diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md new file mode 100644 index 000000000..12ff9ba51 --- /dev/null +++ b/.github/ISSUE_TEMPLATE.md @@ -0,0 +1,53 @@ +### Instructions + +- Use a **concise** yet **descriptive** title; +- Determine whether your issue is a **bug report**, a **feature request**, or a **documentation request** (for tool gatkdocs only; for forum docs see [the support issues repo](https://github.com/broadinstitute/dsde-docs/issues)); +- Choose the corresponding template block below and fill it in, replacing or deleting text in italics (surrounded by `_`) as appropriate; +- If the issue will be added to the public tracker (using the `public` label), it must conform to [these guidelines](http://gatkforums.broadinstitute.org/dsde/discussion/6801/guidelines-for-tagging-issues-with-the-public-tag#latest); +- Delete the other template blocks and this header. + +---- + +## Bug Report + +### Affected tool(s) +_Tool name(s), special parameters?_ + +### Affected version(s) +- [ ] Latest public release version [version?] +- [ ] Latest development/master branch as of [date of test?] + +### Description +_Describe the problem below. Provide **screenshots** , **stacktrace** , **logs** where appropriate._ + +#### Steps to reproduce +_Tell us how to reproduce this issue. If possible, include command lines that reproduce the problem on a test case on one of the gsa* servers._ + +#### Expected behavior +_Tell us what should happen_ + +#### Actual behavior +_Tell us what happens instead_ + +---- + +## Feature request + +### Tool(s) involved +_Tool name(s), special parameters?_ + +### Description +_Specify whether you want a modification of an existing behavior or addition of a new capability._ +_Provide **examples**, **screenshots**, where appropriate._ + +---- + +## Documentation request + +### Tool(s) involved +_Tool name(s), parameters?_ + +### Description +_Describe what needs to be added or modified._ + +---- diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 000000000..75309b858 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,30 @@ +### Description + +_Please explain the changes you made here._ +_Explain the **motivation** for making this change. What existing problem does the pull request solve?_ +_Mention any issues fixed, addressed or otherwise related to this pull request, including issue numbers or hard links for issues in other repos._ + +---- + +### Checklist (never delete this) + +Never delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below. + +#### Content +- [ ] Added or modified tests to cover changes and any new functionality +- [ ] All tests passing on Bamboo (including license tests!) + +#### Form +- [ ] Rebased, squashed and reworded to produce a single commit (exemptions may be made -- sparingly) that is _uncluttered by excess lines_ (lines that just say "addressed review", "fixed" etc left over from squashing) +- [ ] Both the PR and the final rebased commit have a **concise** yet **descriptive** title (they are used when we compile version notes) +- [ ] Edited the README / documentation accordingly and got sign-off from support team (private code is exempt) + +#### Review +- [ ] Suggest a reviewer or ask your team lead to suggest one +- [ ] Final (thumbsup) from the reviewer(s) + +#### GATK4 Implications +- [ ] If your fix/change is applicable to GATK4 as well, and is reasonably small and self-contained (< ~50 lines or so), port the change to GATK4 and open a PR against https://github.com/broadinstitute/gatk or https://github.com/broadinstitute/gatk-protected as appropriate, or at least make a "best effort" attempt to do so. +- [ ] If your fix/change cannot yet be ported to GATK4 because the tool in question hasn't been ported yet, or has only been partially ported, or it would be difficult/burdensome to port the change, or you tried to port the change and failed, then add the ticket to our list of [GATK3 PRs to be eventually ported to GATK4](https://docs.google.com/document/d/1DjEHw57k5h0i8MZRGYPlQA3InvURKwQ7pCoi_Eigc4M/edit) + +Once everything is checked off, you can go ahead and merge the PR. Don't forget to also delete the branch. diff --git a/.gitignore b/.gitignore index 819c120a6..bf5088a0c 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ +.idea/ +.queue/ /*.bam /*.bai /*.bed @@ -5,7 +7,6 @@ /*.vcf /*.txt /*.csh -/.* /*.pdf /*.eval *.ipr @@ -13,11 +14,9 @@ *.iml *.pyc .DS_Store -queueScatterGather /foo* /bar* integrationtests/ -public/testdata/onTheFlyOutputTest.vcf build/ dist/ dump/ diff --git a/licensing/private_license.txt b/licensing/private_license.txt index bbb8dcf9e..5818179e0 100644 --- a/licensing/private_license.txt +++ b/licensing/private_license.txt @@ -4,7 +4,7 @@ BROAD INSTITUTE SOFTWARE LICENSE AGREEMENT FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -20,11 +20,11 @@ The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other th 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. 3. PHONE-HOME FEATURE -LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. 4. OWNERSHIP OF INTELLECTUAL PROPERTY LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -Copyright 2012-2015 Broad Institute, Inc. +Copyright 2012-2016 Broad Institute, Inc. Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. diff --git a/licensing/protected_license.txt b/licensing/protected_license.txt index bbb8dcf9e..f8543c6e1 100644 --- a/licensing/protected_license.txt +++ b/licensing/protected_license.txt @@ -4,7 +4,7 @@ BROAD INSTITUTE SOFTWARE LICENSE AGREEMENT FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -20,11 +20,11 @@ The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other th 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. 3. PHONE-HOME FEATURE -LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. 4. OWNERSHIP OF INTELLECTUAL PROPERTY LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -Copyright 2012-2015 Broad Institute, Inc. +Copyright 2012-2016 Broad Institute, Inc. Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. diff --git a/licensing/public_license.txt b/licensing/public_license.txt index c53c5b34a..cf46512f1 100644 --- a/licensing/public_license.txt +++ b/licensing/public_license.txt @@ -1,4 +1,4 @@ -Copyright 2012-2015 Broad Institute, Inc. +Copyright 2012-2016 Broad Institute, Inc. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation diff --git a/pom.xml b/pom.xml index afd3bc23b..3da58fc29 100644 --- a/pom.xml +++ b/pom.xml @@ -13,7 +13,7 @@ org.broadinstitute.gatk gatk-root - 3.5 + 3.6-SNAPSHOT public/gatk-root @@ -32,6 +32,7 @@ false -build-timestamp "${maven.build.timestamp}" + html ${gatk.basedir}/public/src/main/scripts/shell ${gatk.basedir}/public/src/main/assembly @@ -768,7 +769,7 @@ false true private - -build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${gatk.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs + -build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${gatk.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs -output-file-extension ${gatkdocs.extension} diff --git a/protected/gatk-package-distribution/pom.xml b/protected/gatk-package-distribution/pom.xml index a56f962e4..edca647d1 100644 --- a/protected/gatk-package-distribution/pom.xml +++ b/protected/gatk-package-distribution/pom.xml @@ -5,7 +5,7 @@ org.broadinstitute.gatk gatk-aggregator - 3.5 + 3.6-SNAPSHOT ../.. @@ -61,6 +61,11 @@ commons-httpclient commons-httpclient + + + colt + colt + the reference allele for(int iii = 0; iii < eventsAtThisLoc.size(); iii++) { @@ -258,34 +254,25 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine it = allelesToDrop.iterator(); + final StringBuilder builder = new StringBuilder(); + for (int i = 0; i < MAX_DROPPED_ALTERNATIVE_ALLELES_TO_LOG; i++) { + builder.append(it.next().toString()).append(", "); + } + allelesToDropString = builder.append(it.next().toString()).append(" and ").append(allelesToDrop.size() - 20).append(" more").toString(); + } + logger.warn(String.format("location %s: too many alternative alleles found (%d) larger than the maximum requested with -%s (%d), the following will be dropped: %s.", location, + readAlleleLikelihoods.alleleCount() - 1, GenotypeCalculationArgumentCollection.MAX_ALTERNATE_ALLELES_SHORT_NAME, configuration.genotypeArgs.MAX_ALTERNATE_ALLELES, + allelesToDropString)); + readAlleleLikelihoods.dropAlleles(allelesToDrop); + } + + /** + * Returns the set of alleles that should be dropped in order to bring down the number + * of alternative alleles to the maximum allowed. + * + *

+ * The alleles that put forward for removal are those with the lowest estimated allele count. + *

+ *

+ * Allele counts are estimated herein as the weighted average count + * across samples and phased genotypes where the weight is the genotype likelihood-- we apply + * a uniform prior to all genotypes configurations. + *

+ *

+ * In case of a tie, unlikely for non trivial likelihoods, we keep the alleles with the lower index. + *

+ * + * @param genotypeLikelihoods target genotype likelihoods. + * @param maxAlternativeAlleles maximum number of alternative alleles allowed. + * @return never {@code null}. + */ + private Set excessAlternativeAlleles(final GenotypingLikelihoods genotypeLikelihoods, final int maxAlternativeAlleles) { + final int alleleCount = genotypeLikelihoods.alleleCount(); + final int excessAlternativeAlleleCount = Math.max(0, alleleCount - 1 - maxAlternativeAlleles); + if (excessAlternativeAlleleCount <= 0) { + return Collections.emptySet(); + } + + final double log10NumberOfAlleles = MathUtils.Log10Cache.get(alleleCount); // log10(Num of Alleles); e.g. log10(2) for diploids. + final double[] log10EstimatedACs = new double[alleleCount]; // where we store the AC estimates. + // Set allele counts to 0 (i.e. exp(-Inf)) at the start. + Arrays.fill(log10EstimatedACs, Double.NEGATIVE_INFINITY); + + for (int i = 0; i < genotypeLikelihoods.sampleCount(); i++) { + final GenotypeLikelihoodCalculator calculator = GenotypeLikelihoodCalculators.getInstance(genotypeLikelihoods.samplePloidy(i), alleleCount); + final int numberOfUnphasedGenotypes = calculator.genotypeCount(); + // unphased genotype log10 likelihoods + final double[] log10Likelihoods = genotypeLikelihoods.sampleLikelihoods(i).getAsVector(); + // total number of phased genotypes for all possible combinations of allele counts. + final double log10NumberOfPhasedGenotypes = calculator.ploidy() * log10NumberOfAlleles; + for (int j = 0; j < numberOfUnphasedGenotypes; j++) { + final GenotypeAlleleCounts alleleCounts = calculator.genotypeAlleleCountsAt(j); + // given the current unphased genotype, how many phased genotypes there are: + final double log10NumberOfPhasedGenotypesForThisUnphasedGenotype = alleleCounts.log10CombinationCount(); + final double log10GenotypeLikelihood = log10Likelihoods[j]; + for (int k = 0; k < alleleCounts.distinctAlleleCount(); k++) { + final int alleleIndex = alleleCounts.alleleIndexAt(k); + final int alleleCallCount = alleleCounts.alleleCountAt(k); + final double log10AlleleCount = MathUtils.Log10Cache.get(alleleCallCount); + final double log10Weight = log10GenotypeLikelihood + log10NumberOfPhasedGenotypesForThisUnphasedGenotype + - log10NumberOfPhasedGenotypes; + // update the allele AC adding the contribution of this unphased genotype at this sample. + log10EstimatedACs[alleleIndex] = MathUtils.log10sumLog10(log10EstimatedACs[alleleIndex], + log10Weight + log10AlleleCount); + } + } + } + + final PriorityQueue lessFrequentFirst = new PriorityQueue<>(alleleCount, new Comparator() { + @Override + public int compare(final Allele a1, final Allele a2) { + final int index1 = genotypeLikelihoods.alleleIndex(a1); + final int index2 = genotypeLikelihoods.alleleIndex(a2); + final double freq1 = log10EstimatedACs[index1]; + final double freq2 = log10EstimatedACs[index2]; + if (freq1 != freq2) { + return Double.compare(freq1, freq2); + } else { + return Integer.compare(index2, index1); + } + } + }); + + for (int i = 1; i < alleleCount; i++) { + lessFrequentFirst.add(genotypeLikelihoods.alleleAt(i)); + } + + final Set result = new HashSet<>(excessAlternativeAlleleCount); + for (int i = 0; i < excessAlternativeAlleleCount; i++) { + result.add(lessFrequentFirst.remove()); + } + return result; + } + /** * Tries to phase the individual alleles based on pairwise comparisons to the other alleles based on all called haplotypes * @@ -322,13 +451,14 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine> constructHaplotypeMapping(final List originalCalls, + @VisibleForTesting + static Map> constructHaplotypeMapping(final List originalCalls, final Set calledHaplotypes) { final Map> haplotypeMap = new HashMap<>(originalCalls.size()); for ( final VariantContext call : originalCalls ) { // don't try to phase if there is not exactly 1 alternate allele if ( ! isBiallelic(call) ) { - haplotypeMap.put(call, Collections.emptySet()); + haplotypeMap.put(call, Collections.emptySet()); continue; } @@ -359,10 +489,11 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine originalCalls, - final Map> haplotypeMap, - final int totalAvailableHaplotypes, - final Map> phaseSetMapping) { + @VisibleForTesting + static int constructPhaseSetMapping(final List originalCalls, + final Map> haplotypeMap, + final int totalAvailableHaplotypes, + final Map> phaseSetMapping) { final int numCalls = originalCalls.size(); int uniqueCounter = 0; @@ -454,9 +585,10 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine constructPhaseGroups(final List originalCalls, - final Map> phaseSetMapping, - final int indexTo) { + @VisibleForTesting + static List constructPhaseGroups(final List originalCalls, + final Map> phaseSetMapping, + final int indexTo) { final List phasedCalls = new ArrayList<>(originalCalls); // if we managed to find any phased groups, update the VariantContexts @@ -558,6 +690,10 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine(new HashSet<>(call.getAlleles()))); + } + // Skim the filtered map based on the location so that we do not add filtered read that are going to be removed // right after a few lines of code bellow. final Map> overlappingFilteredReads = overlappingFilteredReads(perSampleFilteredReadList, loc); @@ -684,15 +820,12 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine readLikelihoods, final VariantContext mergedVC, final List noCallAlleles ) { - final List vcAlleles = mergedVC.getAlleles(); - final AlleleList alleleList = readLikelihoods.alleleCount() == vcAlleles.size() ? readLikelihoods : new IndexedAlleleList<>(vcAlleles); - final GenotypingLikelihoods likelihoods = genotypingModel.calculateLikelihoods(alleleList,new GenotypingData<>(ploidyModel,readLikelihoods)); + private GenotypesContext calculateGLsForThisEvent(final ReadLikelihoods readLikelihoods, final List noCallAlleles) { + final GenotypingLikelihoods likelihoods = genotypingModel.calculateLikelihoods(readLikelihoods, new GenotypingData<>(ploidyModel, readLikelihoods)); final int sampleCount = samples.sampleCount(); final GenotypesContext result = GenotypesContext.create(sampleCount); for (int s = 0; s < sampleCount; s++) @@ -706,7 +839,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine haplotypes ) { + private static void cleanUpSymbolicUnassembledEvents(final List haplotypes) { final List haplotypesToRemove = new ArrayList<>(); for( final Haplotype h : haplotypes ) { for( final VariantContext vc : h.getEventMap().getVariantContexts() ) { @@ -739,9 +872,9 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine> eventMapper = new LinkedHashMap<>(eventsAtThisLoc.size()+1); final Event refEvent = new Event(null); - eventMapper.put(refEvent, new ArrayList()); + eventMapper.put(refEvent, new ArrayList<>()); for( final VariantContext vc : eventsAtThisLoc ) { - eventMapper.put(new Event(vc), new ArrayList()); + eventMapper.put(new Event(vc), new ArrayList<>()); } for( final Haplotype h : haplotypes ) { @@ -761,11 +894,12 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine generateVCsFromAlignment( final Haplotype haplotype, final byte[] ref, final GenomeLoc refLoc, final String sourceNameToAdd ) { + @VisibleForTesting + static Map generateVCsFromAlignment(final Haplotype haplotype, final byte[] ref, final GenomeLoc refLoc, final String sourceNameToAdd) { return new EventMap(haplotype, ref, refLoc, sourceNameToAdd); } - protected static boolean containsVCWithMatchingAlleles( final List list, final VariantContext vcToTest ) { + private static boolean containsVCWithMatchingAlleles( final List list, final VariantContext vcToTest ) { for( final VariantContext vc : list ) { if( vc.hasSameAllelesAs(vcToTest) ) { return true; @@ -777,7 +911,8 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine clearedGTs = new ArrayList<>(oldGTs.size()); + for ( final Genotype oldGT : oldGTs ) { + // set GT to no-call when GQ is 0 + if (oldGT.hasGQ() && oldGT.getGQ() == 0) { + final int ploidy = oldGT.getPloidy(); + final List noCallAlleles = GATKVariantContextUtils.noCallAlleles(ploidy); + final Genotype noCallGT = new GenotypeBuilder().alleles(noCallAlleles).make(); + clearedGTs.add(noCallGT); + } else { + clearedGTs.add(oldGT); + } + } + return new VariantContextBuilder(VC).genotypes(clearedGTs).make(); + } } \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java index 47706085b..efcadc463 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java index 77a77ba38..3d32b1ea4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeResolver.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeRoute.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeRoute.java index 3b7f5cac0..0f0a5022b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeRoute.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeRoute.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java index f8f1fa52e..ed610a698 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounter.java index afdb5cd0e..ac36ac00e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounter.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Kmer.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Kmer.java index b51f130e1..05abfab3f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Kmer.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Kmer.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequence.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequence.java index 411c33871..67a7fe0bf 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequence.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequence.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequenceGraphMap.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequenceGraphMap.java index a74430951..622cf2c74 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequenceGraphMap.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerSequenceGraphMap.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java index a5b1c233e..a446ab724 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java index 8daffb915..d65daad3e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java index 9651d4533..e1a26dba0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngine.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java index 1cd949014..e8ff47c6a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java index fc1ed6a16..9ae44688a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java index 6e14466d2..aa4d212d2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadAnchoring.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadAnchoring.java index 5ad254b79..fb69fa4cc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadAnchoring.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadAnchoring.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadCost.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadCost.java index 60db1fc46..4eab9e3ee 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadCost.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadCost.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrector.java index b307fc47e..902fe6e4d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrector.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java index 42961f812..b332e6bbe 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentComparator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentComparator.java index c6dd5c9c1..1693c0307 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentComparator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentComparator.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentCost.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentCost.java index bb51c7e37..b65a95e2e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentCost.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadSegmentCost.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java index 743b92ce7..7dfe1be29 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java index 3e25e6794..02f5b59bd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RefVsAnyResult.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceMode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceMode.java index 74df4872a..86814889d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceMode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceMode.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java index 18dec15c3..397179f35 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java index fb397963a..628ddab7b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java index 63cb82174..14ea38d68 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdge.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java index 973c9ca27..e9e84df42 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraph.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java index daa9b48f1..d8a36f39d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphIterator.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java index 5fd4f8fff..aea721d9b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertex.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java index 03c8c1424..26875ed38 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java index 4d436282e..15ece6d8d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertex.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java index ecb5b4b87..156a01e09 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java index e0d084c75..937a685be 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java index 7dfbb1b0e..621f519b3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtils.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java index 2f9717757..698d45a28 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotype.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java index 343b6b1c7..bee8dc1c6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java index 2a2ea9a1d..609e5c02d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestSubHaplotypeFinder.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java index 171aa70e6..2e2198e4e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KmerSearchableGraph.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java index 6f6c00b6f..13fcfb120 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPruner.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java index d63d88fb8..2c77fc87d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdge.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java index 1a990e0a1..b8d06f525 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Path.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java index 64a60ab3b..3f15616e9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilder.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java index aedfd127f..d23fdefa6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java index 69166699f..899d34881 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/Route.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java index a4e59005b..2f3a253ef 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteFinder.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java index 7c8d45086..17b9c4d0d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraph.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java index ec5fd5fbe..99a6c1f20 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertex.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java index 66452e229..7f18f5362 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedSequenceMerger.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java index 48cf29ebe..ea1222eb0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java index 96040a64d..7437b24d3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/TestGraph.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java index 27e413cf2..eba163f6f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/VertexOrder.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java index 9ceed6b15..435233af4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java index 79ceeffb5..667d4998b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/HaplotypeGraph.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java index 6053ac550..502109864 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java index 8985ede87..26fd6b560 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java index ace1b80a1..ec886a8c4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java index 3ae440b1b..1d1b4c6e8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmers.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java index 1195c9bb5..b954a4df4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/HaplotypeIndelErrorModel.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java deleted file mode 100644 index 7421311ff..000000000 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java +++ /dev/null @@ -1,142 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.indels; - -import htsjdk.samtools.Cigar; -import htsjdk.samtools.SAMRecord; -import org.broadinstitute.gatk.utils.commandline.Output; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.utils.contexts.ReferenceContext; -import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; -import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.walkers.ReadWalker; -import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; -import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.utils.sam.AlignmentUtils; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; - - -/** - * Left-align indels within reads in a bam file - * - *

This tool left-aligns any indels within read cigars in order to standardize representation when there are multiple valid - * representations possible (i.e. where the same indel can be placed at multiple positions and still represent the same haplotype). - * The standard convention is to place an indel at the left-most position possible, but this is not always followed, so - * this tool can be used to correct the representation of indels.

- * - *

Note

- *

This is only really needed when calling variants with legacy locus-based tools such as UnifiedGenotyper. With more - * sophisticated tools (like HaplotypeCaller) that involve reconstructing haplotypes (eg through reassembly), the problem - * of multiple valid representations is handled internally and does not need to be corrected explicitly.

- * - *

Input

- *

- * A bam file with mapped reads. - *

- * - *

Output

- *

- * A bam file in which indels have been left-aligned where appropriate. - *

- * - *

Usage example

- * 
- * java -jar GenomeAnalysisTK.jar \
- *   -R reference.fasta \
- *   -T LeftAlignIndels \
- *   -I reads.bam \
- *   -o output_with_leftaligned_indels.bam
- *
- * - */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} ) -public class LeftAlignIndels extends ReadWalker { - - @Output(required=false, doc="Output bam") - protected GATKSAMFileWriter writer = null; - - public void initialize() {} - - private void emit(final SAMRecord read) { - if ( writer != null ) - writer.addAlignment(read); - } - - public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) { - // we can not deal with screwy records - if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) { - emit(read); - return 0; - } - - // move existing indels (for 1 indel reads only) to leftmost position within identical sequence - int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read); - if ( numBlocks == 2 ) { - Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0, true); - newCigar = IndelRealigner.reclipCigar(newCigar, read); - read.setCigar(newCigar); - } - - emit(read); - return 1; - } - - public Integer reduceInit() { - return 0; - } - - public Integer reduce(Integer value, Integer sum) { - return sum + value; - } - - public void onTraversalDone(Integer result) {} -} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java index dd502a354..e2f3ec395 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java deleted file mode 100644 index 9d9975cea..000000000 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java +++ /dev/null @@ -1,128 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.indels; - -import com.google.java.contract.Requires; -import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.HasGenomeLocation; -import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; - -import java.util.ArrayList; -import java.util.List; - -/** -* User: carneiro -* Date: 2/16/13 -* Time: 11:15 PM -*/ -class ReadBin implements HasGenomeLocation { - - private final ArrayList reads = new ArrayList(); - private byte[] reference = null; - private GenomeLoc loc = null; - private final GenomeLocParser parser; - private final int referencePadding; - - public ReadBin(final GenomeLocParser parser, final int referencePadding) { - this.parser = parser; - this.referencePadding = referencePadding; - } - - // Return false if we can't process this read bin because the reads are not correctly overlapping. - // This can happen if e.g. there's a large known indel with no overlapping reads. - public void add(GATKSAMRecord read) { - - final int readStart = read.getSoftStart(); - final int readStop = read.getSoftEnd(); - if ( loc == null ) - loc = parser.createGenomeLoc(read.getReferenceName(), readStart, Math.max(readStop, readStart)); // in case it's all an insertion - else if ( readStop > loc.getStop() ) - loc = parser.createGenomeLoc(loc.getContig(), loc.getStart(), readStop); - - reads.add(read); - } - - public List getReads() { - return reads; - } - - @Requires("referenceReader.isUppercasingBases()") - public byte[] getReference(CachingIndexedFastaSequenceFile referenceReader) { - // set up the reference if we haven't done so yet - if ( reference == null ) { - // first, pad the reference to handle deletions in narrow windows (e.g. those with only 1 read) - int padLeft = Math.max(loc.getStart()- referencePadding, 1); - int padRight = Math.min(loc.getStop()+ referencePadding, referenceReader.getSequenceDictionary().getSequence(loc.getContig()).getSequenceLength()); - loc = parser.createGenomeLoc(loc.getContig(), loc.getContigIndex(), padLeft, padRight); - reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases(); - } - - return reference; - } - - public GenomeLoc getLocation() { - return loc; - } - - public int size() { - return reads.size(); - } - - public void clear() { - reads.clear(); - reference = null; - loc = null; - } - -} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/AllelePair.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/AllelePair.java index 47c80c9f3..88b446987 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/AllelePair.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/AllelePair.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/BaseArray.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/BaseArray.java index 100c31d36..d21079811 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/BaseArray.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/BaseArray.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CardinalityCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CardinalityCounter.java index db9162fe4..796682d4f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CardinalityCounter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CardinalityCounter.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CloneableIteratorLinkedList.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CloneableIteratorLinkedList.java index cfbd823b7..36aebd06b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CloneableIteratorLinkedList.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/CloneableIteratorLinkedList.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/DisjointSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/DisjointSet.java index f3dad23e0..dc9551543 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/DisjointSet.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/DisjointSet.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/Haplotype.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/Haplotype.java index 1a96368e2..328ddbae1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/Haplotype.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/Haplotype.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java index 5513c0b51..b6f31a9e4 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java index 6938784ee..84fc325cb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmission.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -140,7 +140,7 @@ import java.util.*; * * */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} ) public class PhaseByTransmission extends RodWalker, HashMap> { @ArgumentCollection diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java index d2e4f95c2..511956c2f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraph.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java index 6151e5706..fd5d445e3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingGraphEdge.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java index f68955b40..fc1244e80 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingRead.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java index 24060876b..8dbf65730 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtils.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -297,8 +297,8 @@ class PhasingUtils { */ static boolean mergeIntoMNPvalidationCheck(GenomeLocParser genomeLocParser, VariantContext vc1, VariantContext vc2) { // Can only merge "simple" base strings (i.e., SNPs or MNPs, but not indels): - final boolean vc1CanBeMerged = vc1.isSNP() || vc1.isMNP(); - final boolean vc2CanBeMerged = vc2.isSNP() || vc2.isMNP(); + final boolean vc1CanBeMerged = (vc1.isSNP() || vc1.isMNP()) && !vc1.hasAllele(Allele.SPAN_DEL); + final boolean vc2CanBeMerged = (vc2.isSNP() || vc2.isMNP()) && !vc2.hasAllele(Allele.SPAN_DEL); if (!vc1CanBeMerged || !vc2CanBeMerged) return false; @@ -363,7 +363,7 @@ class PhasingUtils { * * @param gt1 genotype 1 * @param gt2 genotype 2 - * @return true if genotypes have the same number of chromosomes, haplotype, phased, number of attributes + * @return true if genotypes have the same number of chromosomes, haplotype, number of attributes * as chromosomes, and either genotype is homozygous, false otherwise */ static boolean alleleSegregationIsKnown(Genotype gt1, Genotype gt2) { @@ -371,10 +371,6 @@ class PhasingUtils { if (gt1.getPloidy() != gt2.getPloidy()) return false; - // If gt1 or gt2 are not phased, then can not be merged. - if (!gt1.isPhased() || !gt2.isPhased()) - return false; - // If gt1 or gt2 are homozygous, then could be merged. if (gt1.isHom() || gt2.isHom()) return true; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java index 81d16670a..8f43c1e7a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/PreciseNonNegativeDouble.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java index a5d4f38f5..19928c3fd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasing.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -52,6 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.phasing; import org.broadinstitute.gatk.engine.walkers.*; +import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.Hidden; @@ -63,6 +64,7 @@ import org.broadinstitute.gatk.utils.contexts.ReferenceContext; import org.broadinstitute.gatk.engine.filters.MappingQualityZeroFilter; import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.sam.ReadUtils; import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; @@ -110,8 +112,20 @@ import static org.broadinstitute.gatk.engine.GATKVCFUtils.getVCFHeadersFromRods; * *

Output

*

- * Phased VCF file. + * Phased VCF file using HP tags to link alleles at (possibly non-consecutive) genotypes of the same sample. *

+ *

Example

+ * 
+ *     GT:GQ:HP    0/1:99:17690409-1,17690409-2
+ *     GT:GQ:HP    0/1:99:17690409-2,17690409-1:1258.14
+ *
+ *

The second site's alternate allele (1) is on the same physical haplotype as the first site's reference allele (0), + * and vice versa [second site's 0 goes with first site's 1]. This is based on the fact that the HP pairs line up in + * reverse order between these two genotypes.

+ *

In an old notation that RBP used to output in much earlier versions, the genotypes would have been: 0/1 and 1|0, + * respectively. This was changed because depending on the case it caused ambiguity, incompleteness, and possible + * inconsistency with trio-based phasing. In contrast, the HP tag is much more explicitl for linking alleles, especially + * if the genotypes are non-consecutive.

* *

Usage example

* 
@@ -338,6 +352,7 @@ public class ReadBackedPhasing extends RodWalker processQueue(PhasingStats phaseStats, boolean processAll) {
         List oldPhasedList = new LinkedList();
 
+        VariantAndReads prevVr = null;
         while (!unphasedSiteQueue.isEmpty()) {
             if (!processAll) { // otherwise, phase until the end of unphasedSiteQueue
                 VariantContext nextToPhaseVc = unphasedSiteQueue.peek().variant;
@@ -354,10 +369,35 @@ public class ReadBackedPhasing extends RodWalker sampleReadBases;
+        public Set variantReadNames;
 
         public VariantAndReads(VariantContext variant, HashMap sampleReadBases) {
             this.variant = variant;
@@ -1232,6 +1282,22 @@ public class ReadBackedPhasing extends RodWalker();
+                        for ( final GATKSAMRecord read : pileup.getReads() ) {
+                            // get the SNP position in the read
+                            Pair pair = ReadUtils.getReadCoordinateForReferenceCoordinate(read, variant.getStart());
+
+                            // get the reads containing the SNP
+                            for (final Allele altAllele : variant.getAlternateAlleles()) {
+                                if (read.getReadBases()[pair.first] == altAllele.getBases()[0]) {
+                                    variantReadNames.add(read.getReadName());
+                                }
+                            }
+                        }
+                    }
                 }
             }
         }
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java
index 416dc538b..6e3ce282d 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBase.java
@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java
index 1fd05ed0f..c1facb880 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBasesAtPosition.java
@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java
index 3c38794c3..e5743c3a7 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/phasing/SNPallelePair.java
@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java
index 809f97214..2be1a11af 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManager.java
@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java
index ced1e9ce5..73463ec43 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReads.java
@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java
index 616b36a4b..2024bb70a 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java
@@ -5,7 +5,7 @@
 * SOFTWARE LICENSE AGREEMENT
 * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
 * 
-* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”).
+* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE").
 * 
 * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
 * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
@@ -21,11 +21,11 @@
 * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
 * 
 * 3. PHONE-HOME FEATURE
-* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
+* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM.  Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time.  Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation.
 * 
 * 4. OWNERSHIP OF INTELLECTUAL PROPERTY
 * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
-* Copyright 2012-2015 Broad Institute, Inc.
+* Copyright 2012-2016 Broad Institute, Inc.
 * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
 * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
 * 
@@ -106,7 +106,7 @@ import java.util.*;
  *
* */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class}, gotoDev = HelpConstants.EB) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class}) @Reference(window=@Window(start=-200,stop=200)) public class SimulateReadsForVariants extends RodWalker { private static Logger logger = Logger.getLogger(SimulateReadsForVariants.class); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java deleted file mode 100644 index ca3da994c..000000000 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/GenotypeAndValidate.java +++ /dev/null @@ -1,551 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.validation; - -import htsjdk.variant.vcf.*; -import org.broadinstitute.gatk.engine.GenomeAnalysisEngine; -import org.broadinstitute.gatk.engine.walkers.*; -import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider; -import org.broadinstitute.gatk.utils.commandline.*; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.utils.contexts.AlignmentContext; -import org.broadinstitute.gatk.utils.contexts.ReferenceContext; -import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.tools.walkers.genotyper.*; -import org.broadinstitute.gatk.engine.SampleUtils; -import org.broadinstitute.gatk.utils.help.HelpConstants; -import org.broadinstitute.gatk.engine.GATKVCFUtils; -import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; -import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; -import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; -import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.variantcontext.VariantContextBuilder; -import htsjdk.variant.variantcontext.writer.VariantContextWriter; - -import java.util.Map; -import java.util.Set; - -import static org.broadinstitute.gatk.utils.IndelUtils.isInsideExtendedIndel; - -/** - * Genotype and validate a dataset and the calls of another dataset using the Unified Genotyper - * - *

Note that this is an old tool that makes use of the UnifiedGenotyper, which has since been - * deprecated in favor of the HaplotypeCaller.

- *

- * Genotype and Validate is a tool to evaluate the quality of a dataset for calling SNPs - * and Indels given a secondary (validation) data source. The data sources are BAM or VCF - * files. You can use them interchangeably (i.e. a BAM to validate calls in a VCF or a VCF - * to validate calls on a BAM). - *

- * - *

- * The simplest scenario is when you have a VCF of hand annotated SNPs and Indels, and you - * want to know how well a particular technology performs calling these snps. With a - * dataset (BAM file) generated by the technology in test, and the hand annotated VCF, you - * can run GenotypeAndValidate to asses the accuracy of the calls with the new technology's - * dataset. - *

- * - *

- * Another option is to validate the calls on a VCF file, using a deep coverage BAM file - * that you trust the calls on. The GenotypeAndValidate walker will make calls using the - * reads in the BAM file and take them as truth, then compare to the calls in the VCF file - * and produce a truth table. - *

- * - * - *

Input

- *

- * A BAM file to make calls on and a VCF file to use as truth validation dataset. - * - * You also have the option to invert the roles of the files using the command line options listed below. - *

- * - *

Output

- *

- * GenotypeAndValidate has two outputs. The truth table and the optional VCF file. The truth table is a - * 2x2 table correlating what was called in the dataset with the truth of the call (whether it's a true - * positive or a false positive). The table should look like this: - *

- *
- * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - *
ALTREFPredictive Value
called altTrue Positive (TP)False Positive (FP)Positive PV
called refFalse Negative (FN)True Negative (TN)Negative PV
- *
- * - *

- * The positive predictive value (PPV) is the proportion of subjects with positive test results - * who are correctly diagnosed. - *

- *

- * The negative predictive value (NPV) is the proportion of subjects with a negative test result - * who are correctly diagnosed. - *

- *

- * The VCF file will contain only the variants that were called or not called, excluding the ones that - * were uncovered or didn't pass the filters. This file is useful if you are trying to compare - * the PPV and NPV of two different technologies on the exact same sites (so you can compare apples to - * apples). - *

- * - *

- * Here is an example of an annotated VCF file (info field clipped for clarity) - * - * 

- * #CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA12878
- * 1   20568807    .   C   T   0    HapMapHet        AC=1;AF=0.50;AN=2;DP=0;GV=T  GT  0/1
- * 1   22359922    .   T   C   282  WG-CG-HiSeq      AC=2;AF=0.50;GV=T;AN=4;DP=42 GT:AD:DP:GL:GQ  1/0 ./. 0/1:20,22:39:-72.79,-11.75,-67.94:99    ./.
- * 13  102391461   .   G   A   341  Indel;SnpCluster AC=1;GV=F;AF=0.50;AN=2;DP=45 GT:AD:DP:GL:GQ  ./. ./. 0/1:32,13:45:-50.99,-13.56,-112.17:99   ./.
- * 1   175516757   .   C   G   655  SnpCluster,WG    AC=1;AF=0.50;AN=2;GV=F;DP=74 GT:AD:DP:GL:GQ  ./. ./. 0/1:52,22:67:-89.02,-20.20,-191.27:99   ./.
- *
- * - *

- * - *

Additional Details

- *
    - *
  • - * You should always use -L on your VCF track, so that the GATK only looks at the sites on the VCF file. - * This speeds up the process a lot. - *
    • - *
  • - * The total number of visited bases may be greater than the number of variants in the original - * VCF file because of extended indels, as they trigger one call per new insertion or deletion. - * (i.e. ACTG/- will count as 4 genotyper calls, but it's only one line in the VCF). - *
    • - *
- * - *

Usage examples

- *

Genotypes BAM file from new technology using the VCF as a truth dataset

- * 
- *  java
- *      -jar GenomeAnalysisTK.jar \
- *      -T  GenotypeAndValidate \
- *      -R reference.fasta \
- *      -I myNewTechReads.bam \
- *      -alleles handAnnotatedVCF.vcf \
- *      -L handAnnotatedVCF.vcf \
- *      -o output.vcf
- *
- * - *

Genotypes BAM file from new technology a BAM file as the truth dataset

- * 
- *  java
- *      -jar GenomeAnalysisTK.jar \
- *      -T  GenotypeAndValidate \
- *      -R reference.fasta \
- *      -I myTruthDataset.bam \
- *      -alleles callsToValidate.vcf \
- *      -L callsToValidate.vcf \
- *      -bt \
- *      -o output.vcf
- *
- * - */ - -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} ) -@Requires(value={DataSource.READS, DataSource.REFERENCE}) -@Allows(value={DataSource.READS, DataSource.REFERENCE}) -@By(DataSource.REFERENCE) -@Reference(window=@Window(start=-200,stop=200)) -public class GenotypeAndValidate extends RodWalker implements TreeReducible { - - /** - * The optional output file that will have all the variants used in the Genotype and Validation essay. - * The new annotation `callStatus` will carry the value called in the validation VCF or BAM file." - */ - @Output(doc="Output VCF file with annotated variants", required=false) - protected VariantContextWriter vcfWriter = null; - - /** - * The callset to be used as truth (default) or validated (if BAM file is set to truth). - */ - @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype", required=true) - public RodBinding alleles; - - /** - * Makes the Unified Genotyper calls to the BAM file the truth dataset and validates the alleles ROD binding callset. - */ - @Argument(fullName ="set_bam_truth", shortName ="bt", doc="Use the calls on the reads (bam file) as the truth dataset and validate the calls on the VCF", required=false) - private boolean bamIsTruth = false; - - /** - * The minimum base quality score necessary for a base to be considered when calling a genotype. This argument is passed to the Unified Genotyper. - */ - @Argument(fullName="minimum_base_quality_score", shortName="mbq", doc="Minimum base quality score for calling a genotype", required=false) - private int mbq = -1; - - /** - * The maximum deletion fraction allowed in a site for calling a genotype. This argument is passed to the Unified Genotyper. - */ - @Argument(fullName="maximum_deletion_fraction", shortName="deletions", doc="Maximum deletion fraction for calling a genotype", required=false) - private double deletions = -1; - - /** - * the minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. This argument is passed to the Unified Genotyper. - */ - @Argument(fullName="standard_min_confidence_threshold_for_calling", shortName="stand_call_conf", doc="the minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls", required=false) - private double callConf = -1; - - /** - * the minimum phred-scaled Qscore threshold to emit low confidence calls. This argument is passed to the Unified Genotyper. - */ - @Argument(fullName="standard_min_confidence_threshold_for_emitting", shortName="stand_emit_conf", doc="the minimum phred-scaled Qscore threshold to emit low confidence calls", required=false) - private double emitConf = -1; - - /** - * Only validate sites that have at least a given depth - */ - @Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false) - private int minDepth = -1; - - /** - * Print out discordance sites to standard out. - */ - @Hidden - @Argument(fullName ="print_interesting_sites", shortName ="print_interesting", doc="Print out interesting sites to standard out", required=false) - private boolean printInterestingSites = false; - - private UnifiedGenotypingEngine snpEngine; - private UnifiedGenotypingEngine indelEngine; - private Set samples; - - private enum GVstatus { - T, F, NONE - } - - public static class CountedData { - private long nAltCalledAlt = 0L; - private long nAltCalledRef = 0L; - private long nAltNotCalled = 0L; - private long nRefCalledAlt = 0L; - private long nRefCalledRef = 0L; - private long nRefNotCalled = 0L; - private long nNoStatusCalledAlt = 0L; - private long nNoStatusCalledRef = 0L; - private long nNoStatusNotCalled = 0L; - private long nNotConfidentCalls = 0L; - private long nUncovered = 0L; - - /** - * Adds the values of other to this, returning this - * @param other the other object - */ - public void add(CountedData other) { - nAltCalledAlt += other.nAltCalledAlt; - nAltCalledRef += other.nAltCalledRef; - nAltNotCalled += other.nAltNotCalled; - nRefCalledAlt += other.nRefCalledAlt; - nRefCalledRef += other.nRefCalledRef; - nRefNotCalled += other.nRefNotCalled; - nNoStatusCalledAlt += other.nNoStatusCalledAlt; - nNoStatusCalledRef += other.nNoStatusCalledRef; - nNoStatusNotCalled += other.nNoStatusNotCalled; - nUncovered += other.nUncovered; - nNotConfidentCalls += other.nNotConfidentCalls; - } - } - - - - //--------------------------------------------------------------------------------------------------------------- - // - // initialize - // - //--------------------------------------------------------------------------------------------------------------- - - public void initialize() { - - // Initialize VCF header - if (vcfWriter != null) { - Map header = GATKVCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName()); - samples = SampleUtils.getSampleList(header, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); - Set headerLines = VCFUtils.smartMergeHeaders(header.values(), true); - headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate")); - headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.GENOTYPE_AND_VALIDATE_STATUS_KEY)); - vcfWriter.writeHeader(new VCFHeader(headerLines, samples)); - } - - // Filling in SNP calling arguments for UG - UnifiedArgumentCollection uac = new UnifiedArgumentCollection(); - uac.outputMode = OutputMode.EMIT_ALL_SITES; - uac.alleles = alleles; - - // TODO -- if we change this tool to actually validate against the called allele, then this if statement is needed; - // TODO -- for now, though, we need to be able to validate the right allele (because we only test isVariant below) [EB] - //if (!bamIsTruth) - uac.genotypingOutputMode = GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES; - - if (mbq >= 0) uac.MIN_BASE_QUALTY_SCORE = mbq; - if (deletions >= 0) - uac.MAX_DELETION_FRACTION = deletions; - else - uac.MAX_DELETION_FRACTION = 1.0; - if (emitConf >= 0) uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_EMITTING = emitConf; - if (callConf >= 0) uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING = callConf; - - final GenomeAnalysisEngine toolkit = getToolkit(); - uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP; - snpEngine = new UnifiedGenotypingEngine(uac, - FixedAFCalculatorProvider.createThreadSafeProvider(toolkit, uac, logger),toolkit); - - - // Adding the INDEL calling arguments for UG - UnifiedArgumentCollection uac_indel = uac.clone(); - uac_indel.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL; - indelEngine = new UnifiedGenotypingEngine(uac_indel, - FixedAFCalculatorProvider.createThreadSafeProvider(toolkit, uac, logger),toolkit); - - // make sure we have callConf set to the threshold set by the UAC so we can use it later. - callConf = uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING; - } - - //--------------------------------------------------------------------------------------------------------------- - // - // map - // - //--------------------------------------------------------------------------------------------------------------- - - public CountedData map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) { - - final CountedData counter = new CountedData(); - - // For some reason RodWalkers get map calls with null trackers - if( tracker == null ) - return counter; - - VariantContext vcComp = tracker.getFirstValue(alleles); - if( vcComp == null ) - return counter; - - //todo - not sure I want this, may be misleading to filter extended indel events. - if (isInsideExtendedIndel(vcComp, ref)) - return counter; - - // Do not operate on variants that are not covered to the optional minimum depth - if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) { - counter.nUncovered = 1L; - final GVstatus status = getGVstatus(vcComp); - if ( status == GVstatus.T ) - counter.nAltNotCalled = 1L; - else if ( status == GVstatus.F ) - counter.nRefNotCalled = 1L; - else - counter.nNoStatusNotCalled = 1L; - - return counter; - } - - VariantCallContext call; - if ( vcComp.isSNP() ) { - call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0); - } else if ( vcComp.isIndel() ) { - call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0); - } else if ( bamIsTruth ) { - // assume it's a SNP if no variation is present; this is necessary so that we can test supposed monomorphic sites against the truth bam - call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context).get(0); - } else { - logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles()); - return counter; - } - - - boolean writeVariant = true; - - if (bamIsTruth) { - if (call.confidentlyCalled) { - // If truth is a confident REF call - if (call.isVariant()) { - if (vcComp.isVariant()) - counter.nAltCalledAlt = 1L; - else { - counter.nAltCalledRef = 1L; - if ( printInterestingSites ) - System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart()); - } - } - // If truth is a confident ALT call - else { - if (vcComp.isVariant()) { - counter.nRefCalledAlt = 1L; - if ( printInterestingSites ) - System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart()); - } else - counter.nRefCalledRef = 1L; - } - } - else { - counter.nNotConfidentCalls = 1L; - if ( printInterestingSites ) - System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart()); - writeVariant = false; - } - } - else { -// if (!vcComp.hasExtendedAttribute("GV")) -// throw new UserException.BadInput("Variant has no GV annotation in the INFO field. " + vcComp.getChr() + ":" + vcComp.getStart()); - - final GVstatus status = getGVstatus(vcComp); - if (call.isCalledAlt(callConf)) { - if ( status == GVstatus.T ) - counter.nAltCalledAlt = 1L; - else if ( status == GVstatus.F ) { - counter.nRefCalledAlt = 1L; - if ( printInterestingSites ) - System.out.println("Truth=REF Call=ALT at " + call.getChr() + ":" + call.getStart()); - } - else - counter.nNoStatusCalledAlt = 1L; - } - else if (call.isCalledRef(callConf)) { - if ( status == GVstatus.T ) { - counter.nAltCalledRef = 1L; - if ( printInterestingSites ) - System.out.println("Truth=ALT Call=REF at " + call.getChr() + ":" + call.getStart()); - } - else if ( status == GVstatus.F ) - counter.nRefCalledRef = 1L; - - else - counter.nNoStatusCalledRef = 1L; - } - else { - counter.nNotConfidentCalls = 1L; - if ( status == GVstatus.T ) - counter.nAltNotCalled = 1L; - else if ( status == GVstatus.F ) - counter.nRefNotCalled = 1L; - else - counter.nNoStatusNotCalled = 1L; - - if ( printInterestingSites ) - System.out.println("Truth is not confident at " + call.getChr() + ":" + call.getStart()); - writeVariant = false; - } - } - - if (vcfWriter != null && writeVariant) { - if (!vcComp.hasAttribute(GATKVCFConstants.GENOTYPE_AND_VALIDATE_STATUS_KEY)) { - vcfWriter.add(new VariantContextBuilder(vcComp).attribute(GATKVCFConstants.GENOTYPE_AND_VALIDATE_STATUS_KEY, call.isCalledAlt(callConf) ? "ALT" : "REF").make()); - } - else - vcfWriter.add(vcComp); - } - return counter; - } - - private GVstatus getGVstatus(final VariantContext vc) { - return ( !vc.hasAttribute("GV") ) ? GVstatus.NONE : (vc.getAttribute("GV").equals("T") ? GVstatus.T : GVstatus.F); - } - - //--------------------------------------------------------------------------------------------------------------- - // - // reduce - // - //--------------------------------------------------------------------------------------------------------------- - - public CountedData reduceInit() { - return new CountedData(); - } - - public CountedData treeReduce( final CountedData sum1, final CountedData sum2) { - sum2.add(sum1); - return sum2; - } - - public CountedData reduce( final CountedData mapValue, final CountedData reduceSum ) { - reduceSum.add(mapValue); - return reduceSum; - } - - public void onTraversalDone( CountedData reduceSum ) { - double ppv = 100 * ((double) reduceSum.nAltCalledAlt /( reduceSum.nAltCalledAlt + reduceSum.nRefCalledAlt)); - double npv = 100 * ((double) reduceSum.nRefCalledRef /( reduceSum.nRefCalledRef + reduceSum.nAltCalledRef)); - double sensitivity = 100 * ((double) reduceSum.nAltCalledAlt /( reduceSum.nAltCalledAlt + reduceSum.nAltCalledRef)); - double specificity = (reduceSum.nRefCalledRef + reduceSum.nRefCalledAlt > 0) ? 100 * ((double) reduceSum.nRefCalledRef /( reduceSum.nRefCalledRef + reduceSum.nRefCalledAlt)) : 100; - logger.info(String.format("Resulting Truth Table Output\n\n" + - "------------------------------------------------------------------\n" + - "\t\t|\tALT\t|\tREF\t|\tNo Status\n" + - "------------------------------------------------------------------\n" + - "called alt\t|\t%d\t|\t%d\t|\t%d\n" + - "called ref\t|\t%d\t|\t%d\t|\t%d\n" + - "not called\t|\t%d\t|\t%d\t|\t%d\n" + - "------------------------------------------------------------------\n" + - "positive predictive value: %f%%\n" + - "negative predictive value: %f%%\n" + - "------------------------------------------------------------------\n" + - "sensitivity: %f%%\n" + - "specificity: %f%%\n" + - "------------------------------------------------------------------\n" + - "not confident: %d\n" + - "not covered: %d\n" + - "------------------------------------------------------------------\n", reduceSum.nAltCalledAlt, reduceSum.nRefCalledAlt, reduceSum.nNoStatusCalledAlt, reduceSum.nAltCalledRef, reduceSum.nRefCalledRef, reduceSum.nNoStatusCalledRef, reduceSum.nAltNotCalled, reduceSum.nRefNotCalled, reduceSum.nNoStatusNotCalled, ppv, npv, sensitivity, specificity, reduceSum.nNotConfidentCalls, reduceSum.nUncovered)); - } -} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java index b9228f23c..1910dc75e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/FrequencyModeSelector.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java index 6d2cf5296..2f26b19f5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GLBasedSampleSelector.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java index a7d716c24..01369e348 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GTBasedSampleSelector.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java index 78bc3b5f9..6c2928ae9 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/GenomeEvent.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java index 897ef9a81..873d98302 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java index dc6c1ba58..c95b85153 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/NullSampleSelector.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java index c2e86faa9..31185cf77 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/SampleSelector.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java index 7e459c021..01a1ed757 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java index c64070cff..35fe33d43 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -52,6 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector; import org.broadinstitute.gatk.utils.commandline.*; +import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; import org.broadinstitute.gatk.utils.contexts.ReferenceContext; @@ -60,11 +61,11 @@ import org.broadinstitute.gatk.engine.walkers.RodWalker; import org.broadinstitute.gatk.utils.GenomeLocParser; import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; + import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; -import org.broadinstitute.gatk.engine.GATKVCFUtils; -import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.writer.VariantContextWriter; @@ -134,7 +135,7 @@ import java.util.*; * * */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) public class ValidationSiteSelector extends RodWalker { public enum AF_COMPUTATION_MODE { diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java index b6ef38ade..d350af102 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,6 +51,8 @@ package org.broadinstitute.gatk.tools.walkers.variantrecalibration; +import htsjdk.variant.variantcontext.Allele; +import org.broadinstitute.gatk.tools.walkers.annotator.AnnotationUtils; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; @@ -74,6 +76,8 @@ import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; import java.io.File; import java.util.*; +import java.util.regex.Matcher; +import java.util.regex.Pattern; /** * Apply a score cutoff to filter variants based on a recalibration table @@ -115,26 +119,45 @@ import java.util.*; * *

Usage example for filtering SNPs

* 
- * java -Xmx3g -jar GenomeAnalysisTK.jar \
+ * java -jar GenomeAnalysisTK.jar \
  *   -T ApplyRecalibration \
  *   -R reference.fasta \
- *   -input NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf \
+ *   -input raw_variants.vcf \
  *   --ts_filter_level 99.0 \
- *   -tranchesFile path/to/output.tranches \
- *   -recalFile path/to/output.recal \
+ *   -tranchesFile output.tranches \
+ *   -recalFile output.recal \
  *   -mode SNP \
  *   -o path/to/output.recalibrated.filtered.vcf
  *
* + *

Allele-specific usage

+ * 
+ * java -jar GenomeAnalysisTK.jar \
+ *   -T ApplyRecalibration \
+ *   -R reference.fasta \
+ *   -input raw_variants.withASannotations.vcf \
+ *   -AS \
+ *   --ts_filter_level 99.0 \
+ *   -tranchesFile output.AS.tranches \
+ *   -recalFile output.AS.recal \
+ *   -mode SNP \
+ *   -o path/to/output.recalibrated.ASfiltered.vcf
+ *
+ * Each allele will be annotated by its corresponding entry in the AS_FilterStatus INFO field annotation. Allele-specific VQSLOD and culprit are also carried through from VariantRecalibrator and stored in the AS_VQSLOD and AS_culprit INFO fields, respectively. + * The site-level filter is set to the most lenient of any of the allele filters. That is, if one allele passes, the whole site will be PASS. If no alleles pass, the site-level filter will be set to the lowest sensitivity tranche among all the alleles. + * + * Note that the .tranches and .recal files should be derived from an allele-specific run of VariantRecalibrator + * Also note that the AS_culprit, AS_FilterStatus, and AS_VQSLOD fields will have placeholder values (NA or NaN) for alleles of a type that have not yet been processed by ApplyRecalibration + * The spanning deletion allele (*) will not be recalibrated because it represents missing data. Its VQSLOD will remain NaN and it's culprit and FilterStatus will be NA. + * *

Caveats

* *
    - *
  • The tranche values used in the example above is only a general example. You should determine the level of sensitivity + *
  • The tranche values used in the example above are only meant to be a general example. You should determine the level of sensitivity * that is appropriate for your specific project. Remember that higher sensitivity (more power to detect variants, yay!) comes * at the cost of specificity (more false negatives, boo!). You have to choose at what point you want to set the tradeoff.
    • *
  • In order to create the tranche reporting plots (which are only generated for SNPs, not indels!) Rscript needs to be - * in your environment PATH (this is the scripting version of R, not the interactive version). - * See http://www.r-project.org for more info on how to download and install R.
    • + * in your environment PATH (this is the scripting version of R, not the interactive version). *
*/ @@ -145,6 +168,9 @@ public class ApplyRecalibration extends RodWalker implements T public static final String LOW_VQSLOD_FILTER_NAME = "LOW_VQSLOD"; private final double DEFAULT_VQSLOD_CUTOFF = 0.0; + boolean foundSNPTranches = false; + boolean foundINDELTranches = false; + ///////////////////////////// // Inputs ///////////////////////////// @@ -169,6 +195,14 @@ public class ApplyRecalibration extends RodWalker implements T ///////////////////////////// @Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering", required=false) protected Double TS_FILTER_LEVEL = null; + + /** + * Filter the input file based on allele-specific recalibration data. See tool docs for site-level and allele-level filtering details. + * Requires a .recal file produced using an allele-specific run of VariantRecalibrator + */ + @Argument(fullName="useAlleleSpecificAnnotations", shortName="AS", doc="If specified, the tool will attempt to apply a filter to each allele based on the input tranches and allele-specific .recal file.", required=false) + public boolean useASannotations = false; + @Advanced @Argument(fullName="lodCutoff", shortName="lodCutoff", doc="The VQSLOD score below which to start filtering", required=false) protected Double VQSLOD_CUTOFF = null; @@ -191,6 +225,12 @@ public class ApplyRecalibration extends RodWalker implements T final private List tranches = new ArrayList<>(); final private Set inputNames = new HashSet<>(); final private Set ignoreInputFilterSet = new TreeSet<>(); + final static private String listPrintSeparator = ","; + final static private String trancheFilterString = "VQSRTranche"; + final static private String arrayParseRegex = "[\\[\\]\\s]"; + final static private String emptyStringValue = "NA"; + final static private String emptyFloatValue = "NaN"; + //--------------------------------------------------------------------------------------------------------------- // @@ -219,11 +259,19 @@ public class ApplyRecalibration extends RodWalker implements T // setup the header fields final Set hInfo = new HashSet<>(); - hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames)); + final Set inputHeaders = GATKVCFUtils.getHeaderFields(getToolkit(), inputNames); + hInfo.addAll(inputHeaders); addVQSRStandardHeaderLines(hInfo); + if (useASannotations) + addAlleleSpecificVQSRHeaderLines(hInfo); + + checkForPreviousApplyRecalRun(Collections.unmodifiableSet(inputHeaders)); + final TreeSet samples = new TreeSet<>(); samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)); + //generate headers from tranches file + //TODO: throw away old tranche headers if we're ignoring filters if( TS_FILTER_LEVEL != null ) { // if the user specifies both ts_filter_level and lodCutoff then throw a user error if( VQSLOD_CUTOFF != null ) { @@ -255,6 +303,20 @@ public class ApplyRecalibration extends RodWalker implements T vcfWriter.writeHeader(vcfHeader); } + private boolean trancheIntervalIsValid(final String sensitivityLimits) { + final String[] vals = sensitivityLimits.split("to"); + if(vals.length != 2) + return false; + try { + double lowerLimit = Double.parseDouble(vals[0]); + double upperLimit = Double.parseDouble(vals[1].replace("+","")); //why does our last tranche end with 100+? Is there anything greater than 100 percent? Really??? + } + catch(NumberFormatException e) { + throw new UserException("Poorly formatted tranche filter name does not contain two sensitivity interval end points."); + } + return true; + } + public static void addVQSRStandardHeaderLines(final Set hInfo) { hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY)); hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.VQS_LOD_KEY)); @@ -263,6 +325,40 @@ public class ApplyRecalibration extends RodWalker implements T hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.NEGATIVE_LABEL_KEY)); } + public static void addAlleleSpecificVQSRHeaderLines(final Set hInfo) { + hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_FILTER_STATUS_KEY)); + hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_CULPRIT_KEY)); + hInfo.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VQS_LOD_KEY)); + } + + /** + * Check the filter declarations in the input VCF header to see if any ApplyRecalibration mode has been run + * Here we assume that the tranches are named with a specific format: VQSRTranche[SNP|INDEL][lowerLimit]to[upperLimit] + * @param inputHeaders + */ + private void checkForPreviousApplyRecalRun(final Set inputHeaders) { + for(final VCFHeaderLine header : inputHeaders) { + if(header instanceof VCFFilterHeaderLine) { + final String filterName = ((VCFFilterHeaderLine)header).getID(); + if(filterName.length() < 12 || !filterName.substring(0, 11).equalsIgnoreCase(trancheFilterString)) { + continue; + } + if(filterName.charAt(11) == 'S') { + //for SNP tranches, get sensitivity limit + final String sensitivityLimits = filterName.substring(14); + if(trancheIntervalIsValid(sensitivityLimits)) + foundSNPTranches = true; + } + else if(filterName.charAt(11) == 'I') { + //for INDEL tranches, get sensitivity limit + final String sensitivityLimits = filterName.substring(16); + if(trancheIntervalIsValid(sensitivityLimits)) + foundINDELTranches = true; + } + } + } + } + //--------------------------------------------------------------------------------------------------------------- // // map @@ -280,38 +376,26 @@ public class ApplyRecalibration extends RodWalker implements T for( final VariantContext vc : VCs ) { - if( VariantDataManager.checkVariationClass( vc, MODE ) && (IGNORE_ALL_FILTERS || vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters())) ) { + final boolean evaluateThisVariant = useASannotations || VariantDataManager.checkVariationClass( vc, MODE ); + final boolean variantIsNotFiltered = IGNORE_ALL_FILTERS || vc.isNotFiltered() || (!ignoreInputFilterSet.isEmpty() && ignoreInputFilterSet.containsAll(vc.getFilters())); //vc.isNotFiltered is true for PASS; vc.filtersHaveBeenApplied covers PASS and filters + if( evaluateThisVariant && variantIsNotFiltered) { - final VariantContext recalDatum = getMatchingRecalVC(vc, recals); - if( recalDatum == null ) { - throw new UserException("Encountered input variant which isn't found in the input recal file. Please make sure VariantRecalibrator and ApplyRecalibration were run on the same set of input variants. First seen at: " + vc ); + + String filterString; + final VariantContextBuilder builder = new VariantContextBuilder(vc); + if (!useASannotations) { + filterString = doSiteSpecificFiltering(vc, recals, builder); + } + else { //allele-specific mode + filterString = doAlleleSpecificFiltering(vc, recals, builder); } - final String lodString = recalDatum.getAttributeAsString(GATKVCFConstants.VQS_LOD_KEY, null); - if( lodString == null ) { - throw new UserException("Encountered a malformed record in the input recal file. There is no lod for the record at: " + vc ); - } - final double lod; - try { - lod = Double.valueOf(lodString); - } catch (NumberFormatException e) { - throw new UserException("Encountered a malformed record in the input recal file. The lod is unreadable for the record at: " + vc ); - } - - VariantContextBuilder builder = new VariantContextBuilder(vc); - - // Annotate the new record with its VQSLOD and the worst performing annotation - builder.attribute(GATKVCFConstants.VQS_LOD_KEY, lod); - builder.attribute(GATKVCFConstants.CULPRIT_KEY, recalDatum.getAttribute(GATKVCFConstants.CULPRIT_KEY)); - if ( recalDatum.hasAttribute(GATKVCFConstants.POSITIVE_LABEL_KEY)) - builder.attribute(GATKVCFConstants.POSITIVE_LABEL_KEY, true); - if ( recalDatum.hasAttribute(GATKVCFConstants.NEGATIVE_LABEL_KEY)) - builder.attribute(GATKVCFConstants.NEGATIVE_LABEL_KEY, true); - - final String filterString = generateFilterString(lod); + //for both non-AS and AS modes: if( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) { builder.passFilters(); + } else if(filterString.equals(VCFConstants.UNFILTERED)) { + builder.unfiltered(); } else { builder.filters(filterString); } @@ -328,6 +412,78 @@ public class ApplyRecalibration extends RodWalker implements T return 1; // This value isn't used for anything } + public double parseFilterLowerLimit(final String trancheFilter) { + final Pattern pattern = Pattern.compile("VQSRTranche\\S+(\\d+\\.\\d+)to(\\d+\\.\\d+)"); + final Matcher m = pattern.matcher(trancheFilter); + return m.find() ? Double.parseDouble(m.group(1)) : -1; + } + + /** + * Generate the VCF filter string for this record based on the ApplyRecalibration modes run so far + * @param vc the input VariantContext (with at least one ApplyRecalibration mode already run) + * @param bestLod best LOD from the alleles we've seen in this recalibration mode + * @return the String to use as the VCF filter field + */ + protected String generateFilterStringFromAlleles(final VariantContext vc, final double bestLod) { + String filterString = "."; + + final boolean bothModesWereRun = (MODE == VariantRecalibratorArgumentCollection.Mode.SNP && foundINDELTranches) || (MODE == VariantRecalibratorArgumentCollection.Mode.INDEL && foundSNPTranches); + final boolean onlyOneModeNeeded = !vc.isMixed() && VariantDataManager.checkVariationClass( vc, MODE ); + + //if both SNP and INDEL modes have not yet been run (and need to be), leave this variant as unfiltered and add the filters for the alleles in this mode to the INFO field + if (!bothModesWereRun && !onlyOneModeNeeded) { + return VCFConstants.UNFILTERED; + } + + //if both SNP and INDEL modes have been run or the site is not mixed, generate a filter string for this site based on both models + + //pull out the allele filter status from the info field (there may be more than one entry in the list if there were multiple snp/indel alleles assessed in the other mode) + final String prevFilterStatus = vc.getAttributeAsString(GATKVCFConstants.AS_FILTER_STATUS_KEY, null); + + //if this site hasn't had a filter applied yet + if (prevFilterStatus != null && !prevFilterStatus.equals(VCFConstants.UNFILTERED)) { + final String prevAllelesFilterStatusString = vc.getAttributeAsString(GATKVCFConstants.AS_FILTER_STATUS_KEY, null); + final String[] prevAllelesFilterStatusList = prevAllelesFilterStatusString.split(listPrintSeparator); + //start with the current best allele filter as the most lenient filter across all modes and all alleles + String mostLenientFilterName = generateFilterString(bestLod); + //if the current mode's best allele passes the tranche filter, then let the whole site pass + if (mostLenientFilterName.equals(VCFConstants.PASSES_FILTERS_v4)) { + filterString = mostLenientFilterName; + } + //if the current mode's best allele does not pass the tranche filter, compare the most lenient filter of this mode with those from the previous mode + else { + double mostLenientSensitivityLowerLimit = parseFilterLowerLimit(mostLenientFilterName); + for (int i = 0; i < prevAllelesFilterStatusList.length; i++) { + final String alleleFilterString = prevAllelesFilterStatusList[i].replaceAll(arrayParseRegex, "").trim(); + //if any allele from the previous mode passed the tranche filter, then let the whole site pass + if (alleleFilterString.equals(VCFConstants.PASSES_FILTERS_v4)) { //this allele is PASS + mostLenientFilterName = alleleFilterString; + break; + } + //if there's no PASS, then we need to parse the filters to find out how lenient they are + else { + final double alleleLowerLimit = parseFilterLowerLimit(alleleFilterString); + if (alleleLowerLimit == -1) + continue; + if (alleleLowerLimit < mostLenientSensitivityLowerLimit) { + mostLenientSensitivityLowerLimit = alleleLowerLimit; + mostLenientFilterName = alleleFilterString; + } + } + + } + filterString = mostLenientFilterName; + } + } + + //if both modes have been run, but the previous mode didn't apply a filter, use the current mode's best allele VQSLOD filter (shouldn't get run, but just in case) + else { + filterString = generateFilterString(bestLod); + } + + return filterString; + } + /** * Generate the VCF filter string for this record based on the provided lod score * @param lod non-null double @@ -358,16 +514,164 @@ public class ApplyRecalibration extends RodWalker implements T return filterString; } - private static VariantContext getMatchingRecalVC(final VariantContext target, final List recalVCs) { + private VariantContext getMatchingRecalVC(final VariantContext target, final List recalVCs, final Allele allele) { for( final VariantContext recalVC : recalVCs ) { if ( target.getEnd() == recalVC.getEnd() ) { - return recalVC; + if (!useASannotations) + return recalVC; + else if (allele.equals(recalVC.getAlternateAllele(0))) + return recalVC; } } - return null; } + /** + * + * @param altIndex current alt allele + * @param prevCulpritList culprits from previous ApplyRecalibration run + * @param prevLodList lods from previous ApplyRecalibration run + * @param prevASfiltersList AS_filters from previous ApplyRecalibration run + * @param culpritString + * @param lodString + * @param AS_filterString + */ + private void updateAnnotationsWithoutRecalibrating(final int altIndex, final String[] prevCulpritList, final String[] prevLodList, final String[] prevASfiltersList, + final List culpritString, final List lodString, final List AS_filterString) { + if (foundINDELTranches || foundSNPTranches) { + if (altIndex < prevCulpritList.length) { + culpritString.add(prevCulpritList[altIndex].replaceAll(arrayParseRegex, "").trim()); + lodString.add(prevLodList[altIndex].replaceAll(arrayParseRegex, "").trim()); + AS_filterString.add(prevASfiltersList[altIndex].replaceAll(arrayParseRegex, "").trim()); + } + } else { //if the other allele type hasn't been processed yet, make sure there are enough entries + culpritString.add(emptyStringValue); + lodString.add(emptyFloatValue); + AS_filterString.add(emptyStringValue); + } + } + + /** + * Calculate the allele-specific filter status of vc + * @param vc + * @param recals + * @param builder is modified by adding attributes + * @return a String with the filter status for this site + */ + private String doAlleleSpecificFiltering(final VariantContext vc, final List recals, final VariantContextBuilder builder) { + double bestLod = VariantRecalibratorEngine.MIN_ACCEPTABLE_LOD_SCORE; + final List culpritStrings = new ArrayList<>(); + final List lodStrings = new ArrayList<>(); + final List AS_filterStrings = new ArrayList<>(); + + String[] prevCulpritList = null; + String[] prevLodList = null; + String[] prevASfiltersList = null; + + //get VQSR annotations from previous run of ApplyRecalibration, if applicable + if(foundINDELTranches || foundSNPTranches) { + final String prevCulprits = vc.getAttributeAsString(GATKVCFConstants.AS_CULPRIT_KEY,""); + prevCulpritList = prevCulprits.isEmpty()? new String[0] : prevCulprits.split(listPrintSeparator); + final String prevLodString = vc.getAttributeAsString(GATKVCFConstants.AS_VQS_LOD_KEY,""); + prevLodList = prevLodString.isEmpty()? new String[0] : prevLodString.split(listPrintSeparator); + final String prevASfilters = vc.getAttributeAsString(GATKVCFConstants.AS_FILTER_STATUS_KEY,""); + prevASfiltersList = prevASfilters.isEmpty()? new String[0] : prevASfilters.split(listPrintSeparator); + } + + //for each allele in the current VariantContext + for (int altIndex = 0; altIndex < vc.getNAlleles()-1; altIndex++) { + final Allele allele = vc.getAlternateAllele(altIndex); + + //if the current allele is not part of this recalibration mode, add its annotations to the list and go to the next allele + if (!VariantDataManager.checkVariationClass(vc, allele, MODE)) { + updateAnnotationsWithoutRecalibrating(altIndex, prevCulpritList, prevLodList, prevASfiltersList, culpritStrings, lodStrings, AS_filterStrings); + continue; + } + + //if the current allele does need to have recalibration applied... + + //initialize allele-specific VQSR annotation data with values for spanning deletion + String alleleLodString = emptyFloatValue; + String alleleFilterString = emptyStringValue; + String alleleCulpritString = emptyStringValue; + + //if it's not a spanning deletion, replace those allele strings with the real values + if (!allele.equals(Allele.SPAN_DEL)) { + VariantContext recalDatum = getMatchingRecalVC(vc, recals, allele); + if (recalDatum == null) { + throw new UserException("Encountered input allele which isn't found in the input recal file. Please make sure VariantRecalibrator and ApplyRecalibration were run on the same set of input variants with flag -AS. First seen at: " + vc); + } + + //compare VQSLODs for all alleles in the current mode for filtering later + final double lod = recalDatum.getAttributeAsDouble(GATKVCFConstants.VQS_LOD_KEY, VariantRecalibratorEngine.MIN_ACCEPTABLE_LOD_SCORE); + if (lod > bestLod) + bestLod = lod; + + alleleLodString = String.format("%.4f", lod); + alleleFilterString = generateFilterString(lod); + alleleCulpritString = recalDatum.getAttributeAsString(GATKVCFConstants.CULPRIT_KEY, "."); + + if(recalDatum != null) { + if (recalDatum.hasAttribute(GATKVCFConstants.POSITIVE_LABEL_KEY)) + builder.attribute(GATKVCFConstants.POSITIVE_LABEL_KEY, true); + if (recalDatum.hasAttribute(GATKVCFConstants.NEGATIVE_LABEL_KEY)) + builder.attribute(GATKVCFConstants.NEGATIVE_LABEL_KEY, true); + } + } + + //append per-allele VQSR annotations + lodStrings.add(alleleLodString); + AS_filterStrings.add(alleleFilterString); + culpritStrings.add(alleleCulpritString); + } + + // Annotate the new record with its VQSLOD, AS_FilterStatus, and the worst performing annotation + if(!AS_filterStrings.isEmpty() ) + builder.attribute(GATKVCFConstants.AS_FILTER_STATUS_KEY, AnnotationUtils.encodeStringList(AS_filterStrings)); + if(!lodStrings.isEmpty()) + builder.attribute(GATKVCFConstants.AS_VQS_LOD_KEY, AnnotationUtils.encodeStringList(lodStrings)); + if(!culpritStrings.isEmpty()) + builder.attribute(GATKVCFConstants.AS_CULPRIT_KEY, AnnotationUtils.encodeStringList(culpritStrings)); + + return generateFilterStringFromAlleles(vc, bestLod); + } + + /** + * Calculate the filter status for a given VariantContext using the combined data from all alleles at a site + * @param vc + * @param recals + * @param builder is modified by adding attributes + * @return a String with the filter status for this site + */ + private String doSiteSpecificFiltering(final VariantContext vc, final List recals, final VariantContextBuilder builder) { + VariantContext recalDatum = getMatchingRecalVC(vc, recals, null); + if( recalDatum == null ) { + throw new UserException("Encountered input variant which isn't found in the input recal file. Please make sure VariantRecalibrator and ApplyRecalibration were run on the same set of input variants. First seen at: " + vc ); + } + + final String lodString = recalDatum.getAttributeAsString(GATKVCFConstants.VQS_LOD_KEY, null); + if( lodString == null ) { + throw new UserException("Encountered a malformed record in the input recal file. There is no lod for the record at: " + vc ); + } + final double lod; + try { + lod = Double.valueOf(lodString); + } catch (NumberFormatException e) { + throw new UserException("Encountered a malformed record in the input recal file. The lod is unreadable for the record at: " + vc ); + } + + builder.attribute(GATKVCFConstants.VQS_LOD_KEY, lod); + builder.attribute(GATKVCFConstants.CULPRIT_KEY, recalDatum.getAttribute(GATKVCFConstants.CULPRIT_KEY)); + if(recalDatum != null) { + if (recalDatum.hasAttribute(GATKVCFConstants.POSITIVE_LABEL_KEY)) + builder.attribute(GATKVCFConstants.POSITIVE_LABEL_KEY, true); + if (recalDatum.hasAttribute(GATKVCFConstants.NEGATIVE_LABEL_KEY)) + builder.attribute(GATKVCFConstants.NEGATIVE_LABEL_KEY, true); + } + + return generateFilterString(lod); + } + //--------------------------------------------------------------------------------------------------------------- // // reduce diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java index 624b6c062..0995fc10c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/GaussianMixtureModel.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -58,6 +58,7 @@ import org.broadinstitute.gatk.utils.Utils; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.List; /** @@ -70,7 +71,7 @@ public class GaussianMixtureModel { protected final static Logger logger = Logger.getLogger(GaussianMixtureModel.class); - private final ArrayList gaussians; + private final List gaussians; private final double shrinkage; private final double dirichletParameter; private final double priorCounts; @@ -97,6 +98,21 @@ public class GaussianMixtureModel { empiricalSigma.setMatrix(0, empiricalMu.length - 1, 0, empiricalMu.length - 1, Matrix.identity(empiricalMu.length, empiricalMu.length).times(200.0).inverse()); } + //this is used for the model output unit test + protected GaussianMixtureModel(final List gaussians, final double shrinkage, final double dirichletParameter, final double priorCounts ) { + this.gaussians = gaussians; + final int numAnnotations = gaussians.get(0).mu.length; + this.shrinkage = shrinkage; + this.dirichletParameter = dirichletParameter; + this.priorCounts = priorCounts; + empiricalMu = new double[numAnnotations]; + empiricalSigma = new Matrix(numAnnotations, numAnnotations); + isModelReadyForEvaluation = false; + Arrays.fill(empiricalMu, 0.0); + empiricalSigma.setMatrix(0, empiricalMu.length - 1, 0, empiricalMu.length - 1, Matrix.identity(empiricalMu.length, empiricalMu.length).times(200.0).inverse()); + + } + public void initializeRandomModel( final List data, final int numKMeansIterations ) { // initialize random Gaussian means // BUGBUG: this is broken up this way to match the order of calls to rand.nextDouble() in the old code @@ -295,4 +311,8 @@ public class GaussianMixtureModel { } return Math.log10( sumPVarInGaussian / ((double) numRandomDraws) ); } + + protected List getModelGaussians() {return Collections.unmodifiableList(gaussians);} + + protected int getNumAnnotations() {return empiricalMu.length;} } \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java index 7365340f2..db46b0c33 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/MultivariateGaussian.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java index 55a26bc42..1423c2cc8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrainingSet.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java index f6167e8c4..642fc7af3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/Tranche.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java index 2290f3c76..10b79c1e3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/TrancheManager.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java index cac206083..b1b19433c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -58,7 +58,6 @@ import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.vcf.VCFConstants; -import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import htsjdk.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.gatk.utils.help.HelpConstants; import org.broadinstitute.gatk.utils.collections.ExpandingArrayList; @@ -85,7 +84,7 @@ public class VariantDataManager { protected final static Logger logger = Logger.getLogger(VariantDataManager.class); protected final List trainingSets; private static final double SAFETY_OFFSET = 0.01; //To use for example as 1/(X + SAFETY_OFFSET) to protect against dividing or taking log of X=0. - private static final double PRECISION = 0.01; //To use mainly with MathUrils.compareDoubles(a,b,PRECISON) + private static final double PRECISION = 0.01; //To use mainly with MathUtils.compareDoubles(a,b,PRECISION) public VariantDataManager( final List annotationKeys, final VariantRecalibratorArgumentCollection VRAC ) { this.data = Collections.emptyList(); @@ -111,7 +110,7 @@ public class VariantDataManager { final double theSTD = standardDeviation(theMean, iii, true); logger.info( annotationKeys.get(iii) + String.format(": \t mean = %.2f\t standard deviation = %.2f", theMean, theSTD) ); if( Double.isNaN(theMean) ) { - throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See " + HelpConstants.forumPost("discussion/49/using-variant-annotator")); + throw new UserException.BadInput("Values for " + annotationKeys.get(iii) + " annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations."); } foundZeroVarianceAnnotation = foundZeroVarianceAnnotation || (theSTD < 1E-5); @@ -148,6 +147,14 @@ public class VariantDataManager { logger.info("Annotations are now ordered by their information content: " + annotationKeys.toString()); } + public double[] getMeanVector() { + return meanVector; + } + + public double[] getVarianceVector() { + return varianceVector; + } + /** * Get a list of indices which give the ascending sort order of the data array * @param inputVector the data to consider @@ -336,7 +343,7 @@ public class VariantDataManager { int iii = 0; for( final String key : annotationKeys ) { isNull[iii] = false; - annotations[iii] = decodeAnnotation( key, vc, jitter, VRAC ); + annotations[iii] = decodeAnnotation( key, vc, jitter, VRAC, datum ); if( Double.isNaN(annotations[iii]) ) { isNull[iii] = true; } iii++; } @@ -348,19 +355,31 @@ public class VariantDataManager { return Math.log((x - xmin)/(xmax - x)); } - private static double decodeAnnotation( final String annotationKey, final VariantContext vc, final boolean jitter, final VariantRecalibratorArgumentCollection vrac ) { + private static double decodeAnnotation( final String annotationKey, final VariantContext vc, final boolean jitter, final VariantRecalibratorArgumentCollection vrac, final VariantDatum datum ) { double value; final double LOG_OF_TWO = 0.6931472; try { - value = vc.getAttributeAsDouble( annotationKey, Double.NaN ); + //if we're in allele-specific mode and an allele-specific annotation has been requested, parse the appropriate value from the list + if(vrac.useASannotations && annotationKey.startsWith(GATKVCFConstants.ALLELE_SPECIFIC_PREFIX)) { + final List valueList = vc.getAttributeAsList(annotationKey); + if (vc.hasAllele(datum.alternateAllele)) { + final int altIndex = vc.getAlleleIndex(datum.alternateAllele)-1; //-1 is to convert the index from all alleles (including reference) to just alternate alleles + value = Double.parseDouble((String)valueList.get(altIndex)); + } + //if somehow our alleles got mixed up + else + throw new IllegalStateException("VariantDatum allele " + datum.alternateAllele + " is not contained in the input VariantContext."); + } + else + value = vc.getAttributeAsDouble( annotationKey, Double.NaN ); if( Double.isInfinite(value) ) { value = Double.NaN; } - if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } - if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } - if( jitter && annotationKey.equalsIgnoreCase("InbreedingCoeff") && MathUtils.compareDoubles(value, 0.0, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } - if( jitter && annotationKey.equalsIgnoreCase("SOR") && MathUtils.compareDoubles(value, LOG_OF_TWO, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } //min SOR is 2.0, then we take ln - if( jitter && annotationKey.equalsIgnoreCase("MQ")) { + if( jitter && annotationKey.equalsIgnoreCase(GATKVCFConstants.HAPLOTYPE_SCORE_KEY) && MathUtils.compareDoubles(value, 0.0, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } + if( jitter && (annotationKey.equalsIgnoreCase(GATKVCFConstants.FISHER_STRAND_KEY) || annotationKey.equalsIgnoreCase(GATKVCFConstants.AS_FILTER_STATUS_KEY)) && MathUtils.compareDoubles(value, 0.0, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } + if( jitter && annotationKey.equalsIgnoreCase(GATKVCFConstants.INBREEDING_COEFFICIENT_KEY) && MathUtils.compareDoubles(value, 0.0, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } + if( jitter && (annotationKey.equalsIgnoreCase(GATKVCFConstants.STRAND_ODDS_RATIO_KEY) || annotationKey.equalsIgnoreCase(GATKVCFConstants.AS_STRAND_ODDS_RATIO_KEY)) && MathUtils.compareDoubles(value, LOG_OF_TWO, PRECISION) == 0 ) { value += 0.01 * Utils.getRandomGenerator().nextGaussian(); } //min SOR is 2.0, then we take ln + if( jitter && (annotationKey.equalsIgnoreCase(VCFConstants.RMS_MAPPING_QUALITY_KEY) || annotationKey.equalsIgnoreCase(GATKVCFConstants.AS_RMS_MAPPING_QUALITY_KEY))) { if( vrac.MQ_CAP > 0) { value = logitTransform(value, -SAFETY_OFFSET, vrac.MQ_CAP + SAFETY_OFFSET); if (MathUtils.compareDoubles(value, logitTransform(vrac.MQ_CAP, -SAFETY_OFFSET, vrac.MQ_CAP + SAFETY_OFFSET), PRECISION) == 0 ) { @@ -386,6 +405,8 @@ public class VariantDataManager { for( final TrainingSet trainingSet : trainingSets ) { for( final VariantContext trainVC : tracker.getValues(trainingSet.rodBinding, genomeLoc) ) { + if (VRAC.useASannotations && !doAllelesMatch(trainVC, datum)) + continue; if( isValidVariant( evalVC, trainVC, TRUST_ALL_POLYMORPHIC ) ) { datum.isKnown = datum.isKnown || trainingSet.isKnown; datum.atTruthSite = datum.atTruthSite || trainingSet.isTruth; @@ -405,6 +426,11 @@ public class VariantDataManager { (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphicInSamples()); } + private boolean doAllelesMatch(final VariantContext trainVC, final VariantDatum datum) { + //only do this check in the allele-specific case, where each datum represents one allele + return datum.alternateAllele == null || trainVC.getAlternateAlleles().contains(datum.alternateAllele); + } + protected static boolean checkVariationClass( final VariantContext evalVC, final VariantContext trainVC ) { switch( trainVC.getType() ) { case SNP: @@ -428,7 +454,21 @@ public class VariantDataManager { case BOTH: return true; default: - throw new ReviewedGATKException( "Encountered unknown recal mode: " + mode ); + throw new IllegalStateException( "Encountered unknown recal mode: " + mode ); + } + } + + protected static boolean checkVariationClass( final VariantContext evalVC, final Allele allele, final VariantRecalibratorArgumentCollection.Mode mode ) { + switch( mode ) { + case SNP: + //note that spanning deletions are considered SNPs by this logic + return evalVC.getReference().length() == allele.length(); + case INDEL: + return (evalVC.getReference().length() != allele.length()) || allele.isSymbolic(); + case BOTH: + return true; + default: + throw new IllegalStateException( "Encountered unknown recal mode: " + mode ); } } @@ -440,9 +480,11 @@ public class VariantDataManager { }} ); // create dummy alleles to be used - final List alleles = Arrays.asList(Allele.create("N", true), Allele.create("", false)); + List alleles = Arrays.asList(Allele.create("N", true), Allele.create("", false)); for( final VariantDatum datum : data ) { + if (VRAC.useASannotations) + alleles = Arrays.asList(datum.referenceAllele, datum.alternateAllele); //use the alleles to distinguish between multiallelics in AS mode VariantContextBuilder builder = new VariantContextBuilder("VQSR", datum.loc.getContig(), datum.loc.getStart(), datum.loc.getStop(), alleles); builder.attribute(VCFConstants.END_KEY, datum.loc.getStop()); builder.attribute(GATKVCFConstants.VQS_LOD_KEY, String.format("%.4f", datum.lod)); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java index 8fe785769..ca14e0ae6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDatum.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,6 +51,7 @@ package org.broadinstitute.gatk.tools.walkers.variantrecalibration; +import htsjdk.variant.variantcontext.Allele; import org.broadinstitute.gatk.utils.GenomeLoc; import java.io.Serializable; @@ -79,8 +80,11 @@ public class VariantDatum { public int consensusCount; public GenomeLoc loc; public int worstAnnotation; + public double worstValue; public MultivariateGaussian assignment; // used in K-means implementation public boolean isAggregate; // this datum was provided to aid in modeling but isn't part of the input callset + public Allele referenceAllele; + public Allele alternateAllele; public static class VariantDatumLODComparator implements Comparator, Serializable { @Override diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java index 09a5dc985..416d72c67 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,6 +51,7 @@ package org.broadinstitute.gatk.tools.walkers.variantrecalibration; +import htsjdk.variant.variantcontext.Allele; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; @@ -64,6 +65,8 @@ import org.broadinstitute.gatk.utils.QualityUtils; import org.broadinstitute.gatk.utils.R.RScriptExecutor; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; @@ -79,19 +82,13 @@ import java.io.FileNotFoundException; import java.io.PrintStream; import java.util.*; +import Jama.Matrix; + /** * Build a recalibration model to score variant quality for filtering purposes * *

- * This tool performs the first pass in a two-stage process called VQSR; the second pass is performed by the - * ApplyRecalibration tool. - * In brief, the first pass consists of creating a Gaussian mixture model by looking at the distribution of annotation - * values over a high quality subset of the input call set, and then scoring all input variants according to the model. - * The second pass consists of filtering variants based on score cutoffs identified in the first pass. - *

- * - *

- * The purpose of the variant recalibrator is to assign a well-calibrated probability to each variant call in a call set. + * The purpose of variant recalibration is to assign a well-calibrated probability to each variant call in a call set. * You can then create highly accurate call sets by filtering based on this single estimate for the accuracy of each call. * The approach taken by variant quality score recalibration is to develop a continuous, covarying estimate of the relationship * between SNP call annotations (such as QD, MQ, and ReadPosRankSum, for example) and the probability that a SNP is a true genetic @@ -101,6 +98,14 @@ import java.util.*; * probability that each call is real. The score that gets added to the INFO field of each variant is called the VQSLOD. It is * the log odds of being a true variant versus being false under the trained Gaussian mixture model. *

+ * + *

+ * This tool performs the first pass in a two-stage process called VQSR; the second pass is performed by the + * ApplyRecalibration tool. + * In brief, the first pass consists of creating a Gaussian mixture model by looking at the distribution of annotation + * values over a high quality subset of the input call set, and then scoring all input variants according to the model. + * The second pass consists of filtering variants based on score cutoffs identified in the first pass. + *

* *

VQSR is probably the hardest part of the Best Practices to get right, so be sure to read the * method documentation, @@ -110,7 +115,10 @@ import java.util.*; * *

Inputs

*
    - *
  • The input raw variants to be recalibrated.
    • + *
  • The input raw variants to be recalibrated. These variant calls must be annotated with the annotations that will be used for modeling. + * If the calls come from multiple samples, they must have been obtained by joint calling the samples, either directly (running HaplotypeCaller + * on all samples together) or via the GVCF workflow (HaplotypeCaller with -ERC GVCF per-sample then GenotypeGVCFs on the resulting gVCFs) + * which is more scalable.
    • *
  • Known, truth, and training sets to be used by the algorithm. See the method documentation for more details.
    • *
* @@ -130,7 +138,7 @@ import java.util.*; * -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \ * -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf \ * -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.vcf - * -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_135.b37.vcf \ + * -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_135.b37.vcf \ * -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff \ * -mode SNP \ * -recalFile output.recal \ @@ -138,6 +146,26 @@ import java.util.*; * -rscriptFile output.plots.R * * + *

Allele-specfic usage

+ * 
+ * java -Xmx4g -jar GenomeAnalysisTK.jar \
+ *   -T VariantRecalibrator \
+ *   -R reference.fasta \
+ *   -input raw_variants.withASannotations.vcf \
+ *   -AS \
+ *   -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \
+ *   -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf \
+ *   -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.vcf
+ *   -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_135.b37.vcf \
+ *   -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff \
+ *   -mode SNP \
+ *   -recalFile output.AS.recal \
+ *   -tranchesFile output.AS.tranches \
+ *   -rscriptFile output.plots.AS.R
+ *
+ * The input VCF must have been produced using allele-specific annotations in HaplotypeCaller. + * Note that each allele will have a separate line in the output .recal file with its own VQSLOD and culprit that will be transferred to the final VCF in ApplyRecalibration. + * *

Caveats

* *
    @@ -166,9 +194,13 @@ public class VariantRecalibrator extends RodWalker> inputCollections; final private List> input = new ArrayList<>(); @@ -233,11 +265,38 @@ public class VariantRecalibrator extends RodWalker replicate = new ArrayList<>(); + /** + * The statistical model being built by this tool may fail due to simple statistical sampling + * issues. Rather than dying immediately when the initial model fails, this argument allows the + * tool to restart with a different random seed and try to build the model again. The first + * successfully built model will be kept. + * + * Note that the most common underlying cause of model building failure is that there is insufficient data to + * build a really robust model. This argument provides a workaround for that issue but it is + * preferable to provide this tool with more data (typically by including more samples or more territory) + * in order to generate a more robust model. + */ + @Advanced + @Argument(fullName="max_attempts", shortName = "max_attempts", doc="Number of attempts to build a model before failing", required=false) + protected int max_attempts = 1; + ///////////////////////////// // Debug Arguments ///////////////////////////// @@ -341,23 +400,16 @@ public class VariantRecalibrator extends RodWalker variants, final boolean isInput, final RefMetaDataTracker tracker, final AlignmentContext context, final VariantContext vc, final Allele refAllele, final Allele altAllele) { + final VariantDatum datum = new VariantDatum(); + + // Populate the datum with lots of fields from the VariantContext, unfortunately the VC is too big so we just pull in only the things we absolutely need. + datum.referenceAllele = refAllele; + datum.alternateAllele = altAllele; + dataManager.decodeAnnotations(datum, vc, true); //BUGBUG: when run with HierarchicalMicroScheduler this is non-deterministic because order of calls depends on load of machine + datum.loc = (isInput ? getToolkit().getGenomeLocParser().createGenomeLoc(vc) : null); + datum.originalQual = vc.getPhredScaledQual(); + datum.isSNP = vc.isSNP() && vc.isBiallelic(); + datum.isTransition = datum.isSNP && GATKVariantContextUtils.isTransition(vc); + datum.isAggregate = !isInput; + + // Loop through the training data sets and if they overlap this locus (and allele, if applicable) then update the prior and training status appropriately + dataManager.parseTrainingSets(tracker, context.getLocation(), vc, datum, TRUST_ALL_POLYMORPHIC); + final double priorFactor = QualityUtils.qualToProb(datum.prior); + datum.prior = Math.log10(priorFactor) - Math.log10(1.0 - priorFactor); + + variants.add(datum); + } + + //--------------------------------------------------------------------------------------------------------------- // // reduce @@ -396,51 +474,154 @@ public class VariantRecalibrator extends RodWalker reduceSum ) { - dataManager.setData( reduceSum ); - dataManager.normalizeData(); // Each data point is now (x - mean) / standard deviation + for (int i = 1; i <= max_attempts; i++) { + try { + dataManager.setData(reduceSum); + dataManager.normalizeData(); // Each data point is now (x - mean) / standard deviation - // Generate the positive model using the training data and evaluate each variant - final List positiveTrainingData = dataManager.getTrainingData(); - final GaussianMixtureModel goodModel = engine.generateModel( positiveTrainingData, VRAC.MAX_GAUSSIANS ); - engine.evaluateData( dataManager.getData(), goodModel, false ); + // Generate the positive model using the training data and evaluate each variant + final List positiveTrainingData = dataManager.getTrainingData(); + final GaussianMixtureModel goodModel = engine.generateModel(positiveTrainingData, VRAC.MAX_GAUSSIANS); + engine.evaluateData(dataManager.getData(), goodModel, false); - // Generate the negative model using the worst performing data and evaluate each variant contrastively - final List negativeTrainingData = dataManager.selectWorstVariants(); - final GaussianMixtureModel badModel = engine.generateModel( negativeTrainingData, Math.min(VRAC.MAX_GAUSSIANS_FOR_NEGATIVE_MODEL, VRAC.MAX_GAUSSIANS)); - dataManager.dropAggregateData(); // Don't need the aggregate data anymore so let's free up the memory - engine.evaluateData( dataManager.getData(), badModel, true ); + // Generate the negative model using the worst performing data and evaluate each variant contrastively + final List negativeTrainingData = dataManager.selectWorstVariants(); + final GaussianMixtureModel badModel = engine.generateModel(negativeTrainingData, Math.min(VRAC.MAX_GAUSSIANS_FOR_NEGATIVE_MODEL, VRAC.MAX_GAUSSIANS)); + dataManager.dropAggregateData(); // Don't need the aggregate data anymore so let's free up the memory + engine.evaluateData(dataManager.getData(), badModel, true); - if( badModel.failedToConverge || goodModel.failedToConverge ) { - throw new UserException("NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider " + (badModel.failedToConverge ? "raising the number of variants used to train the negative model (via --minNumBadVariants 5000, for example)." : "lowering the maximum number of Gaussians allowed for use in the model (via --maxGaussians 4, for example).") ); + if (badModel.failedToConverge || goodModel.failedToConverge) { + throw new UserException("NaN LOD value assigned. Clustering with this few variants and these annotations is unsafe. Please consider " + (badModel.failedToConverge ? "raising the number of variants used to train the negative model (via --minNumBadVariants 5000, for example)." : "lowering the maximum number of Gaussians allowed for use in the model (via --maxGaussians 4, for example).")); + } + + if (outputModel) { + GATKReport report = writeModelReport(goodModel, badModel, USE_ANNOTATIONS); + report.print(modelReport); + } + + engine.calculateWorstPerformingAnnotation(dataManager.getData(), goodModel, badModel); + + // Find the VQSLOD cutoff values which correspond to the various tranches of calls requested by the user + final int nCallsAtTruth = TrancheManager.countCallsAtTruth(dataManager.getData(), Double.NEGATIVE_INFINITY); + final TrancheManager.SelectionMetric metric = new TrancheManager.TruthSensitivityMetric(nCallsAtTruth); + final List tranches = TrancheManager.findTranches(dataManager.getData(), TS_TRANCHES, metric, VRAC.MODE); + tranchesStream.print(Tranche.tranchesString(tranches)); + + logger.info("Writing out recalibration table..."); + dataManager.writeOutRecalibrationTable(recalWriter); + if (RSCRIPT_FILE != null) { + logger.info("Writing out visualization Rscript file..."); + createVisualizationScript(dataManager.getRandomDataForPlotting(1000, positiveTrainingData, negativeTrainingData, dataManager.getEvaluationData()), goodModel, badModel, 0.0, dataManager.getAnnotationKeys().toArray(new String[USE_ANNOTATIONS.size()])); + } + + if (VRAC.MODE == VariantRecalibratorArgumentCollection.Mode.INDEL) { + // Print out an info message to make it clear why the tranches plot is not generated + logger.info("Tranches plot will not be generated since we are running in INDEL mode"); + } else { + // Execute the RScript command to plot the table of truth values + RScriptExecutor executor = new RScriptExecutor(); + executor.addScript(new Resource(PLOT_TRANCHES_RSCRIPT, VariantRecalibrator.class)); + executor.addArgs(TRANCHES_FILE.getAbsoluteFile(), TARGET_TITV); + // Print out the command line to make it clear to the user what is being executed and how one might modify it + logger.info("Executing: " + executor.getApproximateCommandLine()); + executor.exec(); + } + return; + } catch (Exception e) { + if (i == max_attempts) { + throw e; + } else { + logger.info(String.format("Exception occurred on attempt %d of %d. Trying again. Message was: '%s'", i, max_attempts, e.getMessage())); + } + } + } + } + + protected GATKReport writeModelReport(final GaussianMixtureModel goodModel, final GaussianMixtureModel badModel, List annotationList) { + final String formatString = "%.3f"; + final GATKReport report = new GATKReport(); + + if (dataManager != null) { //for unit test + final double[] meanVector = dataManager.getMeanVector(); + GATKReportTable annotationMeans = makeVectorTable("AnnotationMeans", "Mean for each annotation, used to normalize data", dataManager.annotationKeys, meanVector, "Mean", formatString); + report.addTable(annotationMeans); + + final double[] varianceVector = dataManager.getVarianceVector(); //"varianceVector" is actually stdev + GATKReportTable annotationVariances = makeVectorTable("AnnotationStdevs", "Standard deviation for each annotation, used to normalize data", dataManager.annotationKeys, varianceVector, "Standard deviation", formatString); + report.addTable(annotationVariances); } - engine.calculateWorstPerformingAnnotation( dataManager.getData(), goodModel, badModel ); + //The model and Gaussians don't know what the annotations are, so get them from this class + //VariantDataManager keeps the annotation in the same order as the argument list + GATKReportTable positiveMeans = makeMeansTable("PositiveModelMeans", "Vector of annotation values to describe the (normalized) mean for each Gaussian in the positive model", annotationList, goodModel, formatString); + report.addTable(positiveMeans); - // Find the VQSLOD cutoff values which correspond to the various tranches of calls requested by the user - final int nCallsAtTruth = TrancheManager.countCallsAtTruth( dataManager.getData(), Double.NEGATIVE_INFINITY ); - final TrancheManager.SelectionMetric metric = new TrancheManager.TruthSensitivityMetric( nCallsAtTruth ); - final List tranches = TrancheManager.findTranches( dataManager.getData(), TS_TRANCHES, metric, VRAC.MODE ); - tranchesStream.print(Tranche.tranchesString( tranches )); + GATKReportTable positiveCovariance = makeCovariancesTable("PositiveModelCovariances", "Matrix to describe the (normalized) covariance for each Gaussian in the positive model; covariance matrices are joined by row", annotationList, goodModel, formatString); + report.addTable(positiveCovariance); - logger.info( "Writing out recalibration table..." ); - dataManager.writeOutRecalibrationTable( recalWriter ); - if( RSCRIPT_FILE != null ) { - logger.info( "Writing out visualization Rscript file..."); - createVisualizationScript( dataManager.getRandomDataForPlotting( 1000, positiveTrainingData, negativeTrainingData, dataManager.getEvaluationData() ), goodModel, badModel, 0.0, dataManager.getAnnotationKeys().toArray(new String[USE_ANNOTATIONS.size()]) ); + //do the same for the negative model means + GATKReportTable negativeMeans = makeMeansTable("NegativeModelMeans", "Vector of annotation values to describe the (normalized) mean for each Gaussian in the negative model", annotationList, badModel, formatString); + report.addTable(negativeMeans); + + GATKReportTable negativeCovariance = makeCovariancesTable("NegativeModelCovariances", "Matrix to describe the (normalized) covariance for each Gaussian in the negative model; covariance matrices are joined by row", annotationList, badModel, formatString); + report.addTable(negativeCovariance); + + return report; + } + + protected GATKReportTable makeVectorTable(final String tableName, final String tableDescription, final List annotationList, final double[] perAnnotationValues, final String columnName, final String formatString) { + GATKReportTable vectorTable = new GATKReportTable(tableName, tableDescription, annotationList.size(), GATKReportTable.TableSortingWay.DO_NOT_SORT); + vectorTable.addColumn("Annotation"); + vectorTable.addColumn(columnName, formatString); + for (int i = 0; i < perAnnotationValues.length; i++) { + vectorTable.addRowIDMapping(annotationList.get(i), i, true); + vectorTable.set(i, 1, perAnnotationValues[i]); } + return vectorTable; + } - if(VRAC.MODE == VariantRecalibratorArgumentCollection.Mode.INDEL) { - // Print out an info message to make it clear why the tranches plot is not generated - logger.info("Tranches plot will not be generated since we are running in INDEL mode"); - } else { - // Execute the RScript command to plot the table of truth values - RScriptExecutor executor = new RScriptExecutor(); - executor.addScript(new Resource(PLOT_TRANCHES_RSCRIPT, VariantRecalibrator.class)); - executor.addArgs(TRANCHES_FILE.getAbsoluteFile(), TARGET_TITV); - // Print out the command line to make it clear to the user what is being executed and how one might modify it - logger.info("Executing: " + executor.getApproximateCommandLine()); - executor.exec(); + private GATKReportTable makeMeansTable(final String tableName, final String tableDescription, final List annotationList, final GaussianMixtureModel model, final String formatString) { + GATKReportTable meansTable = new GATKReportTable(tableName, tableDescription, annotationList.size(), GATKReportTable.TableSortingWay.DO_NOT_SORT); + meansTable.addColumn("Gaussian"); + for (final String annotationName : annotationList) { + meansTable.addColumn(annotationName, formatString); } + final List modelGaussians = model.getModelGaussians(); + for (int i = 0; i < modelGaussians.size(); i++) { + final MultivariateGaussian gaussian = modelGaussians.get(i); + final double[] meanVec = gaussian.mu; + if (meanVec.length != annotationList.size()) + throw new IllegalStateException("Gaussian mean vector does not have the same size as the list of annotations"); + meansTable.addRowIDMapping(i, i, true); + for (int j = 0; j < annotationList.size(); j++) + meansTable.set(i, annotationList.get(j), meanVec[j]); + } + return meansTable; + } + + private GATKReportTable makeCovariancesTable(final String tableName, final String tableDescription, final List annotationList, final GaussianMixtureModel model, final String formatString) { + GATKReportTable modelCovariances = new GATKReportTable(tableName, tableDescription, annotationList.size()+2, GATKReportTable.TableSortingWay.DO_NOT_SORT); //+2 is for Gaussian and Annotation columns + modelCovariances.addColumn("Gaussian"); + modelCovariances.addColumn("Annotation"); + for (final String annotationName : annotationList) { + modelCovariances.addColumn(annotationName, formatString); + } + final List modelGaussians = model.getModelGaussians(); + for (int i = 0; i < modelGaussians.size(); i++) { + final MultivariateGaussian gaussian = modelGaussians.get(i); + final Matrix covMat = gaussian.sigma; + if (covMat.getRowDimension() != annotationList.size() || covMat.getColumnDimension() != annotationList.size()) + throw new IllegalStateException("Gaussian covariance matrix does not have the same size as the list of annotations"); + for (int j = 0; j < annotationList.size(); j++) { + modelCovariances.set(j + i * annotationList.size(), "Gaussian", i); + modelCovariances.set(j + i * annotationList.size(), "Annotation", annotationList.get(j)); + for (int k = 0; k < annotationList.size(); k++) { + modelCovariances.set(j + i * annotationList.size(), annotationList.get(k), covMat.get(j, k)); + + } + } + } + return modelCovariances; } private void createVisualizationScript( final List randomData, final GaussianMixtureModel goodModel, final GaussianMixtureModel badModel, final double lodCutoff, final String[] annotationKeys ) { diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java index 4d11f3ef8..83b5a3262 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -83,6 +83,13 @@ public class VariantRecalibratorArgumentCollection { @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ", required = true) public VariantRecalibratorArgumentCollection.Mode MODE = VariantRecalibratorArgumentCollection.Mode.SNP; + /** + * Generate a VQSR model using per-allele data instead of the default per-site data, assuming that the input VCF contains allele-specific annotations. + * Annotations should be specified using their full names with AS_ prefix. Non-allele-specific (scalar) annotations will be applied to all alleles. + */ + @Argument(fullName="useAlleleSpecificAnnotations", shortName="AS", doc="If specified, the variant recalibrator will attempt to use the allele-specific versions of the specified annotations.", required=false) + public boolean useASannotations = false; + /** * This parameter determines the maximum number of Gaussians that should be used when building a positive model * using the variational Bayes algorithm. @@ -196,7 +203,8 @@ public class VariantRecalibratorArgumentCollection { ///////////////////////////// // Deprecated Arguments - // Keeping them here is meant to provide users with error messages that are more informative than "arg not defined" when they use an argument that has been put out of service + // Keeping them here is meant to provide users with error messages that are more informative than "arg not defined" + // when they use an argument that has been put out of service ///////////////////////////// @Hidden diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java index ddaf5d400..f86099113 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorEngine.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -123,15 +123,17 @@ public class VariantRecalibratorEngine { for( final VariantDatum datum : data ) { int worstAnnotation = -1; double minProb = Double.MAX_VALUE; + double worstValue = -1; for( int iii = 0; iii < datum.annotations.length; iii++ ) { final Double goodProbLog10 = goodModel.evaluateDatumInOneDimension(datum, iii); final Double badProbLog10 = badModel.evaluateDatumInOneDimension(datum, iii); if( goodProbLog10 != null && badProbLog10 != null ) { final double prob = goodProbLog10 - badProbLog10; - if(prob < minProb) { minProb = prob; worstAnnotation = iii; } + if(prob < minProb) { minProb = prob; worstAnnotation = iii; worstValue = datum.annotations[iii];} } } datum.worstAnnotation = worstAnnotation; + datum.worstValue = worstValue; } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java index dc9b06354..224caa97f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -186,7 +186,7 @@ import java.util.*; * * */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} ) public class CalculateGenotypePosteriors extends RodWalker { /** diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java index 324e3e1e0..ca2988d81 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -54,6 +54,7 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.gatk.utils.commandline.*; import org.broadinstitute.gatk.engine.CommandLineGATK; import org.broadinstitute.gatk.utils.contexts.AlignmentContext; @@ -129,7 +130,7 @@ public class CombineGVCFs extends RodWalker implements AnnotatorCompatible, TreeReducible { - /** * The gVCF files to merge together */ @@ -169,7 +171,7 @@ public class GenotypeGVCFs extends RodWalker annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{"Standard"})); + protected List annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{StandardAnnotation.class.getSimpleName()})); /** @@ -210,21 +212,20 @@ public class GenotypeGVCFs extends RodWalker vcfRods = GATKVCFUtils.getVCFHeadersFromRods(toolkit, variants); - final GATKVariantContextUtils.GenotypeMergeType mergeType; - if(uniquifySamples) { - mergeType = GATKVariantContextUtils.GenotypeMergeType.UNIQUIFY; - } - else - mergeType = GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE; - + final GATKVariantContextUtils.GenotypeMergeType mergeType = uniquifySamples ? + GATKVariantContextUtils.GenotypeMergeType.UNIQUIFY : GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE; final SampleList samples = new IndexedSampleList(SampleUtils.getSampleList(vcfRods, mergeType)); - // create the annotation engine + annotationEngine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, Collections.emptyList(), this, toolkit); // create the genotyping engine - boolean doAlleleSpecificGenotyping = annotationsToUse.contains(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY) || annotationGroupsToUse.contains("AS_Standard"); - genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(), GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit, genotypeArgs, logger), - toolkit.getArguments().BAQMode, doAlleleSpecificGenotyping); + // when checking for presence of AS_StandardAnnotation we must deal with annoying feature that + // the class name with or without the trailing "Annotation" are both valid command lines + boolean doAlleleSpecificGenotyping = annotationsToUse.contains(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY) + || annotationGroupsToUse.contains(AS_StandardAnnotation.class.getSimpleName()) + || annotationGroupsToUse.contains(AS_StandardAnnotation.class.getSimpleName().replace("Annotation", "")); + genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(), + GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit, genotypeArgs, logger), toolkit.getArguments().BAQMode, doAlleleSpecificGenotyping); // take care of the VCF headers final Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); @@ -249,15 +250,18 @@ public class GenotypeGVCFs extends RodWalker vcsAtThisLocus = tracker.getPrioritizedValue(variants, loc); + final Byte refBase = INCLUDE_NON_VARIANTS ? ref.getBase() : null; + final boolean removeNonRefSymbolicAllele = !INCLUDE_NON_VARIANTS; + final VariantContext combinedVC = ReferenceConfidenceVariantContextMerger.merge(vcsAtThisLocus, loc, + refBase, removeNonRefSymbolicAllele, uniquifySamples, annotationEngine); + return combinedVC == null ? null : regenotypeVC(tracker, ref, combinedVC); } /** @@ -269,65 +273,67 @@ public class GenotypeGVCFs extends RodWalker 0 ) { + result = genotypingEngine.calculateGenotypes(originalVC); + } + + if (result == null || (!isProperlyPolymorphic(result) && !INCLUDE_NON_VARIANTS)) { + return null; + } + + result = addGenotypingAnnotations(originalVC.getAttributes(), result); //At this point we should already have DP and AD annotated - VariantContext result = annotationEngine.finalizeAnnotations(rawResult, originalVC); + result = annotationEngine.finalizeAnnotations(result, originalVC); //do trimming after allele-specific annotation reduction or the mapping is difficult result = GATKVariantContextUtils.reverseTrimAlleles(result); - // if it turned monomorphic then we either need to ignore or fix such sites - boolean createRefGTs = false; - if ( result.isMonomorphicInSamples() ) { - if ( !INCLUDE_NON_VARIANTS ) - return null; - createRefGTs = true; - } // Re-annotate and fix/remove some of the original annotations. // Note that the order of these actions matters and is different for polymorphic and monomorphic sites. // For polymorphic sites we need to make sure e.g. the SB tag is sent to the annotation engine and then removed later. // For monomorphic sites we need to make sure e.g. the hom ref genotypes are created and only then are passed to the annotation engine. // We could theoretically make 2 passes to re-create the genotypes, but that gets extremely expensive with large sample sizes. - if ( createRefGTs ) { + if (result.isPolymorphicInSamples()) { + result = annotationEngine.annotateContext(tracker, ref, null, result); + result = new VariantContextBuilder(result).genotypes(cleanupGenotypeAnnotations(result, false)).make(); + } else if (INCLUDE_NON_VARIANTS) { result = new VariantContextBuilder(result).genotypes(cleanupGenotypeAnnotations(result, true)).make(); result = annotationEngine.annotateContext(tracker, ref, null, result); } else { - result = annotationEngine.annotateContext(tracker, ref, null, result); - result = new VariantContextBuilder(result).genotypes(cleanupGenotypeAnnotations(result, false)).make(); + return null; } - return result; } /** - * Determines whether the provided VariantContext has real alternate alleles + * Determines whether the provided VariantContext has real alternate alleles. + * + * There is a bit of a hack to handle the case because it is not defined in htsjdk.Allele + * We check for this as a biallelic symbolic allele. * * @param vc the VariantContext to evaluate * @return true if it has proper alternate alleles, false otherwise */ private boolean isProperlyPolymorphic(final VariantContext vc) { - return ( vc != null && - !vc.getAlternateAlleles().isEmpty() && - (!vc.isBiallelic() || - (!vc.getAlternateAllele(0).equals(Allele.SPAN_DEL) && - !vc.getAlternateAllele(0).equals(GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED)) - ) - ); + //obvious cases + if (vc == null || vc.getAlternateAlleles().isEmpty()) { + return false; + } else if (vc.isBiallelic()) { + return !(vc.getAlternateAllele(0).equals(Allele.SPAN_DEL) || + vc.getAlternateAllele(0).equals(GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED) || + vc.isSymbolic()); + } else { + return true; + } } /** @@ -429,6 +435,9 @@ public class GenotypeGVCFs extends RodWalker * */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} ) public class RegenotypeVariants extends RodWalker implements TreeReducible { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java index c56cba9af..fb830e41e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/SequenceComplexity.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/cancer/TestingReadUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/cancer/TestingReadUtils.java index bb8105ec1..8855681d1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/cancer/TestingReadUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/cancer/TestingReadUtils.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java index 55c4b43b5..6eefb6228 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/CountSet.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java index 91b08a61b..4111d4fc2 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/collections/IntMaxHeap.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java index c386272e7..62abd11e6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gga/GenotypingGivenAllelesUtils.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java index 3b287a1f1..18379f990 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriter.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java index eba6d6771..cb77de1ab 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlock.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java index 9824e08fa..de6b43f55 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java index 97aacb559..7631844a1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/DroppedReadsTracker.java similarity index 55% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/DroppedReadsTracker.java index 54ed375e0..b4bfc1519 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/DroppedReadsTracker.java @@ -1,44 +1,44 @@ /* * By downloading the PROGRAM you agree to the following terms of use: -* +* * BROAD INSTITUTE * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* +* +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). +* * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. * NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* +* * 1. DEFINITIONS * 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* +* * 2. LICENSE * 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. * The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. * 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* +* * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* +* * 5. INDEMNIFICATION * LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* +* * 6. NO REPRESENTATIONS OR WARRANTIES * THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. * IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* +* * 7. ASSIGNMENT * This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* +* * 8. MISCELLANEOUS * 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. * 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. @@ -49,130 +49,164 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.engine.recalibration; +package org.broadinstitute.gatk.utils.haplotypeBAMWriter; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.Utils; -import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; -import org.testng.Assert; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; +import com.google.common.hash.HashFunction; +import com.google.common.hash.Hashing; +import htsjdk.samtools.SAMTag; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.LinkedList; -import java.util.List; +import java.util.*; -public final class RecalUtilsUnitTest extends BaseTest { - private class Row { - int rg, qual, ne, no; +/** + * Class for tracking and emitting reads dropped by HaplotypeCaller due to filtering, trimming, etc. Reads are + * categorized per ActiveRegion by reason, and then emitted to the HaplotypeBAMWriter's bamout read destination, + * with an "FT" attribute with a value corresponding to the reason the reads were dropped. + */ +public class DroppedReadsTracker { - private Row(final Row copy) { - this(copy.rg, copy.qual, copy.ne, copy.no); + private final Map> droppedReads = new HashMap<>(Reason.values().length); + private final static HashFunction murmurHasher = Hashing.murmur3_32(); + + // Enum of reasons that reads are dropped and tracked. + public enum Reason { + TRIMMMED { + String reasonName() { return "Trimmed"; } + }, + DOWNSAMPLED { + String reasonName() { return "Downsampled"; } + }, + REALIGNMENT_FAILURE { + String reasonName() { return "Failed realignment"; } + }, + FILTERED { + String reasonName() { return "Filtered"; } + }, + NOT_INFORMATIVE { + String reasonName() { return "Not informative"; } + }; + + abstract String reasonName(); + } + + // Private wrapper for a GATKSAMRecord that provides an alternate hashCode + // suitable for maintaining record identity across mutations that occur during + // filtering, trimming, etc. Used by addReadsFromDelta to + private class GATKSAMRecordHashWrapper { + private GATKSAMRecord samRec; + + public GATKSAMRecordHashWrapper() { + samRec = null; } - private Row(int rg, int qual, int ne, int no) { - this.rg = rg; - this.qual = qual; - this.ne = ne; - this.no = no; + public GATKSAMRecordHashWrapper(GATKSAMRecord rec) { + samRec = rec; + } + + public GATKSAMRecordHashWrapper set(GATKSAMRecord rec) { + samRec = rec; + return this; } @Override - public String toString() { - return "Row{" + - "" + rg + - ", " + qual + - ", " + ne + - ", " + no + - '}'; + public boolean equals(Object o) { + if (this == o) { + return true; + } + if (!(o instanceof GATKSAMRecordHashWrapper)) { + return false; + } + + GATKSAMRecord other = ((GATKSAMRecordHashWrapper) o).samRec; + return samRec.getReadName().equals(other.getReadName()) && samRec.getFlags() == other.getFlags(); + } + + // Calculate a read hash that remains invariant as reads are mutated during + // filtering/trimming etc., but that distinguishes paired reads from their mate, secondary etc. + public int hashCode() { + // Use a murmur hash of the flags to distribute the values more uniformly over the full range of int + return samRec.getReadName().hashCode() + (31 * murmurHasher.hashLong(samRec.getFlags()).asInt()); } } - @DataProvider(name = "CombineTablesProvider") - public Object[][] createCombineTablesProvider() { - List tests = new ArrayList(); - - final List rows = new ArrayList(); - for ( final int rg : Arrays.asList(0, 1) ) { - for ( final int qual : Arrays.asList(0, 1) ) { - rows.add(new Row(rg, qual, 1, 10)); + /** + * Add reads that have been dropped for the specified reason to the dropped list. + */ + public void addReads(final Reason reason, final Collection reads) { + Set readsForReason = droppedReads.get(reason); + if (null == readsForReason) { + readsForReason = new HashSet<>(reads.size()); + } + for (final GATKSAMRecord rec: reads) { + if (!previouslyDropped(rec)) { + // tag the original read so we can track the ones we've already seen and + // only add them to the dropped list once + rec.setAttribute(SAMTag.FT.name(), reason.reasonName()); + readsForReason.add(rec); } } - logger.warn("Number of rows " + rows.size()); - - List> permutations = new LinkedList>(); - permutations.addAll(Utils.makePermutations(rows, 1, false)); - permutations.addAll(Utils.makePermutations(rows, 2, false)); - permutations.addAll(Utils.makePermutations(rows, 3, false)); - - // adding 1 row to 2 - for ( final List table1 : permutations ) { - for ( final Row table2 : rows ) { - tests.add(new Object[]{table1, Arrays.asList(table2)}); - } - } - - // adding 2 rows to 1 - for ( final List table1 : permutations ) { - for ( final Row table2 : rows ) { - tests.add(new Object[]{Arrays.asList(table2), table1}); - } - } - - for ( final List table1 : permutations ) { - for ( final List table2 : permutations ) { - tests.add(new Object[]{table1, table2}); - } - } - - return tests.toArray(new Object[][]{}); + droppedReads.put(reason, readsForReason); } - @Test(dataProvider = "CombineTablesProvider") - public void testCombineTables(final List table1, final List table2) { - final NestedIntegerArray nia1 = makeTable(table1); - final NestedIntegerArray nia2 = makeTable(table2); - final List expectedRows = makeExpected(table1, table2); - final NestedIntegerArray expected = makeTable(expectedRows); - RecalUtils.combineTables(nia1, nia2); + /** + * Figure out the delta between the preReads list and the postReads list by hashing on the combination of read name and + * first_of_pair flag; any read not in the postReads list is added to the dropped list for the specified reason. + */ + public void addReadsFromDelta(final Reason reason, final Collection preReads, final Collection postReads) { + final HashSet postReadsSet = new HashSet<>(postReads.size()); - Assert.assertEquals(nia1.getDimensions(), expected.getDimensions()); - Assert.assertEquals(nia1.getAllValues().size(), expected.getAllValues().size()); - - for ( final NestedIntegerArray.Leaf leaf : expected.getAllLeaves() ) { - final RecalDatum actual = nia1.get(leaf.keys); - Assert.assertEquals(actual.getNumMismatches(), leaf.value.getNumMismatches()); - Assert.assertEquals(actual.getNumObservations(), leaf.value.getNumObservations()); + for (final GATKSAMRecord postRead : postReads) { + final GATKSAMRecordHashWrapper hashWrapper = new GATKSAMRecordHashWrapper(postRead); + postReadsSet.add(hashWrapper); } - } - public List makeExpected(final List table1, final List table2) { - final List combined = new LinkedList(); - for ( final Row t1 : table1 ) combined.add(new Row(t1)); - for ( final Row t2 : table2 ) { - combine(combined, t2); - } - return combined; - } + final int estimatedDropSize = preReads.size() - postReads.size(); + final List newlyDropped = new ArrayList<>(estimatedDropSize > 0 ? estimatedDropSize : 5); - private void combine(final List combined, final Row row) { - for ( final Row c : combined ) { - if ( c.rg == row.rg && c.qual == row.qual ) { - c.ne += row.ne; - c.no += row.no; - return; + GATKSAMRecordHashWrapper hashWrapper = new GATKSAMRecordHashWrapper(); + for (final GATKSAMRecord preRead: preReads) { + if (!postReadsSet.contains(hashWrapper.set(preRead))) { + newlyDropped.add(preRead); } } - combined.add(new Row(row)); + addReads(reason, newlyDropped); } - public NestedIntegerArray makeTable(final List rows) { - final NestedIntegerArray x = new NestedIntegerArray(3, 3); - for ( final Row r : rows ) - x.put(new RecalDatum((long)r.no, (double)r.ne, (byte)10), r.rg, r.qual); - return x; + /** + * Emit the accumulated dropped reads and reset/clear the cache. + * + * @param readDestination destination to receive the reads + */ + public void writeDroppedReads(final ReadDestination readDestination) { + for (final DroppedReadsTracker.Reason reason : droppedReads.keySet()) { + final Set droppedRecords = droppedReads.get(reason); + for (final GATKSAMRecord originalRec : droppedRecords) { + // We want to set the vendor quality check flag on the read emitted to + // the bamout, so clone the read before update it so we don't affect + // subsequent filtering/trimming, etc. in the event the original read + // gets processed again + final GATKSAMRecord clonedRec = (GATKSAMRecord)originalRec.clone(); + clonedRec.setReadFailsVendorQualityCheckFlag(true); + readDestination.add(clonedRec); + } + } + + // clear and reset the cache + droppedReads.clear(); + } + + /* + * Check to see if the read is marked as having been previously dropped. + */ + private boolean previouslyDropped(GATKSAMRecord rec) { + final String reasonDesc = rec.getStringAttribute(SAMTag.FT.name()); + for (final Reason reason : Reason.values()) { + if (reason.reasonName().equals(reasonDesc)) { + return true; + } + } + return false; } } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java index 026a249e7..d712a995e 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -84,6 +84,8 @@ public abstract class HaplotypeBAMWriter { private boolean writeHaplotypesAsWell = true; private boolean onlyRealignInformativeReads = false; + protected final DroppedReadsTracker droppedReadsTracker = new DroppedReadsTracker(); + /** * Possible modes for writing haplotypes to BAMs */ @@ -149,6 +151,35 @@ public abstract class HaplotypeBAMWriter { this.output = output; } + /** + * Figure out the delta between the preReads list and the postReads list by hashing on the combination of read name and + * first_of_pair flag; any read not in the postReads list is added to the dropped list for the specified reason. + */ + public void addDroppedReadsFromDelta( + final DroppedReadsTracker.Reason reason, + final Collection preReads, + final Collection postReads) { + droppedReadsTracker.addReadsFromDelta(reason, preReads, postReads); + } + + /** + * Add reads that have been dropped for the specified reason to the dropped list. + * + * @param reason -reason category these reads were dropped + * @param reads - reads to write out for this reason + * + */ + public void addDroppedReads(final DroppedReadsTracker.Reason reason, final Collection reads) { + droppedReadsTracker.addReads(reason, reads); + } + + /** + * Emit the accumulated dropped reads and reset/clear the droppedReads cache. + */ + public void writeDroppedReads() { + droppedReadsTracker.writeDroppedReads(output); + } + /** * Write out a BAM representing for the haplotype caller at this site * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java index f8d8ead57..9eab1e239 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/ReadDestination.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -84,9 +84,9 @@ public abstract class ReadDestination { bamHeader.setSequenceDictionary(header.getSequenceDictionary()); bamHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate); - // include the original read groups plus a new artificial one for the haplotypes - final List readGroups = new ArrayList(header.getReadGroups()); - final SAMReadGroupRecord rg = new SAMReadGroupRecord(readGroupID); + // include the original read groups plus an artificial one for haplotypes + final List readGroups = new ArrayList<>(header.getReadGroups()); + SAMReadGroupRecord rg = new SAMReadGroupRecord(readGroupID); rg.setSample("HC"); rg.setSequencingCenter("BI"); readGroups.add(rg); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java index a03ea8303..480674339 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/ArrayLoglessPairHMM.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java index 7beb8b04a..4ce3661e5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMM.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java index 0e6f92510..645039614 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java index e27856c40..df3c7306d 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMM.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java index 654b36e23..d6685ba8b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/FlexibleHMM.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java index a73f20edd..f362b7791 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/JNILoglessPairHMM.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java index ad9fa20f0..2a68bd626 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/LoglessPairHMM.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java index 368150335..f535cf2ac 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java index 40bdb12c6..c9a6cee99 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/sam/ClippedGATKSAMRecord.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java index 965ef04fc..ada4e0f02 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/TandemRepeatFinder.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibrationUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibrationUnitTest.java deleted file mode 100644 index 218377582..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibrationUnitTest.java +++ /dev/null @@ -1,116 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.engine.recalibration; - -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.QualityUtils; -import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.testng.Assert; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - -public class BaseRecalibrationUnitTest { - - @Test - public void repeatedAndUnorderedFixedQualities() { - // Test both repeated quals, and quals that aren't input in order - List quantizedQualsOrdered = Arrays.asList(11, 19); - List quantizedQualsUnordered = Arrays.asList(19, 11, 19, 19); - - // Unordered and Ordered qmapping should be identical - byte[] qmappingUnordered = BaseRecalibration.constructStaticQuantizedMapping(quantizedQualsUnordered, true); - byte[] qmappingOrdered = BaseRecalibration.constructStaticQuantizedMapping(quantizedQualsOrdered, true); - Assert.assertEquals(qmappingOrdered.length, qmappingUnordered.length); - for(int i = 0 ; i < qmappingUnordered.length ; i++) { - Assert.assertEquals(qmappingOrdered[i], qmappingUnordered[i]); - } - } - - @Test - public void nearestVsRoundDown() { - List fixedQuantizedQuals = Arrays.asList(10, 20, 30); - - byte[] qmappingRoundDown = BaseRecalibration.constructStaticQuantizedMapping(fixedQuantizedQuals, true); - byte[] qmappingRoundNearest = BaseRecalibration.constructStaticQuantizedMapping(fixedQuantizedQuals, false); - - // Depending on rounding strategy, bin 19 should round to 10 or 20 - Assert.assertEquals(qmappingRoundDown[19], 10); - Assert.assertEquals(qmappingRoundNearest[19], 20); - - // Regarless of rounding strategy, bin 21 should always round down to 20 - Assert.assertEquals(qmappingRoundDown[21], 20); - Assert.assertEquals(qmappingRoundNearest[21], 20); - } - - @Test - public void onlyOneFixedQualUsed() { - // Set all qualities to singleQual value (except for those below MIN_USABLE_Q_SCORE) - int singleQual = 10; - List fixedQuantizedQuals = Arrays.asList(singleQual); - - byte[] qmapping = BaseRecalibration.constructStaticQuantizedMapping(fixedQuantizedQuals, true); - - for(int i = 0 ; i < qmapping.length ; i++) { - if(i >= QualityUtils.MIN_USABLE_Q_SCORE) { - Assert.assertEquals(qmapping[i], singleQual); - } - else { - // Make sure that all values less than MIN_USABLE_Q_SCORE are preserved - Assert.assertEquals(qmapping[i], i); - } - } - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java deleted file mode 100644 index 1cf60d688..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java +++ /dev/null @@ -1,121 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.engine.recalibration; - -import org.broadinstitute.gatk.engine.recalibration.covariates.ContextCovariate; -import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; -import org.broadinstitute.gatk.utils.clipping.ClippingRepresentation; -import org.broadinstitute.gatk.utils.clipping.ReadClipper; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.broadinstitute.gatk.utils.sam.ReadUtils; -import org.testng.Assert; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; - -/** - * @author Mauricio Carneiro - * @since 3/1/12 - */ -public class ContextCovariateUnitTest { - ContextCovariate covariate; - RecalibrationArgumentCollection RAC; - - @BeforeClass - public void init() { - RAC = new RecalibrationArgumentCollection(); - covariate = new ContextCovariate(); - covariate.initialize(RAC); - } - - @BeforeMethod - public void initCache() { - ReadCovariates.clearKeysCache(); - } - - @Test(enabled = true) - public void testSimpleContexts() { - GATKSAMRecord read = ReadUtils.createRandomRead(1000); - GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, RAC.LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS); - ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); - covariate.recordValues(read, readCovariates); - - verifyCovariateArray(readCovariates.getMismatchesKeySet(), RAC.MISMATCHES_CONTEXT_SIZE, clippedRead, covariate); - verifyCovariateArray(readCovariates.getInsertionsKeySet(), RAC.INDELS_CONTEXT_SIZE, clippedRead, covariate); - verifyCovariateArray(readCovariates.getDeletionsKeySet(), RAC.INDELS_CONTEXT_SIZE, clippedRead, covariate); - } - - public static void verifyCovariateArray(int[][] values, int contextSize, GATKSAMRecord read, Covariate contextCovariate) { - for (int i = 0; i < values.length; i++) - Assert.assertEquals(contextCovariate.formatKey(values[i][0]), expectedContext(read, i, contextSize)); - - } - - public static String expectedContext (GATKSAMRecord read, int offset, int contextSize) { - final String bases = stringFrom(read.getReadBases()); - String expectedContext = null; - if (offset - contextSize + 1 >= 0) { - String context = bases.substring(offset - contextSize + 1, offset + 1); - if (!context.contains("N")) - expectedContext = context; - } - return expectedContext; - } - - private static String stringFrom(byte[] array) { - String s = ""; - for (byte value : array) - s += (char) value; - return s; - } - -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java deleted file mode 100644 index 681f001c1..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java +++ /dev/null @@ -1,140 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.engine.recalibration; - -import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.broadinstitute.gatk.engine.recalibration.covariates.CycleCovariate; -import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.broadinstitute.gatk.utils.sam.ReadUtils; -import org.testng.Assert; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; - -/** - * @author Mauricio Carneiro - * @since 3/1/12 - */ -public class CycleCovariateUnitTest { - CycleCovariate covariate; - RecalibrationArgumentCollection RAC; - - @BeforeClass - public void init() { - RAC = new RecalibrationArgumentCollection(); - covariate = new CycleCovariate(); - covariate.initialize(RAC); - } - - @BeforeMethod - public void initCache() { - ReadCovariates.clearKeysCache(); - } - - @Test(enabled = true) - public void testSimpleCycles() { - short readLength = 10; - GATKSAMRecord read = ReadUtils.createRandomRead(readLength); - read.setReadPairedFlag(true); - read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID")); - read.getReadGroup().setPlatform("illumina"); - - ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); - covariate.recordValues(read, readCovariates); - verifyCovariateArray(readCovariates.getMismatchesKeySet(), 1, (short) 1); - - read.setReadNegativeStrandFlag(true); - covariate.recordValues(read, readCovariates); - verifyCovariateArray(readCovariates.getMismatchesKeySet(), readLength, -1); - - read.setSecondOfPairFlag(true); - covariate.recordValues(read, readCovariates); - verifyCovariateArray(readCovariates.getMismatchesKeySet(), -readLength, 1); - - read.setReadNegativeStrandFlag(false); - covariate.recordValues(read, readCovariates); - verifyCovariateArray(readCovariates.getMismatchesKeySet(), -1, -1); - } - - private void verifyCovariateArray(int[][] values, int init, int increment) { - for (short i = 0; i < values.length; i++) { - short actual = Short.decode(covariate.formatKey(values[i][0])); - int expected = init + (increment * i); - Assert.assertEquals(actual, expected); - } - } - - @Test(enabled = true, expectedExceptions={UserException.class}) - public void testMoreThanMaxCycleFails() { - int readLength = RAC.MAXIMUM_CYCLE_VALUE + 1; - GATKSAMRecord read = ReadUtils.createRandomRead(readLength); - read.setReadPairedFlag(true); - read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID")); - read.getReadGroup().setPlatform("illumina"); - - ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); - covariate.recordValues(read, readCovariates); - } - - @Test(enabled = true) - public void testMaxCyclePasses() { - int readLength = RAC.MAXIMUM_CYCLE_VALUE; - GATKSAMRecord read = ReadUtils.createRandomRead(readLength); - read.setReadPairedFlag(true); - read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID")); - read.getReadGroup().setPlatform("illumina"); - - ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); - covariate.recordValues(read, readCovariates); - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java deleted file mode 100644 index 8229d2586..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java +++ /dev/null @@ -1,148 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.engine.recalibration; - -import org.broadinstitute.gatk.engine.recalibration.covariates.*; -import org.broadinstitute.gatk.utils.Utils; -import org.broadinstitute.gatk.utils.recalibration.EventType; -import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.broadinstitute.gatk.utils.sam.ReadUtils; -import org.testng.Assert; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; - -import java.util.Random; - -/** - * @author carneiro - * @since 4/21/12 - */ -public class ReadCovariatesUnitTest { - - @BeforeMethod - public void init() { - ReadCovariates.clearKeysCache(); - } - - @Test(enabled = false) - public void testCovariateGeneration() { - final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); - final String RGID = "id"; - - ReadGroupCovariate rgCov = new ReadGroupCovariate(); - QualityScoreCovariate qsCov = new QualityScoreCovariate(); - ContextCovariate coCov = new ContextCovariate(); - CycleCovariate cyCov = new CycleCovariate(); - - rgCov.initialize(RAC); - qsCov.initialize(RAC); - coCov.initialize(RAC); - cyCov.initialize(RAC); - - Covariate[] requestedCovariates = new Covariate[4]; - requestedCovariates[0] = rgCov; - requestedCovariates[1] = qsCov; - requestedCovariates[2] = coCov; - requestedCovariates[3] = cyCov; - - final int NUM_READS = 100; - final Random rnd = Utils.getRandomGenerator(); - - final String[] readGroups = {"RG1", "RG2", "RGbla"}; - for (int idx = 0; idx < NUM_READS; idx++) { - for (final String rgs : readGroups) { - final int length = 10 + rnd.nextInt(100); // random read length, at least 10 bp long - final GATKSAMRecord read = ReadUtils.createRandomRead(length, false); - final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(rgs); - rg.setPlatform("illumina"); - read.setReadGroup(rg); - read.setReadNegativeStrandFlag(rnd.nextBoolean()); - final byte[] mQuals = read.getBaseQualities(EventType.BASE_SUBSTITUTION); - final byte[] iQuals = read.getBaseQualities(EventType.BASE_INSERTION); - final byte[] dQuals = read.getBaseQualities(EventType.BASE_DELETION); - ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates); - - // check that the length is correct - Assert.assertEquals(rc.getMismatchesKeySet().length, length); - Assert.assertEquals(rc.getInsertionsKeySet().length, length); - Assert.assertEquals(rc.getDeletionsKeySet().length, length); - - for (int i = 0; i < length; i++) { - // check that read group is always the same - Assert.assertEquals(rgCov.formatKey(rc.getMismatchesKeySet(i)[0]), rgs); - Assert.assertEquals(rgCov.formatKey(rc.getInsertionsKeySet(i)[0]), rgs); - Assert.assertEquals(rgCov.formatKey(rc.getDeletionsKeySet(i)[0]), rgs); - - // check quality score - Assert.assertEquals(qsCov.formatKey(rc.getMismatchesKeySet(i)[1]), "" + mQuals[i]); - Assert.assertEquals(qsCov.formatKey(rc.getInsertionsKeySet(i)[1]), "" + iQuals[i]); - Assert.assertEquals(qsCov.formatKey(rc.getDeletionsKeySet(i)[1]), "" + dQuals[i]); - - // check context - Assert.assertEquals(coCov.formatKey(rc.getMismatchesKeySet(i)[2]), ContextCovariateUnitTest.expectedContext(read, i, RAC.MISMATCHES_CONTEXT_SIZE)); - Assert.assertEquals(coCov.formatKey(rc.getInsertionsKeySet(i)[2]), ContextCovariateUnitTest.expectedContext(read, i, RAC.INDELS_CONTEXT_SIZE)); - Assert.assertEquals(coCov.formatKey(rc.getDeletionsKeySet(i)[2]), ContextCovariateUnitTest.expectedContext(read, i, RAC.INDELS_CONTEXT_SIZE)); - - // check cycle - Assert.assertEquals(cyCov.formatKey(rc.getMismatchesKeySet(i)[3]), "" + (i+1)); - Assert.assertEquals(cyCov.formatKey(rc.getInsertionsKeySet(i)[3]), "" + (i+1)); - Assert.assertEquals(cyCov.formatKey(rc.getDeletionsKeySet(i)[3]), "" + (i+1)); - } - - } - - } - - } - -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java deleted file mode 100644 index 65ce02cc8..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java +++ /dev/null @@ -1,125 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.engine.recalibration; - -import org.broadinstitute.gatk.engine.recalibration.covariates.ReadGroupCovariate; -import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.broadinstitute.gatk.utils.sam.ReadUtils; -import org.testng.Assert; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; - -/** - * @author Mauricio Carneiro - * @since 3/1/12 - */ -public class ReadGroupCovariateUnitTest { - ReadGroupCovariate covariate; - RecalibrationArgumentCollection RAC; - - @BeforeClass - public void init() { - RAC = new RecalibrationArgumentCollection(); - covariate = new ReadGroupCovariate(); - covariate.initialize(RAC); - } - - @BeforeMethod - public void initCache() { - ReadCovariates.clearKeysCache(); - } - - @Test(enabled = true) - public void testSingleRecord() { - final String expected = "SAMPLE.1"; - GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("MY.ID"); - rg.setPlatformUnit(expected); - runTest(rg, expected, covariate); - } - - @Test(enabled = true) - public void testMissingPlatformUnit() { - final String expected = "MY.7"; - GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(expected); - runTest(rg, expected, covariate); - } - - @Test(enabled = true) - public void testForceReadgroup() { - final RecalibrationArgumentCollection forcedRAC = new RecalibrationArgumentCollection(); - forcedRAC.FORCE_READGROUP = "FOO"; - final ReadGroupCovariate forcedCovariate = new ReadGroupCovariate(); - forcedCovariate.initialize(forcedRAC); - - final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("NOT_FOO"); - runTest(rg, "FOO", forcedCovariate); - } - - private static void runTest(final GATKSAMReadGroupRecord rg, final String expected, final ReadGroupCovariate covariate) { - GATKSAMRecord read = ReadUtils.createRandomRead(10); - read.setReadGroup(rg); - ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1); - covariate.recordValues(read, readCovariates); - verifyCovariateArray(readCovariates.getMismatchesKeySet(), expected, covariate); - - } - - private static void verifyCovariateArray(final int[][] values, final String expected, final ReadGroupCovariate covariate) { - for (int[] value : values) { - String actual = covariate.formatKey(value[0]); - Assert.assertEquals(actual, expected); - } - } - -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java deleted file mode 100644 index e6d3d9444..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java +++ /dev/null @@ -1,176 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.engine.recalibration; - -import org.broadinstitute.gatk.engine.recalibration.covariates.*; -import org.broadinstitute.gatk.utils.recalibration.EventType; -import org.broadinstitute.gatk.utils.QualityUtils; -import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; -import org.broadinstitute.gatk.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.broadinstitute.gatk.utils.sam.ReadUtils; -import org.testng.Assert; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; - -import java.util.*; - -/** - * @author carneiro - * @since 4/21/12 - */ -public class RecalibrationReportUnitTest { - @BeforeMethod - public void init() { - ReadCovariates.clearKeysCache(); - } - - private static RecalDatum createRandomRecalDatum(int maxObservations, int maxErrors) { - final Random random = new Random(); - final int nObservations = random.nextInt(maxObservations); - final int nErrors = Math.min(random.nextInt(maxErrors), nObservations); - final int qual = random.nextInt(QualityUtils.MAX_SAM_QUAL_SCORE); - return new RecalDatum((long)nObservations, (double)nErrors, (byte)qual); - } - - @Test - public void testOutput() { - final int length = 100; - - List quals = new ArrayList(QualityUtils.MAX_SAM_QUAL_SCORE + 1); - List counts = new ArrayList(QualityUtils.MAX_SAM_QUAL_SCORE + 1); - - for (int i = 0; i<= QualityUtils.MAX_SAM_QUAL_SCORE; i++) { - quals.add((byte) i); - counts.add(1L); - } - - final QuantizationInfo quantizationInfo = new QuantizationInfo(quals, counts); - final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); - - quantizationInfo.noQuantization(); - final List requiredCovariates = new LinkedList(); - final List optionalCovariates = new LinkedList(); - - final ReadGroupCovariate rgCovariate = new ReadGroupCovariate(); - rgCovariate.initialize(RAC); - requiredCovariates.add(rgCovariate); - - final QualityScoreCovariate qsCovariate = new QualityScoreCovariate(); - qsCovariate.initialize(RAC); - requiredCovariates.add(qsCovariate); - - final ContextCovariate cxCovariate = new ContextCovariate(); - cxCovariate.initialize(RAC); - optionalCovariates.add(cxCovariate); - final CycleCovariate cyCovariate = new CycleCovariate(); - cyCovariate.initialize(RAC); - optionalCovariates.add(cyCovariate); - - final Covariate[] requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()]; - int covariateIndex = 0; - for (final Covariate cov : requiredCovariates) - requestedCovariates[covariateIndex++] = cov; - for (final Covariate cov : optionalCovariates) - requestedCovariates[covariateIndex++] = cov; - - final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("id"); - rg.setPlatform("illumina"); - final GATKSAMRecord read = ReadUtils.createRandomRead(length, false); - read.setReadGroup(rg); - final byte [] readQuals = new byte[length]; - for (int i = 0; i < length; i++) - readQuals[i] = 20; - read.setBaseQualities(readQuals); - - final int expectedKeys = expectedNumberOfKeys(length, RAC.INDELS_CONTEXT_SIZE, RAC.MISMATCHES_CONTEXT_SIZE); - int nKeys = 0; // keep track of how many keys were produced - final ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates); - - final RecalibrationTables recalibrationTables = new RecalibrationTables(requestedCovariates); - final NestedIntegerArray rgTable = recalibrationTables.getReadGroupTable(); - final NestedIntegerArray qualTable = recalibrationTables.getQualityScoreTable(); - - for (int offset = 0; offset < length; offset++) { - - for (EventType errorMode : EventType.values()) { - - final int[] covariates = rc.getKeySet(offset, errorMode); - final int randomMax = errorMode == EventType.BASE_SUBSTITUTION ? 10000 : 100000; - - rgTable.put(createRandomRecalDatum(randomMax, 10), covariates[0], errorMode.ordinal()); - qualTable.put(createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], errorMode.ordinal()); - nKeys += 2; - for (int j = 0; j < optionalCovariates.size(); j++) { - final NestedIntegerArray covTable = recalibrationTables.getTable(RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.ordinal() + j); - final int covValue = covariates[RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.ordinal() + j]; - if ( covValue >= 0 ) { - covTable.put(createRandomRecalDatum(randomMax, 10), covariates[0], covariates[1], covValue, errorMode.ordinal()); - nKeys++; - } - } - } - } - Assert.assertEquals(nKeys, expectedKeys); - } - - private static int expectedNumberOfKeys (int readLength, int indelContextSize, int mismatchesContextSize) { - final int numCovariates = 4; - final int numTables = 3; - final int mismatchContextPadding = mismatchesContextSize - 1; - final int indelContextPadding = 2 * (indelContextSize - 1); - final int indelCyclePadding = 2 * (2 * CycleCovariate.CUSHION_FOR_INDELS); - - return (numCovariates * numTables * readLength) - mismatchContextPadding - indelContextPadding - indelCyclePadding; - } - -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java deleted file mode 100644 index 675e10b87..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java +++ /dev/null @@ -1,203 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.engine.recalibration; - -import org.broadinstitute.gatk.engine.recalibration.covariates.Covariate; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.collections.NestedIntegerArray; -import org.broadinstitute.gatk.utils.recalibration.EventType; -import org.testng.Assert; -import org.testng.annotations.BeforeMethod; -import org.testng.annotations.Test; - -import java.util.Arrays; -import java.util.List; - -public final class RecalibrationTablesUnitTest extends BaseTest { - private RecalibrationTables tables; - private Covariate[] covariates; - private int numReadGroups = 6; - final byte qualByte = 1; - final List combineStates = Arrays.asList(0, 1, 2); - - @BeforeMethod - private void makeTables() { - covariates = RecalibrationTestUtils.makeInitializedStandardCovariates(); - tables = new RecalibrationTables(covariates, numReadGroups); - fillTable(tables); - } - - private void fillTable(final RecalibrationTables tables) { - for ( int iterations = 0; iterations < 10; iterations++ ) { - for ( final EventType et : EventType.values() ) { - for ( final int rg : combineStates) { - final double error = rg % 2 == 0 ? 1 : 0; - RecalUtils.incrementDatumOrPutIfNecessary(tables.getReadGroupTable(), qualByte, error, rg, et.ordinal()); - for ( final int qual : combineStates) { - RecalUtils.incrementDatumOrPutIfNecessary(tables.getQualityScoreTable(), qualByte, error, rg, qual, et.ordinal()); - for ( final int cycle : combineStates) - RecalUtils.incrementDatumOrPutIfNecessary(tables.getTable(2), qualByte, error, rg, qual, cycle, et.ordinal()); - for ( final int context : combineStates) - RecalUtils.incrementDatumOrPutIfNecessary(tables.getTable(3), qualByte, error, rg, qual, context, et.ordinal()); - } - } - } - } - } - - @Test - public void basicTest() { - final Covariate qualCov = covariates[1]; - final Covariate cycleCov = covariates[2]; - final Covariate contextCov = covariates[3]; - - Assert.assertEquals(tables.numTables(), covariates.length); - - Assert.assertNotNull(tables.getReadGroupTable()); - Assert.assertEquals(tables.getReadGroupTable(), tables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE.ordinal())); - testDimensions(tables.getReadGroupTable(), numReadGroups); - - Assert.assertNotNull(tables.getQualityScoreTable()); - Assert.assertEquals(tables.getQualityScoreTable(), tables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE.ordinal())); - testDimensions(tables.getQualityScoreTable(), numReadGroups, qualCov.maximumKeyValue() + 1); - - Assert.assertNotNull(tables.getTable(2)); - testDimensions(tables.getTable(2), numReadGroups, qualCov.maximumKeyValue() + 1, cycleCov.maximumKeyValue() + 1); - - Assert.assertNotNull(tables.getTable(3)); - testDimensions(tables.getTable(3), numReadGroups, qualCov.maximumKeyValue() + 1, contextCov.maximumKeyValue() + 1); - } - - private void testDimensions(final NestedIntegerArray table, final int ... dimensions) { - final int[] dim = new int[dimensions.length+1]; - System.arraycopy(dimensions, 0, dim, 0, dimensions.length); - dim[dimensions.length] = EventType.values().length; - Assert.assertEquals(table.getDimensions().length, dim.length); - - for ( int i = 0; i < dim.length; i++ ) { - Assert.assertEquals(table.getDimensions()[i], dim[i], "Table dimensions not expected at dim " + i); - } - } - - @Test - public void basicMakeQualityScoreTable() { - final Covariate qualCov = covariates[1]; - final NestedIntegerArray copy = tables.makeQualityScoreTable(); - testDimensions(copy, numReadGroups, qualCov.maximumKeyValue()+1); - Assert.assertEquals(copy.getAllValues().size(), 0); - } - - @Test - public void testCombine1() { - final RecalibrationTables merged = new RecalibrationTables(covariates, numReadGroups); - fillTable(merged); - - merged.combine(tables); - - for ( int i = 0; i < tables.numTables(); i++ ) { - NestedIntegerArray table = tables.getTable(i); - NestedIntegerArray mergedTable = merged.getTable(i); - - Assert.assertEquals(table.getAllLeaves().size(), mergedTable.getAllLeaves().size()); - for ( final NestedIntegerArray.Leaf leaf : table.getAllLeaves() ) { - final RecalDatum mergedValue = mergedTable.get(leaf.keys); - Assert.assertNotNull(mergedValue); - Assert.assertEquals(mergedValue.getNumObservations(), leaf.value.getNumObservations() * 2); - Assert.assertEquals(mergedValue.getNumMismatches(), leaf.value.getNumMismatches() * 2); - } - } - } - - @Test - public void testCombineEmptyOther() { - final RecalibrationTables merged = new RecalibrationTables(covariates, numReadGroups); - - merged.combine(tables); - - for ( int i = 0; i < tables.numTables(); i++ ) { - NestedIntegerArray table = tables.getTable(i); - NestedIntegerArray mergedTable = merged.getTable(i); - - Assert.assertEquals(table.getAllLeaves().size(), mergedTable.getAllLeaves().size()); - for ( final NestedIntegerArray.Leaf leaf : table.getAllLeaves() ) { - final RecalDatum mergedValue = mergedTable.get(leaf.keys); - Assert.assertNotNull(mergedValue); - Assert.assertEquals(mergedValue.getNumObservations(), leaf.value.getNumObservations()); - Assert.assertEquals(mergedValue.getNumMismatches(), leaf.value.getNumMismatches()); - } - } - } - - @Test - public void testCombinePartial() { - final RecalibrationTables merged = new RecalibrationTables(covariates, numReadGroups); - for ( final int rg : combineStates) { - RecalUtils.incrementDatumOrPutIfNecessary(merged.getTable(3), qualByte, 1, rg, 0, 0, 0); - } - - merged.combine(tables); - for ( int i = 0; i < tables.numTables(); i++ ) { - NestedIntegerArray table = tables.getTable(i); - NestedIntegerArray mergedTable = merged.getTable(i); - - Assert.assertEquals(table.getAllLeaves().size(), mergedTable.getAllLeaves().size()); - for ( final NestedIntegerArray.Leaf leaf : table.getAllLeaves() ) { - final RecalDatum mergedValue = mergedTable.get(leaf.keys); - Assert.assertNotNull(mergedValue); - - final int delta = i == 3 && leaf.keys[1] == 0 && leaf.keys[2] == 0 && leaf.keys[3] == 0 ? 1 : 0; - Assert.assertEquals(mergedValue.getNumObservations(), leaf.value.getNumObservations() + delta); - Assert.assertEquals(mergedValue.getNumMismatches(), leaf.value.getNumMismatches() + delta); - } - } - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java deleted file mode 100644 index 8f29d42c3..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java +++ /dev/null @@ -1,74 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.engine.recalibration; - -import org.broadinstitute.gatk.engine.recalibration.covariates.*; - -/** - * Created with IntelliJ IDEA. - * User: depristo - * Date: 12/23/12 - * Time: 1:06 PM - * To change this template use File | Settings | File Templates. - */ -public class RecalibrationTestUtils { - public static Covariate[] makeInitializedStandardCovariates() { - final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); - final Covariate[] covariates = new Covariate[4]; - covariates[0] = new ReadGroupCovariate(); - covariates[1] = new QualityScoreCovariate(); - covariates[2] = new ContextCovariate(); - covariates[3] = new CycleCovariate(); - for ( Covariate cov : covariates ) cov.initialize(RAC); - return covariates; - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java index d20b08b2f..4ac503cf6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/WalkerTestIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeffUnitTest.java index 35be76487..b896f6057 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeffUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_InbreedingCoeffUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtilsTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtilsTest.java index 671b31989..3b1fa8a06 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtilsTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/AnnotationUtilsTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHetUnitTest.java index 8b5194485..a28ce0337 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHetUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java index b2f758cd9..d8728c9cb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/GenotypeSummariesUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java index f23079bfe..b42df9043 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java index a3259dd14..5bfd8469e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/QualByDepthUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java index 5bacc7450..3d388fcee 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/RankSumUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -65,7 +65,7 @@ import java.util.List; public class RankSumUnitTest { - List distribution20, distribution30, distribution20_40; + List distribution20, distribution30, distribution20_40; static final int observations = 100; @BeforeClass @@ -86,11 +86,11 @@ public class RankSumUnitTest { Collections.shuffle(distribution20_40, Utils.getRandomGenerator()); } - private static void makeDistribution(final List result, final int target, final int skew, final int numObservations) { + private static void makeDistribution(final List result, final int target, final int skew, final int numObservations) { final int rangeStart = target - skew; final int rangeEnd = target + skew; - int current = rangeStart; + double current = rangeStart; for ( int i = 0; i < numObservations; i++ ) { result.add(current++); if ( current > rangeEnd ) @@ -118,40 +118,33 @@ public class RankSumUnitTest { } @Test(enabled = true, dataProvider = "DistributionData") - public void testDistribution(final List distribution1, final List distribution2, final int numToReduceIn2, final boolean distributionsShouldBeEqual, final String debugString) { - final MannWhitneyU mannWhitneyU = new MannWhitneyU(true); + public void testDistribution(final List distribution1, final List distribution2, final int numToReduceIn2, final boolean distributionsShouldBeEqual, final String debugString) { + final MannWhitneyU mannWhitneyU = new MannWhitneyU(); - for ( final Integer num : distribution1 ) - mannWhitneyU.add(num, MannWhitneyU.USet.SET1); - - final List dist2 = new ArrayList<>(distribution2); + final List dist2 = new ArrayList<>(distribution2); if ( numToReduceIn2 > 0 ) { - int counts = 0; - int quals = 0; + Double counts = 0.0; + Double quals = 0.0; for ( int i = 0; i < numToReduceIn2; i++ ) { counts++; quals += dist2.remove(0); } - final int qual = quals / counts; + final Double qual = quals / counts; for ( int i = 0; i < numToReduceIn2; i++ ) dist2.add(qual); } - for ( final Integer num : dist2 ) - mannWhitneyU.add(num, MannWhitneyU.USet.SET2); - - final Double result = mannWhitneyU.runTwoSidedTest().second; + final Double result = mannWhitneyU.test(RankSumTest.convertToArray(distribution1),RankSumTest.convertToArray(dist2), MannWhitneyU.TestType.TWO_SIDED).getP(); Assert.assertFalse(Double.isNaN(result)); if ( distributionsShouldBeEqual ) { - // TODO -- THIS IS THE FAILURE POINT OF USING REDUCED READS WITH RANK SUM TESTS if ( numToReduceIn2 >= observations / 2 ) return; - Assert.assertTrue(result > 0.1, String.format("%f %d %d", result, numToReduceIn2, dist2.get(0))); + Assert.assertTrue(result > 0.1, String.format("%f %d %f", result, numToReduceIn2, dist2.get(0))); } else { - Assert.assertTrue(result < 0.01, String.format("%f %d %d", result, numToReduceIn2, dist2.get(0))); + Assert.assertTrue(result < 0.01, String.format("%f %d %f", result, numToReduceIn2, dist2.get(0))); } } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java index 7cc76a199..6ce608539 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtilsTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtilsTest.java index 440f14aac..3e963a6bc 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtilsTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTableUtilsTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java index 4be0bbebf..647b285c5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatioUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java index 515888a09..0029f78a6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -53,7 +53,6 @@ package org.broadinstitute.gatk.tools.walkers.annotator; import htsjdk.tribble.readers.LineIterator; import htsjdk.tribble.readers.PositionalBufferedStream; -import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; import org.broadinstitute.gatk.engine.walkers.WalkerTest; @@ -100,7 +99,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("d6cd81fc2f483f29d44fbb27d1772841")); + Arrays.asList("b63baada372925a76c3f279e16eb631d")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -108,7 +107,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("300836de4e2c8424734d2ee0ca4261c1")); + Arrays.asList("6f5856bc2d31f8aae4131717e5ab0b16")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -134,7 +133,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("192f393da4e28aecf16112562e65083a")); + Arrays.asList("7ec5470f742f80cdfbfb203213bea8cc")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -142,7 +141,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("52baff55535f7c87545a7818052a2d5c")); + Arrays.asList("afc47e4f253d0999961f26920be8e834")); + executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -150,7 +150,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testExcludeAnnotations() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "-XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("334915d90fa92ee9fa07d4647912ceac")); + Arrays.asList("a8a87e2a67436e14ed32ce9d355a3440")); executeTest("test exclude annotations", spec); } @@ -183,7 +183,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testOverwritingHeader() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1, - Arrays.asList("ab84654ac412a0aaaec99e86e357f0fd")); + Arrays.asList("fc7958261af93681fde73c1fc6b578a0")); executeTest("test overwriting header", spec); } @@ -191,7 +191,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoReads() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("489a09a8531d9c8ef683ad8cc81db3e8")); + Arrays.asList("2d535a48ec1c66aa9c707f6d498fc81d")); executeTest("not passing it any reads", spec); } @@ -199,7 +199,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithDbsnp() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("a7af6774ea1f7622d999cae1b7f8ea32")); + Arrays.asList("a2a2f9ce8e6f9c933ad46906719ce402")); executeTest("getting DB tag with dbSNP", spec); } @@ -207,7 +207,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testMultipleIdsWithDbsnp() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1, - Arrays.asList("de8cfffe3b61b7c8832096a399e9d954")); + Arrays.asList("ed351765d63d92b1913784fa47b3d859")); executeTest("adding multiple IDs with dbSNP", spec); } @@ -215,7 +215,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithHapMap() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("25443af7099f7de184b8dcdfb659f62e")); + Arrays.asList("114d8300ec0fac613bb2e82f8951adc0")); executeTest("getting DB tag with HM3", spec); } @@ -223,7 +223,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithTwoComps() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf " + STANDARD_ANNOTATIONS + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("ea9b10d2b82a7846c01a017f6f3bb57e")); + Arrays.asList("af59185b6a03d4147d2755019dcc6bf9")); executeTest("getting DB tag with 2 comps", spec); } @@ -239,7 +239,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpression() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("f26d1f849cceca0ab115737f8db670ae")); + Arrays.asList("7bcbd8ad8388f371d1a990fde67d3273")); executeTest("using expression", spec); } @@ -247,7 +247,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpressionAlleleMisMatch() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resourceAlleleConcordance --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-mod.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty-mod.vcf", 1, - Arrays.asList("6f288c4b672ac3a22cb2385981f51d75")); + Arrays.asList("76f716569e33d88914e479b70e08ac88")); executeTest("using expression allele mismatch", spec); } @@ -255,7 +255,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpressionMultiAllele() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1, - Arrays.asList("af92a439f092f45da10adac0f9c8fc8f")); + Arrays.asList("0e3fc86349f5fd28159d00d22d278e84")); executeTest("using expression with multi-alleles", spec); } @@ -264,7 +264,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { /* The order of filters in the output seems platform-dependent. May need to change htsjdk to make the order consistent across platforms. [Sato] */ WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + privateTestDir + "annotationResourceWithFilter.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.FILTER -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1, - Arrays.asList("77bc144fd432b8886ab19ed20bfb9396")); + Arrays.asList("6fe67e72232165a829fde7c3b12c2275")); executeTest("annotate a vcf with the FILTER field of another vcf", spec); } @@ -272,7 +272,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpressionWithID() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("58a86fe8a34c92127eb33e36107941dd")); + Arrays.asList("94b03ee63604ab8d61aacfd3297c5dca")); executeTest("using expression with ID", spec); } @@ -300,7 +300,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile " + validationDataLocation + "snpEff2.0.5.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429", 1, - Arrays.asList("6618f3ae9dc6d4ce6ebd4eb8f9495103") + Arrays.asList("db0c5f273583a54d0cefc4b3c01aae9a") ); executeTest("Testing SnpEff annotations", spec); } @@ -313,7 +313,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { "--snpEffFile " + privateTestDir + "snpEff_unsupported_version_gatk_mode.vcf " + "-L 1:10001292-10012424", 1, - Arrays.asList("7533645a3791ce30d7407f789e1ffbb0") + Arrays.asList("5f952cfcd25653edcffd3916d52e94ec") ); executeTest("Testing SnpEff annotations (unsupported version, GATK mode)", spec); } @@ -326,14 +326,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { "--snpEffFile " + privateTestDir + "snpEff_unsupported_version_no_gatk_mode.vcf " + "-L 1:10001292-10012424", 1, - Arrays.asList("0e201a91a2b2b130debcd5dd7d9328ab") + Arrays.asList("86fb28c2e3886eda194026b3b7d07c77") ); executeTest("Testing SnpEff annotations (unsupported version, no GATK mode)", spec); } @Test(enabled = true) public void testTDTAnnotation() { - final String MD5 = "9532ca341b52be650b35e32d7c765030"; + final String MD5 = "cf65fdfbcd822279e84326989b2f6378"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" + " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1, @@ -344,7 +344,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test(enabled = true) public void testChromosomeCountsPed() { - final String MD5 = "4ab0b4245ba2c5c62424775879f51379"; + final String MD5 = "71045f20e4cd9f5fdaa367f6d7324e59"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" + " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1, @@ -354,7 +354,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test(enabled = true) public void testInbreedingCoeffPed() { - final String MD5 = "914e6882f01bae43f1d6ba1b0023cf91"; + final String MD5 = "0cf7c115316950abc0213935b20a653a"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" + " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1, @@ -364,7 +364,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test(enabled = true) public void testAlleleTrimming() { - final String MD5 = "90f9ee6c34c0820435dce7a0d63b4c1e"; + final String MD5 = "5db0cd72ad0ffc711afb95df58de31fa"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "alleleTrim.vcf.gz" + " -L 1:26608870-26608875 -no_cmdline_in_header --resource:exac " + privateTestDir + "exacAlleleTrim.vcf.gz -E exac.AC_Adj" + @@ -422,36 +422,17 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { } @Test - public void testStrandAlleleCountsBySample() throws IOException { + public void testStrandAlleleCountsBySample() { + final String MD5 = "564aeeefad92353d66dbb2a2222d5108"; final WalkerTestSpec spec = new WalkerTestSpec( "-T HaplotypeCaller --disableDithering " + String.format("-R %s -I %s ", REF, CEUTRIO_BAM) + "--no_cmdline_in_header -o %s -L 20:10130000-10134800 " + "-A StrandBiasBySample -A StrandAlleleCountsBySample", - 1, Arrays.asList("") + 1, Arrays.asList(MD5) ); - spec.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SC - final File outputVCF = executeTest("testStrandAlleleCountsBySample", spec).getFirst().get(0); - - //Confirm that SB and SAC are identical for bi-allelic variants - final VCFCodec codec = new VCFCodec(); - final FileInputStream s = new FileInputStream(outputVCF); - final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s)); - codec.readHeader(lineIterator); - - while (lineIterator.hasNext()) { - final String line = lineIterator.next(); - Assert.assertFalse(line == null); - final VariantContext vc = codec.decode(line); - - if (vc.isBiallelic()) { - for (final Genotype g : vc.getGenotypes()) { - Assert.assertTrue(g.hasExtendedAttribute("SB")); - Assert.assertTrue(g.hasExtendedAttribute("SAC")); - Assert.assertEquals(g.getExtendedAttribute("SB").toString(), g.getExtendedAttribute("SAC").toString()); - } - } - } + spec.disableShadowBCF(); + executeTest("testStrandAlleleCountsBySample", spec); } @Test(enabled = false) @@ -523,4 +504,22 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { Assert.assertFalse(lineIterator.hasNext()); Assert.assertFalse(lineIteratorAnn.hasNext()); } + + @Test + public void testHomopolymerRunWindow() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T VariantAnnotator -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " -A HomopolymerRun --variant:vcf " + privateTestDir + "problem_del.vcf " + + "-U ALLOW_SEQ_DICT_INCOMPATIBILITY -L chr18:44382010-44384010 --reference_window_stop 59 --no_cmdline_in_header -o %s", 1, + Arrays.asList("f3166721ef0380636590b3e860aa06af")); + executeTest("Testing testHomopolymerRunWindow", spec); + } + + @Test + public void testHomopolymerRunTooBig() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T VariantAnnotator -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " -A HomopolymerRun --variant:vcf " + privateTestDir + "problem_del.vcf " + + "-U ALLOW_SEQ_DICT_INCOMPATIBILITY -L chr18:44382010-44384010 --no_cmdline_in_header -o %s", 1, + Arrays.asList("3dba997d03779781c82a25ace69c838e")); + executeTest("Testing HomopolymerRunTooBig", spec); + } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java index d356c629d..010f3bb72 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotatorUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java index dcbe80446..ac747825a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java index 3daffaa3e..d44fe6cda 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGathererUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java index 2c362acd2..4a148698b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java index 2adaec781..ffb8cb6be 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/ReadRecalibrationInfoUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySampleUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySampleUnitTest.java index f507c8b47..1a304891f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySampleUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/BaseQualitySumPerAlleleBySampleUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstIntegrationTest.java index ac1edfaa9..9158e0b68 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -52,6 +52,7 @@ package org.broadinstitute.gatk.tools.walkers.cancer.contamination; import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.Arrays; @@ -100,4 +101,17 @@ public class ContEstIntegrationTest extends WalkerTest { " -isr INTERSECTION",md5sums); executeTest("testArrayFree",spec); } + + @Test(enabled = true) + public void testArrayNoPop(){ + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + "-T ContEst" + + " -I:eval " + ContaminatedBamsDirectory + "HCC1143_BL.small.0.05.contaminated.with.SM-612V3.small.0.95.bam" + + " -I:genotype " + NormalBamsDirectory + "SM-612V4.bam" + + " -R " + b37KGReference + + " --popfile " + validationDataLocation + "hg19_population_stratified_af_hapmap_3.3.fixed_no_pop.vcf", + 0, + UserException.class); + executeTest("testArrayNoPop",spec); + } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstUnitTest.java index 9b8990a08..aa8ce47f3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/contamination/ContEstUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java index f9b18d4b9..bfd0e4911 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -73,12 +73,14 @@ public class MuTect2IntegrationTest extends WalkerTest { final static String DREAM3_FP_INTERVALS_FILE = privateTestDir + "m2_dream3.fp.intervals"; + final String commandLine = + "-T MuTect2 --no_cmdline_in_header -dt NONE --disableDithering -alwaysloadVectorHMM -pairHMM LOGLESS_CACHING -ip 50 -R %s --dbsnp %s --cosmic %s --normal_panel %s -I:tumor %s -I:normal %s -L %s"; private void M2Test(String tumorBam, String normalBam, String intervals, String args, String md5) { final String base = String.format( - "-T MuTect2 --no_cmdline_in_header -dt NONE --disableDithering -alwaysloadVectorHMM -pairHMM LOGLESS_CACHING -ip 50 -R %s --dbsnp %s --cosmic %s --normal_panel %s -I:tumor %s -I:normal %s -L %s", - REF, DBSNP, COSMIC, PON, tumorBam, normalBam, intervals) + - " -o %s "; + commandLine, + REF, DBSNP, COSMIC, PON, tumorBam, normalBam, intervals) + + " -o %s "; final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5)); @@ -89,9 +91,37 @@ public class MuTect2IntegrationTest extends WalkerTest { executeTest("testM2: args=" + args, spec); } + private void m2TumorOnlyTest(String tumorBam, String intervals, String args, String md5) { + final String base = String.format( + "-T MuTect2 --no_cmdline_in_header -dt NONE --disableDithering -alwaysloadVectorHMM -pairHMM LOGLESS_CACHING -ip 50 -R %s --dbsnp %s --cosmic %s --normal_panel %s -I:tumor %s -L %s", + REF, DBSNP, COSMIC, PON, tumorBam, intervals) + + " -o %s "; + + final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5)); + + spec.disableShadowBCF(); + executeTest("testM2TumorOnly: args=" + args, spec); + } + + private void M2TestWithDroppedReads(String tumorBam, String normalBam, String intervals, String args, String md5Variants, String md5Bamout) { + final String base = String.format( + commandLine, + REF, DBSNP, COSMIC, PON, tumorBam, normalBam, intervals) + + " -o %s " + + "-bamout %s --emitDroppedReads"; + + final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5Variants, md5Bamout)); + + // TODO: do we want to enable this and why? It explodes with + // java.lang.RuntimeException: java.lang.ClassCastException: java.lang.Double cannot be cast to java.lang.String + // at htsjdk.variant.variantcontext.writer.BCF2FieldEncoder$StringOrCharacter.javaStringToBCF2String(BCF2FieldEncoder.java:312) + spec.disableShadowBCF(); + executeTest("testM2Dropped: args=" + args, spec); + } + @Test public void testMicroRegression() { - M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "", "617054c6d056cad7448a463cb8d04a55"); + M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "", "a7658ccfb75bf1ce8d3d3cfbf3b552f0"); } /** @@ -101,7 +131,17 @@ public class MuTect2IntegrationTest extends WalkerTest { */ @Test public void testTruePositivesDream3() { - M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_TP_INTERVALS_FILE, "", "f856432679e43445d2939772be4326cf"); + M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_TP_INTERVALS_FILE, "", "91dee82a13275e5568f5d2e680e3162b"); + } + + /** + * Test dropped read tracking on true positives and a narrow interval range. + */ + @Test + public void testTruePositivesDream3TrackedDropped() { + M2TestWithDroppedReads(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, "21:10935369", "", + "4f1337df1de5dd4468e2d389403ca785", + "b536e76870326b4be01b8d6b83c1cf1c"); } /** @@ -110,15 +150,23 @@ public class MuTect2IntegrationTest extends WalkerTest { */ @Test public void testFalsePositivesDream3() { - M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "11357aa543e7c6b2725cd330adba23a0"); + M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "6be3fc318e2c22a28098f58b76c9a5a1"); } - /* + /** * Test that contamination downsampling reduces tumor LOD, rejects more variants */ @Test public void testContaminationCorrection() { - M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "d7947ddf0240fe06a44621312831f44c"); + M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "b1010a6614b0332c41fd6da9d5f6b14e"); + } + + /** + * Test that tumor-only mode does not create an empty vcf + */ + @Test + public void testTumorOnly(){ + m2TumorOnlyTest(CCLE_MICRO_TUMOR_BAM, "2:166000000-167000000", "", "bb0cddfdc29500fbea68a0913d6706a3"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java index e754c3aaf..82b842604 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java index b65fbc1fd..3fc5e7a7e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java index 6b1911448..6ac91a350 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java index 5fd8e8562..dafab495b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java index 8604e05ea..4670f6630 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java index de63ed550..fe807874b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java index 973b6a875..61d92f0bb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -189,7 +189,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference + " --filterExpression 'FS > 60.0' --filterName SNP_FS -V " + privateTestDir + "unfilteredForFiltering.vcf", 1, - Arrays.asList("0febd66699fcd7f521377d1d0d0016fb")); + Arrays.asList("b9fa012770831c984101d23420ef0c38")); executeTest("testUnfilteredBecomesFilteredAndPass", spec); } @@ -234,10 +234,21 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf --setFilteredGtToNocall", 1, - Arrays.asList("454d265ee8b425284ed7fca8ca4774be")); + Arrays.asList("2ff3753215d418712309e50da323f6e8")); executeTest("testSetFilteredGtoNocall", spec); } + + @Test + public void testSetFilteredGtoNocallUpdateInfo() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference + + " -G_filter 'GQ < 20' -G_filterName lowDP -G_filter 'DP<10' -G_filterName lowGQ -V " + privateTestDir + "variantFiltrationInfoField.vcf --setFilteredGtToNocall", + 1, + Arrays.asList("3b074975bb6f70c84b2dd81695bb89ff")); + executeTest("testSetFilteredGtoNocallUpdateInfo", spec); + } + @Test public void testSetVcfFilteredGtoNocall() { String testfile = privateTestDir + "filteredSamples.vcf"; @@ -245,7 +256,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("7771f07a9997296852ab367fac2c7a6c") + Arrays.asList("410c6b7bb62fc43bb41eee627670f757") ); spec.disableShadowBCF(); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java index 32080e3c4..9cf9df648 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java index 367d1810c..cef32f30e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java index d163ccae5..2f5de64bf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java index 44bf0acc3..a0fe57635 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java index 545ead5e9..5f7213ce7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java index 65d56cc2a..e7a9c9467 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java index b185db532..8b4916d0b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java index 2d10c6a66..0d06dd71c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java index d5a26fee0..239dd671a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java index d3e681e84..c723da134 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java index de44779b9..5591ffa13 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java index f9e4ad05f..284e368c2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java index 464e94ab8..c941c5d3a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java index 40f5370a6..7ed81fdb6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java index 1a795edd8..b4cae1373 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java index a894d26bc..76c7ed209 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java index e3ef6e58b..a76f36880 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java index 659832d10..35925fa8b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java index 6c24cb1e1..f727826ae 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollectionUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java index 61cb79428..ff8d7f99a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -133,7 +133,7 @@ public class UnifiedGenotyperEngineUnitTest extends BaseTest { } final VariantContext vc = new VariantContextBuilder("test", "chr1", 1000, 1000, alleles).make(); final boolean result = ugEngine.hasTooManyAlternativeAlleles(vc); - Assert.assertTrue(result == (vc.getNAlleles() > GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)); + Assert.assertTrue(result == (vc.getNAlleles() > GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java index a1de74780..6e21e96d1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -69,17 +69,17 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe @Test(enabled = true) public void testSNP_ACS_Pools() { - executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "bf6012b6e7dec2d44b2bcb402c98c95e"); + executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "ebdf749d404aaef298780a53059a4f93"); } @Test(enabled = true) public void testBOTH_GGA_Pools() { - executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "217d9108c3014261dbe8befa383a2226"); + executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "c3826794a250e32b0497353ceb1deb26"); } @Test(enabled = true) public void testINDEL_GGA_Pools() { - executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "6a7f00e7f26cbc1891f40c9ed8b6579b"); + executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "4eb0d8018da6612cd434491f338ed5a4"); } @Test(enabled = true) @@ -88,6 +88,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe //TODO the old MD5 is kept for the record. //TODO this should be revisit once we get into addressing inaccuracies by the independent allele approach. // executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "b5ff7530827f4b9039a58bdc8a3560d2"); - executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "c0271a4c281991a86490c1955456af26"); + executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "c2fb9b05027c2b0ac9e338d9ddda69b1"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java index 2fb2d11c5..51d7a5a65 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -63,16 +63,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() { - executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","c445bcd828c540c009bc8fc9f48916bc"); + executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","e22846de4567f576e08e00edda2931d0"); } @Test(enabled = true) public void testMT_SNP_DISCOVERY_sp4() { - executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","8d8c7926ca9c68251c41eb03b8efaba2"); + executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","9757563c5e32f59cb47eb9b16f1016ac"); } @Test(enabled = true) public void testMT_SNP_GGA_sp10() { - executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "34242c0ae59b0645fb6df5c322e92f01"); + executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "37f8ccc683dc525c25dddc4f8dad505c"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java index 9930d80ac..efe5abef6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java index f4e03043b..9e524e347 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -78,7 +78,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("b132da42e1017c8825d84a06cf79a1e9")); + Arrays.asList("32bece91e170d623092817738faddb4e")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -92,7 +92,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("23e32822d81f198ee52676f24ef74343")); + Arrays.asList("897c6063236fcd7242c2ff5982585648")); executeTest(String.format("test indel caller in SLX with low min allele count"), spec); } @@ -105,7 +105,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("93580986b871890a4fc86ebf98877efa")); + Arrays.asList("dd66e5f8a6e43be0e473251185a4f38a")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -115,7 +115,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("4da9878ee36d0fb387d5a58631383ffa")); + Arrays.asList("aa56ed44e77162efce45c936c485769e")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec); } @@ -125,7 +125,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("9ab4f5306438b5a64cb2cb90020b7b82")); + Arrays.asList("a4b6434c59c4b119e480ddafc86de234")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); } @@ -140,7 +140,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1, - Arrays.asList("6de8d740908e22b46785d5eba6278eb2")); + Arrays.asList("f9d848fe5e6e6762e0dd5b5d925f74f4")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); } @@ -150,7 +150,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + privateTestDir + vcf + " -I " + validationDataLocation + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1, - Arrays.asList("6e8319e65fef1059c2092c05e6916257")); + Arrays.asList("41aa49e9c15198a006a1bc8e9638d6ec")); executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec); } @@ -162,7 +162,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 20:10,000,000-10,100,000", 1, - Arrays.asList("745eb3eefa93aca72f724aab4734c7ef")); + Arrays.asList("e883a8863bdd44c559c4440183c87078")); executeTest(String.format("test UG with base indel quality scores"), spec); } @@ -181,7 +181,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.0", 1, - Arrays.asList("56673c166ba25f625d026e593d5cc667")); + Arrays.asList("2a82d1586b2148e8d902da5cf8538210")); executeTest("test minIndelFraction 0.0", spec); } @@ -189,7 +189,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction25() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.25", 1, - Arrays.asList("2ce1754313561b9cb134152b8f98bf43")); + Arrays.asList("3184a3f58b3aeafcd97280af708a04bb")); executeTest("test minIndelFraction 0.25", spec); } @@ -197,7 +197,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction100() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 1", 1, - Arrays.asList("c7f190f7cea34a7f9c931cd8de110a48")); + Arrays.asList("990b838ef13b8ccf257eb6cbcc7c7741")); executeTest("test minIndelFraction 1.0", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 44a5ab268..7d45eddb5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinBaseQualityScore() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1, - Arrays.asList("21369e50334d2b77b0e638e47e1b8c64")); + Arrays.asList("52a3064863b97e43d8df878edc29275c")); executeTest("test min_base_quality_score 26", spec); } @@ -94,7 +94,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSLOD() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("e58d9a5758c5b11f86558608260d93d5")); + Arrays.asList("31790ea2bd2fa7e5cec78e3ffbc98c81")); executeTest("test SLOD", spec); } @@ -102,7 +102,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testNDA() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("fc8cdf9eeb475773303809c077f83c65")); + Arrays.asList("2f2d7dd623446fc3cae62a44a016c16d")); executeTest("test NDA", spec); } @@ -110,7 +110,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testCompTrack() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("c98294d321bde3e1e3c4fcee3e88d6d9")); + Arrays.asList("7645a06b917efb1ee799bf21bdf08bc4")); executeTest("test using comp track", spec); } @@ -124,17 +124,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameterSitesOnly() { - testOutputParameters("-sites_only", "5b8938ed55a2b7ae8a52056c9130367b"); + testOutputParameters("-sites_only", "3c0e109190cfbe41d24e7726cc8fe6e3"); } @Test public void testOutputParameterAllConfident() { - testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f353b36db7305f47963446220e39debe"); + testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f6937cc8ec068f2d38b5d277a92be34b"); } @Test public void testOutputParameterAllSites() { - testOutputParameters("--output_mode EMIT_ALL_SITES", "364aec53db79d20698fe0d088828736f"); + testOutputParameters("--output_mode EMIT_ALL_SITES", "1cddd7b1e730765c2b7b55d8a1d69b4c"); } private void testOutputParameters(final String args, final String md5) { @@ -148,7 +148,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testConfidence() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1, - Arrays.asList("ec59b34bedf40d70850ab5ffe42bbddd")); + Arrays.asList("5c7d237e666439edb0ef8c697e37933c")); executeTest("test confidence 1", spec1); } @@ -156,7 +156,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testNoPrior() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.33333 -inputPrior 0.33333", 1, - Arrays.asList("7e8a51e658debdaadbcf17761ed011da")); + Arrays.asList("24b550bbc3c9f0577e069b3fd3122d52")); executeTest("test no prior 1", spec1); } @@ -165,7 +165,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testUserPrior() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.001 -inputPrior 0.495", 1, - Arrays.asList("b3514f5b3510b6667fd2c85ecc529de7")); + Arrays.asList("f60b6705daec1059ce3e533bf8e44c89")); executeTest("test user prior 1", spec1); } @@ -174,7 +174,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void emitPLsAtAllSites() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --output_mode EMIT_ALL_SITES -allSitePLs", 1, - Arrays.asList("6fd14930acb08f0dd9749a8c4d7df831")); + Arrays.asList("ae778a64323abe0da5194f0b936f48aa")); // GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail spec1.disableShadowBCF(); @@ -190,12 +190,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity1() { - testHeterozosity( 0.01, "815f01ef28bf576beb5528ac6fdd5248" ); + testHeterozosity( 0.01, "6b8bdde9d303139806c5177fae53b1fd" ); } @Test public void testHeterozyosity2() { - testHeterozosity( 1.0 / 1850, "8dd14ba8ef6314a99921849b2544b8c6" ); + testHeterozosity( 1.0 / 1850, "b1604d1ba68dfe2fcfb861ef6420a8ba" ); } private void testHeterozosity(final double arg, final String md5) { @@ -274,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("34980dbce4fcd2aa21c46ea0e1897422")); + Arrays.asList("7ed55f70feeacf8ecc6b36f0d741dfc7")); executeTest(String.format("test multiple technologies"), spec); } @@ -293,7 +293,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("5f02a7449305b26aab3ff994dfb53fda")); + Arrays.asList("90224ac1c9e2ce9b77fee8dd6e044efe")); executeTest(String.format("test calling with BAQ"), spec); } @@ -310,7 +310,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " + "-A SnpEff", 1, - Arrays.asList("b61c0dece2d77544f9313c24191e0089")); + Arrays.asList("e99f100fe71bb7f328b485204c16f14a")); executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java index 98f9cad32..e5476e2ba 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java index b652f1047..bdd3eb5c0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -70,7 +70,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("0f9eff0ad2f8cb8e277922bd037825f7")); + Arrays.asList("c759b04ed0d948bda95008e29f3f5c2d")); executeTest("test MultiSample Pilot1", spec); } @@ -78,7 +78,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testWithAllelesPassedIn1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("196979c91f84c01fb5d89e73339c09fa")); + Arrays.asList("c35cadefda8a9f13c497f84193f9f841")); executeTest("test MultiSample Pilot2 with alleles passed in", spec1); } @@ -86,7 +86,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testWithAllelesPassedIn2() { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("391c4e1437a3fa5c99584b466a56d7bb")); + Arrays.asList("06b4ce476bf444305c8d76a765c5ddb6")); executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); } @@ -94,7 +94,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testSingleSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1, - Arrays.asList("41b1d92cdea4581f7843b714345547d6")); + Arrays.asList("281db46f39e3367f207838c620a82bd2")); executeTest("test SingleSample Pilot2", spec); } @@ -102,7 +102,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, - Arrays.asList("4ae7c090dfb85f6286f1187a746def58")); + Arrays.asList("94ca1e00d4fad9c5279271c2779ff797")); executeTest("test Multiple SNP alleles", spec); } @@ -110,7 +110,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testBadRead() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1, - Arrays.asList("67dbab7d307d02b3d879eca8bd15a573")); + Arrays.asList("1d5c55b2df63eb24832de3486c020453")); executeTest("test bad read", spec); } @@ -118,7 +118,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testReverseTrim() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, - Arrays.asList("5c2c49bb5e276df933b2d264e9d4a327")); + Arrays.asList("87dbae957b1df41c1938906e23a88c5e")); executeTest("test reverse trim", spec); } @@ -126,7 +126,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMismatchedPLs() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1, - Arrays.asList("ed5f90897c9a348e4f861eff8992b4e2")); + Arrays.asList("c5aff2572ce09c413e7f5c9e1b3f92d6")); executeTest("test mismatched PLs", spec); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java index eba969d90..5992a66cf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculationUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java index c3e6936b7..b618b1cac 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorPerformanceUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java index f414311b5..e41e852a3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/AFCalculatorResultUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java index 0ded6f8ca..b4bb2a615 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/FixedAFCalculatorProviderUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java index d5f0b7625..73d66c2f5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java index a43d330a6..54e262419 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyFailOverAFCalculatorProviderUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java index aa2c3976f..14e05ad2c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculatorUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java index 8844eb783..c3d3fcba1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AFPriorProviderUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java index cce9708bd..76cd499f2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java index 11921ee3b..56506c729 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java index 908198cbb..178ad494c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/AssemblyResultSetUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java index 6d34f7693..c07aa087e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/Civar.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java index 607bdc985..849cdf9fa 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/CivarUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java index fc6efae37..1ae6d7558 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java index 2ba09aa9f..7877ee59a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java index 336775aac..ab150af82 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java index f14fda293..42649af05 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleComplex1() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "066f1ce9e9826bcfedf6cd80bc560ab8"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "88255eda0e29e4a6e128ddb7177a03ab"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -84,7 +84,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa // TODO -- need a better symbolic allele test @Test public void testHaplotypeCallerSingleSampleSymbolic() { - HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "8a83ab27177f0b7adf50031f061f9cd7"); + HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "e158212aba1d7d229563db11b08b7974"); } private void HCTestComplexGGA(String bam, String args, String md5) { @@ -96,13 +96,13 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "2a5de432f04198737732064206c7d63d"); + "8f8680bd8e1549ad88691c9c8af9977c"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "afaa41101f492d37f57bb18cc638c6bc"); + "82b53501bc3254def885e09866377e7c"); } private void HCTestComplexConsensusMode(String bam, String args, String md5) { @@ -114,7 +114,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleConsensusModeComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337", - "d42ba795fe346d8372cae3c00c9c2f23"); + "353f1895047b15b1fec22b559c9da0c1"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java index 20b089630..0cafbff8e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,13 +51,18 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller; +import org.apache.commons.io.FileUtils; +import org.apache.log4j.Level; import org.broadinstitute.gatk.engine.GATKVCFUtils; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType; +import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import java.io.File; +import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -79,12 +84,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { //TODO this might need to be addressed at some point. //TODO the following test is commented out for the record //tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "7f09c261950bf86e435edfa69ed2ec71"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "02300a1f64e085cc0f4420d8160743c1"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "f71ea433b1334a2d146cc6ad76b46d98"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "daddb5349c34e9190f0563e220894748"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "03e5815cc351f1ec2feed89d2aed8268"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "5d5cca382bdf6987b2aef87918ed374c"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "532888aff96c356397a21ef790636818"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "8d30370465d74fd549d76dd31adc4c0c"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "b7a5f4e40d5ebaf5f6c46a3d4355c817"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0f5e6f2584649a1b7386d94e3dc60f91"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "2e81881e92061ad4eb29025ffdc129c7"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2c67bdc08c8784f2114c2039270b9766"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "63fa5841a21e2c13f1e1a8e2d4ea3380"}); return tests.toArray(new Object[][]{}); } @@ -98,13 +103,13 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; // this functionality can be adapted to provide input data for whatever you might want in your data - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "cfe629c5a3be3b6524258ad1f9145488"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "12fbfffa4bb2b8d520f8021a40b37d19"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a5ea6d4052bbf9e8bba9011bc6f0d203"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "31da2254620f4a9c34ccf7c311cc133f"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "c95f52fe395392331dc3102902d54408"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ae2c7e570855f6d6ca58ddd1089a970"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "22e03f01e91177011ac028d2347751ba"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb3f16bc10e1cc75f2093bec92145d18"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "63ff771eed3e62340c8938b4963d0add"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1122a0b3849f42d1c4a654f93b660e1b"}); - final String NA12878bandedResolutionMD5 = "fbe6099d138a069a65e4713bcae1e873"; + final String NA12878bandedResolutionMD5 = "8d4a51af32cd13ba4b3e33dd00c58398"; tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5}); tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878", ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5}); @@ -121,12 +126,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; // this functionality can be adapted to provide input data for whatever you might want in your data - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "5088d6cf80a6da7c769f97b1ab44c745"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "0895f09731d0ef89ec131c9f75aafe70"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "195017f498d3508e6eee492eb00da97b"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "4f8e3e249509a24da21d5dd8e3594f92"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "ef96f5295b048ef31f5ba82d078a44a2"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "cd809158689ddbbfd18a4eaae016f9a0"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "8bf132d73cf6b0851ae73c6799f19ba9"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "90b25f3050435c9e67aa0ee325c24167"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "5f329540dc5c4556ab029d0e2cfcabcb"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a0be095ed902a8acdb80fb56ca4e8fb4"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "8123d8b68b6fa77ef084f292e191622a"}); return tests.toArray(new Object[][]{}); } @@ -139,12 +144,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; // this functionality can be adapted to provide input data for whatever you might want in your data - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "bb85582fcc2ce45407640fa8a70421ab"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "e01603c5d4c3142978a91b8cd6a98618"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b9e471935b960a7dba3eb2b13939ccaf"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "c724ecdaea7eab5a6239ff4daaa6e034"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "194d27bd2321ff1a8b895a4e9a8d2938"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "4a3dfcfc2f5d27b75725346d63e0b83a"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "6662cfc41393257dfd6c39f1af1e3843"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "70ee4e60d9f86b63aaab09075a71ddd3"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "700d79df3b0b481444e81471204e242e"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "af0fe243e3b96e59097187cd16ba1597"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "228e1d2ec2e729a5f79c37f3f2557708"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "2fc7020457dde4439b4133c098d9ab9b"}); return tests.toArray(new Object[][]{}); } @@ -270,7 +275,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testWrongGVCFNonVariantRecordOrderBugFix() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9b3b232ceeb109f2624826ea20825a82")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("6facd3d2cf9f52877182d627cef1c872")); spec.disableShadowBCF(); executeTest("testMissingGVCFIndexingStrategyException", spec); } @@ -287,7 +292,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testNoCallGVCFMissingPLsBugFix() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("c5a017f1cbd60219506be76f30fc4468")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("d55ccf214fd5095e6d586c1547cb1a7a")); spec.disableShadowBCF(); executeTest("testNoCallGVCFMissingPLsBugFix", spec); } @@ -320,9 +325,92 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("716db262a288eb2a477df3f1957372c7")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("6f6b2fa85cd1bae7f8f72e144fe56c96")); spec.disableShadowBCF(); executeTest(" testAlleleSpecificAnnotations", spec); } + @Test + public void testASMQMateRankSumAnnotation() { + final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A AS_MQMateRankSumTest --disableDithering", + HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9613ec1ec93547cfb0651673e914bee4")); + spec.disableShadowBCF(); + executeTest(" testASMQMateRankSumAnnotation", spec); + } + + @Test + public void testASInsertSizeRankSum() { + final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering -A AS_InsertSizeRankSum", + HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a8765c11b9130c815aae4e06c1f90e45")); + spec.disableShadowBCF(); + executeTest(" testASInsertSizeRankSum", spec); + } + + @Test + public void testHaplotypeCallerMultiAllelicNonRef() { + final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A StrandAlleleCountsBySample", + b37KGReference, privateTestDir + "multiallelic-nonref.bam", "2:47641259-47641859", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("1d9e75bd09a6fc5a1d9156fe8a7d43ce")); + spec.disableShadowBCF(); + executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec); + } + + @Test + public void testHaplotypeCallerMaxNumPLValues() { + final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 70", + b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a4b5c40b1993573c5efd992f3f0db8a9")); + spec.disableShadowBCF(); + executeTest("testHaplotypeCallerMaxNumPLValues", spec); + } + + @Test + public void testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel() throws IOException { + // Need to see log WARN messages + final Level level = logger.getLevel(); + logger.setLevel(Level.WARN); + + final File logFile = createTempFile("testMaxNumPLValuesExceededWithWarnLogLevel.log", ".tmp"); + final String logFileName = logFile.getAbsolutePath(); + + final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s", + b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", + GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("19f5398e4013c06b52c0085fe0b3469e")); + spec.disableShadowBCF(); + executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec); + // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log + Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) exceeded for sample NA12878 at 20:10097101-10097101 with 35 possible genotypes. " + + "No PLs will be output for these genotypes (which may cause incorrect results in subsequent analyses) unless the --max_num_PL_values argument is increased accordingly. " + + "Unless the DEBUG logging level is used, this warning message is output just once per run and further warnings are suppressed.")); + Assert.assertFalse(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) exceeded for sample NA12878 at 20:10316239-10316241 with 70 possible genotypes.")); + Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) was exceeded 2 time(s); the largest number of PLs found was 70.")); + // Set the log level back + logger.setLevel(level); + } + + @Test + public void testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel() throws IOException { + // Need to see log DEBUG messages + final Level level = logger.getLevel(); + logger.setLevel(Level.DEBUG); + + final File logFile = createTempFile("testMaxNumPLValuesExceededWithDebugLogLevel.log", ".tmp"); + final String logFileName = logFile.getAbsolutePath(); + + final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s", + b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", + GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("19f5398e4013c06b52c0085fe0b3469e")); + spec.disableShadowBCF(); + executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec); + // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log + Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) exceeded for sample NA12878 at 20:10097101-10097101 with 35 possible genotypes.")); + Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) exceeded for sample NA12878 at 20:10316239-10316241 with 70 possible genotypes.")); + Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) was exceeded 2 time(s); the largest number of PLs found was 70.")); + // Set the log level back + logger.setLevel(level); + } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java index c07ff16cb..f8dd4b39c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 4ac07e377..09722f5ee 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -94,89 +94,104 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { Assert.assertFalse(FileUtils.readFileToString(outputVCF).contains(VCFConstants.MAPPING_QUALITY_ZERO_KEY)); } + private void HCTestWithBAMOut(String bam, String args, String md5Variants, String md5BAMOut) throws IOException { + final String base = String.format("-T HaplotypeCaller -R %s -I %s ", + REF, NA12878_BAM) + + args + + " --no_cmdline_in_header -o %s -bamout %s --emitDroppedReads"; + + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5Variants, md5BAMOut)); + executeTest("testHaplotypeCallerBamout", spec); + } + + @Test + public void testHaplotypeBAMOutFlags() throws IOException { + HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "08943fb76d1cd5b5b8815e3991754911", "6a81bbefa6c4ed7a6b8d2c3e0e5a4756"); + } + @Test public void testHaplotypeCallerMultiSample() throws IOException { - HCTest(CEUTRIO_BAM, "", "bdc5a942a7df2d4c61388ecc74a163cf"); + HCTest(CEUTRIO_BAM, "", "ad472fbd63864caacf5bc018dcae9df9"); } @Test public void testHaplotypeCallerSingleSample() throws IOException { - HCTest(NA12878_BAM, "", "5941f88fa1372eb598880a4711ac08de"); + HCTest(NA12878_BAM, "", "c04293cb8466a1a217bce4ef419bdabe"); } @Test public void testHaplotypeCallerMultiSampleHaploid() throws IOException { - HCTest(CEUTRIO_BAM, "-ploidy 1", "4c32640204a11fe46a23d97b1012bca2"); + HCTest(CEUTRIO_BAM, "-ploidy 1", "7ee30877f0153257afdc691c638e7684"); } @Test public void testHaplotypeCallerSingleSampleHaploid() throws IOException { - HCTest(NA12878_BAM, "-ploidy 1", "e09c5fd862f86f69289d847e3b293e19"); + HCTest(NA12878_BAM, "-ploidy 1", "9ca97bb743a369a1abb1e61168d63d69"); } @Test public void testHaplotypeCallerSingleSampleTetraploid() throws IOException { - HCTest(NA12878_BAM, "-ploidy 4", "bbae9f77683591200b2034d5461e6425"); + HCTest(NA12878_BAM, "-ploidy 4", "5098645e8b570bc4521570654fa91806"); } @Test public void testHaplotypeCallerMinBaseQuality() throws IOException { - HCTest(NA12878_BAM, "-mbq 15", "5941f88fa1372eb598880a4711ac08de"); + HCTest(NA12878_BAM, "-mbq 15", "c04293cb8466a1a217bce4ef419bdabe"); } @Test public void testHaplotypeCallerMinBaseQualityHaploid() throws IOException { - HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "e09c5fd862f86f69289d847e3b293e19"); + HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "9ca97bb743a369a1abb1e61168d63d69"); } @Test public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException { - HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "bbae9f77683591200b2034d5461e6425"); + HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "5098645e8b570bc4521570654fa91806"); } @Test public void testHaplotypeCallerGraphBasedSingleSample() throws IOException { - HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "9a4ba54146449914b1fbaed5465b692e"); + HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "ba0dc5f416d69558cb5dd3e0a0a5a084"); } @Test public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "5333e3ff4d7fc53624eab801250be4f0"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "129bca18bb9eec23004b2d28aa541de2"); } @Test public void testHaplotypeCallerGraphBasedMultiSample() throws IOException { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "e9759bf254b7b4d06e4a68c94a417cf1"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "2b89c9e102a049e223bc0d91156a08a3"); } @Test public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException { - HCTest(NA12878_BAM, "-D " + b37dbSNP132, "7466c4d9ce6a1d23bcb428fc9f446843"); + HCTest(NA12878_BAM, "-D " + b37dbSNP132, "ff8e142f491b06e17e64e3a5d59737a7"); } @Test public void testHaplotypeCallerMultiSampleGGA() throws IOException { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" + " -isr INTERSECTION -L " + GGA_INTERVALS_FILE, - "c2fe156912e59626c0393b9b47c9419e"); + "af3f54bee3347cafb34734dc7d3516a9"); } @Test public void testHaplotypeCallerMultiSampleGGAHaploid() throws IOException { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 1 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000", - "49f737983375c740361daa2d48ed0249"); + "e60065998227f4ba8002165fb1729a71"); } @Test public void testHaplotypeCallerMultiSampleGGATetraploid() throws IOException { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 4 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000", - "6ba0fa930899f70fee9a7b1161508f93"); + "d7c3aac002701bec6b6d0539c65207be"); } @Test public void testHaplotypeCallerInsertionOnEdgeOfContig() throws IOException { - HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "da1f6b9a7e5913910531b00f3b35ce06"); + HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "60e98012fbad5f429b3b2abc3a7aa454"); } private void HCTestIndelQualityScores(String bam, String args, String md5) { @@ -187,7 +202,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "22028b104dd60b23a399e5e3a877a1fb"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "3625167f0e788d409c7eab1898d5eafe"); } private void HCTestNearbySmallIntervals(String bam, String args, String md5) { @@ -224,7 +239,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerNearbySmallIntervals() { - HCTestNearbySmallIntervals(NA12878_BAM, "", "6e55de7bf49ecdc71f6d4c9565a19853"); + HCTestNearbySmallIntervals(NA12878_BAM, "", "591a58f16104fbb83ccf81c97cef931a"); } // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper @@ -234,14 +249,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void HCTestProblematicReadsModifiedInActiveRegions() { final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965"; - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("f8774326a268f7d394b333818d15d05c")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("eb79b4c0bf9142c955f0a4501e9e6d8f")); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); } @Test public void HCTestStructuralIndels() { final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730"; - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("034c6b151dfde537d5843f70880bf8a4")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8bddb7f343302ed20bc549df4b82825a")); executeTest("HCTestStructuralIndels: ", spec); } @@ -281,7 +296,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testLeftAlignmentBamOutBugFix() { final String base = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT) + " --no_cmdline_in_header -bamout %s -o /dev/null -L 1:11740000-11740700 --allowNonUniqueKmersInRef"; - final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("c1840293b4565ce1cef393c6a0d5fc9a")); + final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("01deba68f7a7d562b0e466f6858d42e3")); executeTest("LeftAlignmentBamOutBugFix", spec); } @@ -296,7 +311,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestDBSNPAnnotationWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1, - Arrays.asList("ab816ff6facc08acb19c55bd6e828f02")); + Arrays.asList("b56895e6d28ea0b9dadeecd0ff61687e")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -305,7 +320,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132 + " -L " + hg19Intervals + " -isr INTERSECTION", 1, - Arrays.asList("fd1a539e14902f6957eb939aac1412f0")); + Arrays.asList("7b52164df8bf76d789836f990bd6066a")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } @@ -313,7 +328,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestDBSNPAnnotationWGSGraphBased() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1, - Arrays.asList("1810c35e8298dff4aa1b7b04fb5f4962")); + Arrays.asList("096826325215f79fe70661d984ae45a4")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -322,7 +337,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132 + " -L " + hg19Intervals + " -isr INTERSECTION", 1, - Arrays.asList("8a06a53388d73ec667b353379f3b351e")); + Arrays.asList("ff3b24412090ce7693d66d750ae84ac9")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } @@ -345,7 +360,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestAggressivePcrIndelModelWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1, - Arrays.asList("be71ab16d55437cbe3005ea3b93cece6")); + Arrays.asList("c2dab66ad3740320004874c83051bbfc")); executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec); } @@ -353,7 +368,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestConservativePcrIndelModelWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1, - Arrays.asList("8a5185d0a9400c8b3f4b12da65181c4b")); + Arrays.asList("a8ea15ac136042891434ccb0b3c3b686")); executeTest("HC calling with conservative indel error modeling on WGS intervals", spec); } @@ -368,12 +383,21 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { executeTest("testGraphBasedNoSuchEdgeBugFix", spec); } + @Test + public void testWriteGVCFStdout() { + final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -dontTrimActiveRegions -ERC GVCF ", + b37KGReferenceWithDecoy, privateTestDir + "graphbased_no_such_edge_bug.bam", privateTestDir + "graphbased_no_such_edge_bug.intervals.bed"); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine, Arrays.asList("")); + spec.disableShadowBCF(); + executeTest("testWriteGVCFStdout", spec); + } + // This test takes longer than 15 secs ... ~ 25-35 , @Test public void testLackSensitivityDueToBadHaplotypeSelectionFix() { final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list"); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("02ec3090c4a6359fa10e6d8b30e1d5a2")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5514cfbcf12954bb12c725b77eaac248")); spec.disableShadowBCF(); executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec); } @@ -382,7 +406,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testMissingKeyAlternativeHaplotypesBugFix() { final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header ", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list"); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("13c9f094b9c54960dc2fd3a1815a2645")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e6d8c32585906122a6407cb40261d00d")); spec.disableShadowBCF(); executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec); } @@ -405,7 +429,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { // but please make sure that both outputs get the same variant, // alleles all with DBSNP ids // We test here that change in active region size does not have an effect in placement of indels. - final String md5 = "6121d05f96eca3b1dbe3a881d968b6c5"; + final String md5 = "87b687b5476eb38b11db6a156b4066c8"; final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList(md5)); executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec); final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList(md5)); @@ -459,12 +483,22 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{ - HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "03738462e7f0b6f149f40b790a3a7261"); + HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "34328c475325b7dfaa57ab5920478e0c"); } @Test public void testHBaseCountsBySample() throws IOException{ - HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "8739d92898113436666f1cff3bc39bc5"); + HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "f5ad4e03c0faaa806ee6ae536af8a479"); + } + + @Test + public void testSetZeroGQsToNoCall() throws IOException{ + final File testBAM = new File(privateTestDir + "set.zero.GQs.no.call.bam"); + final String md5 = "b90da12d97fce42f5127bcb6cad07b09"; + final String base = String.format("-T HaplotypeCaller -R %s -I %s -L 8:17312375-17312975 ", REF, testBAM) + + " --no_cmdline_in_header -o %s"; + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5)); + executeTest("testSetZeroGQsToNoCall", spec); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java index 76c7cfc3e..d1bf66c97 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java index ec2be4041..fdc51094c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java index 8eae1588d..97565b6e0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java index 69138bd65..6f87f147d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java index ffc3ed72f..e514fbbc2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java index d84483615..457a63547 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java index b5fa37df9..d05737082 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/KmerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java index 4819c7f21..f7f931289 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java index 08dc468da..28690d993 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java index 963a7da61..1b055c9d4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java index a07e815a6..c16b2d269 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java index d230ed7b6..74ed3e49a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java index b240e5ffb..97908682e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java index 8973eb9ba..63278e2f4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java index dad8d8e2d..0c3b4b558 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java index 61d568d57..24cceda65 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java index e633ca39c..945093e9b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java index 5c73ce2fe..01a818b2c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java index b94cc75cf..b8a239579 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java index 8a9cedfb3..cb51f5654 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java index b2a530d6c..807122317 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java index 1f28f6b97..3a568029e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java index 60065ea92..4c8756031 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java index c0093c275..def08be21 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java index caeafd16e..de3acd481 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java index a0675e428..330b7bd88 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathBuilderUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java index cbec4b9b2..2498a2aff 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/PathUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java index 8f7513be7..8965a0f0e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/RouteUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java index 9fb138613..3869db9f7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java index 2086234c7..57d2f4506 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java index 8fa4f4ae8..d8419d9dc 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java index ade84cbf6..875ad4dde 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java index cacf2ba2a..f37e7a4c3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java index 83a00412a..b7f5e2e8d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java index c17b8d1b4..059ed760f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java deleted file mode 100644 index 1ef0db5d4..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java +++ /dev/null @@ -1,198 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.indels; - -import htsjdk.samtools.SAMFileHeader; -import htsjdk.samtools.SAMFileWriter; -import htsjdk.samtools.SAMRecord; -import htsjdk.samtools.util.ProgressLoggerInterface; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.testng.Assert; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - -import java.util.ArrayList; -import java.util.List; - - -public class ConstrainedMateFixingManagerUnitTest extends BaseTest { - - private static SAMFileHeader header; - private static GenomeLocParser genomeLocParser; - - @BeforeClass - public void beforeClass() { - header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 10000); - genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); - } - - @Test - public void testSecondaryAlignmentsDoNotInterfere() { - final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false); - final GATKSAMRecord read1 = properReads.get(0); - read1.setAlignmentStart(8); // move the read - read1.setFlags(99); // first in proper pair, mate negative strand - - final GATKSAMRecord read2Primary = properReads.get(1); - read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment - - Assert.assertEquals(read1.getInferredInsertSize(), 21); - - final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); - read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand - - final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 1000, 1000, 1000); - manager.addRead(read1, true, false); - manager.addRead(read2NonPrimary, false, false); - manager.addRead(read2Primary, false, false); - - Assert.assertEquals(manager.getNReadsInQueue(), 3); - - for ( final SAMRecord read : manager.getReadsInQueueForTesting() ) { - if ( read.getFirstOfPairFlag() ) { - Assert.assertEquals(read.getFlags(), 99); - Assert.assertEquals(read.getInferredInsertSize(), 23); - } else if ( read.getNotPrimaryAlignmentFlag() ) { - Assert.assertEquals(read.getFlags(), 393); - Assert.assertEquals(read.getInferredInsertSize(), -21); - } else { - Assert.assertEquals(read.getFlags(), 147); - Assert.assertEquals(read.getInferredInsertSize(), -23); - } - } - } - - @Test - public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() { - final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false); - final GATKSAMRecord read1 = properReads.get(0); - read1.setFlags(99); // first in proper pair, mate negative strand - - final GATKSAMRecord read2Primary = properReads.get(1); - read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment - read2Primary.setAlignmentStart(1596); // move the read - - final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); - read2NonPrimary.setReadName("foo"); - read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand - read2NonPrimary.setAlignmentStart(451); - read2NonPrimary.setMateAlignmentStart(451); - - final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000); - manager.addRead(read2NonPrimary, false, false); - manager.addRead(read1, false, false); - - for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ ) - manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false); - - Assert.assertTrue(manager.forMateMatching.containsKey("foo")); - } - - @Test - public void testSupplementaryAlignmentsDoNotCauseBadMateFixing() { - final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 1000, 2000, true, false); - final GATKSAMRecord read1 = properReads.get(0); - read1.setFlags(99); // first in pair, negative strand - - final GATKSAMRecord read2 = properReads.get(1); - read2.setFlags(161); // second in pair, mate negative strand - - final GATKSAMRecord read2Supp = new GATKSAMRecord(read2); - read2Supp.setReadName("foo"); - read2Supp.setFlags(2209); // second in pair, mate negative strand, supplementary - read2Supp.setAlignmentStart(100); - read2Supp.setMateAlignmentStart(1000); - - final DummyWriter writer = new DummyWriter(); - final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(writer, genomeLocParser, 10000, 200, 10000); - manager.addRead(read2Supp, false, false); - manager.addRead(read1, false, false); - manager.addRead(read2, false, false); - manager.close(); // "write" the reads to our dummy writer - - // check to make sure that none of the mate locations were changed, which is the problem brought to us by a user - for ( final SAMRecord read : writer.reads ) { - final int start = read.getAlignmentStart(); - switch (start) { - case 100: - Assert.assertEquals(read.getMateAlignmentStart(), 1000); - break; - case 1000: - Assert.assertEquals(read.getMateAlignmentStart(), 2000); - break; - case 2000: - Assert.assertEquals(read.getMateAlignmentStart(), 1000); - break; - default: - Assert.assertTrue(false, "We saw a read located at the wrong position"); - } - } - } - - private class DummyWriter implements SAMFileWriter { - - public List reads; - - public DummyWriter() { reads = new ArrayList<>(10); } - - public void addAlignment(final SAMRecord alignment) { reads.add(alignment);} - - public SAMFileHeader getFileHeader() { return null; } - - public void setProgressLogger(final ProgressLoggerInterface progress) {} - - public void close() {} - } -} \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java deleted file mode 100644 index b8703447a..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java +++ /dev/null @@ -1,187 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.indels; - -import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.testng.annotations.Test; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.Map; - -public class IndelRealignerIntegrationTest extends WalkerTest { - - private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.fixmates.bam"; - private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals"; - private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf"; - private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 "; - private static final String baseCommand = baseCommandPrefix + "-o %s "; - private static final String base_md5 = "ab7407d2299d9ba73449cea376eeb9c4"; - private static final String base_md5_with_SW_or_VCF = "fa57bd96b83038ac6a70e58e11bf5364"; - - @Test - public void testDefaults() { - - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommand, - 1, - Arrays.asList(base_md5)); - executeTest("test realigner defaults", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - baseCommand + "-known " + knownIndels, - 1, - Arrays.asList(base_md5_with_SW_or_VCF)); - executeTest("test realigner defaults with VCF", spec2); - } - - @Test - public void testKnownsOnly() { - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels, - 1, - Arrays.asList("c42b6f3e1270e43cce2b6f75b6a38f30")); - executeTest("realigner known indels only from VCF", spec1); - } - - @Test - public void testUseSW() { - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel USE_SW -known " + knownIndels, - 1, - Arrays.asList(base_md5_with_SW_or_VCF)); - executeTest("realigner use SW from VCF", spec1); - } - - @Test - public void testLods() { - HashMap e = new HashMap(); - e.put("-LOD 60", base_md5); - e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "0c4597e48b4e194de32ebe494704ea6b" ); - - for ( Map.Entry entry : e.entrySet() ) { - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + entry.getKey(), - 1, - Arrays.asList(entry.getValue())); - executeTest(String.format("realigner [%s]", entry.getKey()), spec); - } - } - - @Test - public void testLongRun() { - WalkerTestSpec spec = new WalkerTestSpec( - "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s", - 1, - Arrays.asList("19e6859b9ef09c7e0a79a19626908b17")); - executeTest("realigner long run", spec); - } - - @Test - public void testNoTags() { - WalkerTestSpec spec = new WalkerTestSpec( - baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW", - 1, - Arrays.asList("8f5684359d7b26acaacfa657ef395a0c")); - executeTest("realigner no output tags", spec); - } - - @Test - public void testStats() { - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommandPrefix + "-stats %s -o /dev/null", - 1, - Arrays.asList("7ed8d4eed635613fd031598a5c9ef5a3")); - executeTest("realigner stats", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - baseCommandPrefix + "-LOD 60 -stats %s -o /dev/null", - 1, - Arrays.asList("e8b02bfc5debec55fe936a38c59463cc")); - executeTest("realigner stats", spec2); - } - - @Test - public void testMaxReadsInMemory() { - HashMap e = new HashMap(); - e.put("--maxReadsInMemory 10000", "236c64f2da0047534b44444d9d699378"); - e.put( "--maxReadsInMemory 40000", base_md5 ); - - for ( Map.Entry entry : e.entrySet() ) { - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + entry.getKey(), - 1, - Arrays.asList(entry.getValue())); - executeTest(String.format("realigner [%s]", entry.getKey()), spec); - } - } - - @Test - public void testNWayOut() { - WalkerTestSpec spec1 = new WalkerTestSpec( - baseCommandPrefix + " -nWayOut .clean.bam ", - 1, - Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")); - executeTest("test realigner nWayOut", spec1); - } - - @Test - public void testBadCigarStringDoesNotFail() { - // Just making sure the test runs without an error, don't care about the MD5 value - WalkerTestSpec spec = new WalkerTestSpec( - "-T IndelRealigner -R " + b37KGReference + " -I " + privateTestDir + "Realigner.error.bam -L 19:5787200-5787300 -targetIntervals 19:5787205-5787300 -o %s", - 1, - Arrays.asList("")); - executeTest("test bad cigar string does not fail", spec); - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java deleted file mode 100644 index 4dc1b23e4..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java +++ /dev/null @@ -1,108 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.indels; - -import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.testng.annotations.Test; - -import java.util.ArrayList; - -public class IndelRealignerLargeScaleTest extends WalkerTest { - @Test( timeOut = 18000000 ) - public void testHighCoverage() { - WalkerTestSpec spec = new WalkerTestSpec( - - "-R " + b36KGReference + - " -T IndelRealigner" + - " -I " + validationDataLocation + "indelRealignerTest.pilot1.veryHighCoverage.bam" + - " -L 20:49,500-55,500" + - " -o /dev/null" + - " -targetIntervals " + validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals", - 0, - new ArrayList(0)); - executeTest("testIndelRealignerHighCoverage", spec); - } - - @Test( timeOut = 18000000 ) - public void testRealigner() { - WalkerTestSpec spec1 = new WalkerTestSpec( - - "-R " + hg18Reference + - " -T IndelRealigner" + - " -LOD 5" + - " -maxConsensuses 100" + - " -greedy 100" + - " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + - " -o /dev/null" + - " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + - " -L chr1:1-5,650,000" + - " -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals", - 0, - new ArrayList(0)); - executeTest("testIndelRealignerWholeGenome", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - "-R " + hg18Reference + - " -T IndelRealigner" + - " -LOD 5" + - " -maxConsensuses 100" + - " -greedy 100" + - " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + - " -o /dev/null" + - " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + - " -L chr1:1-150,000,000" + - " -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals", - 0, - new ArrayList(0)); - executeTest("testIndelRealignerWholeExome", spec2); - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java index ce78b68f6..60f7f0fdf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModelUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java deleted file mode 100644 index 97e658a5d..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java +++ /dev/null @@ -1,117 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.indels; - -import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import org.broadinstitute.gatk.utils.sam.ReadUtils; -import org.testng.Assert; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; - -/** - * User: carneiro - * Date: 2/16/13 - * Time: 11:48 PM - */ -public class ReadBinUnitTest { - private GenomeLocParser parser; - private ReadBin readBin; - - private final int readLength = 100; // all reads will have the same size - private final int referencePadding = 10; // standard reference padding - - @BeforeClass - public void init() { - parser = new GenomeLocParser(ArtificialSAMUtils.createArtificialSamHeader().getSequenceDictionary()); - readBin = new ReadBin(parser, referencePadding); - } - - @DataProvider(name = "reads") - public Object[][] reads() { - - return new Object[][]{ - {"20S80M", 80}, - {"80M20S", 1}, - {"20S60M20S", 50}, - {"50I", 60}, - {"100M", 500} - }; - } - - /** - * Tests the GenomeLoc variable in the ReadBin after adding arbitrary reads - * - * @param cigarString the read's cigar string - * @param alignmentStart the read's alignment start - */ - @Test(enabled = true, dataProvider = "reads") - public void testAddingReads(String cigarString, int alignmentStart) { - final GATKSAMRecord read = createReadAndAddToBin(cigarString, alignmentStart); - final GenomeLoc readLoc = parser.createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getSoftStart(), Math.max(read.getSoftStart(), read.getSoftEnd())); - Assert.assertEquals(readBin.getLocation(), readLoc); - readBin.clear(); - } - - public GATKSAMRecord createReadAndAddToBin(String cigarString, int alignmentStart) { - final GATKSAMRecord read = ReadUtils.createRandomRead(readLength); - read.setCigarString(cigarString); - read.setAlignmentStart(alignmentStart); - readBin.add(read); - return read; - } -} - - diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java deleted file mode 100644 index 23881d330..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java +++ /dev/null @@ -1,159 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.indels; - -import htsjdk.samtools.reference.ReferenceSequenceFile; -import htsjdk.samtools.util.Interval; -import htsjdk.samtools.util.IntervalList; -import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.GenomeLoc; -import org.broadinstitute.gatk.utils.GenomeLocParser; -import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.gatk.utils.interval.IntervalUtils; -import org.testng.Assert; -import org.testng.annotations.DataProvider; -import org.testng.annotations.Test; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; - -public class RealignerTargetCreatorIntegrationTest extends WalkerTest { - - @DataProvider(name = "intervals1") - public Object[][] intervals1() { - String arguments = "-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000"; - return new Object[][]{ - {"test standard nt=1", arguments}, - {"test standard nt=4", "-nt 4 " + arguments} - }; - } - - @DataProvider(name = "intervals2") - public Object[][] intervals2() { - String arguments = "-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000"; - return new Object[][]{ - {"test with dbsnp nt=1", arguments}, - {"test with dbsnp nt=4", "-nt 4 " + arguments} - }; - } - - @Test(dataProvider = "intervals1") - public void testIntervals1(String testName, String arguments) { - String md5 = "3f0b63a393104d0c4158c7d1538153b8"; - - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5)); - executeTest(testName, spec); - } - - @Test(dataProvider = "intervals2") - public void testIntervals2(String testName, String arguments) { - String md5 = "d073237694175c75d37bd4f40b8c64db"; - - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5)); - executeTest(testName, spec); - } - - @Test - public void testKnownsOnly() { - WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - "-T RealignerTargetCreator -R " + b36KGReference + " --known " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s", - 1, - Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96")); - executeTest("test rods only", spec3); - } - - @Test() - public void testBadCigarStringDoesNotFail() { - // Just making sure the test runs without an error, don't care about the MD5 value - WalkerTestSpec spec = new WalkerTestSpec( - "-T RealignerTargetCreator -R " + b37KGReference + " -I " + privateTestDir + "Realigner.error.bam -L 19:5787200-5787300 -o %s", - 1, - Arrays.asList("")); - executeTest("test bad cigar string string does not fail", spec); - } - - @Test(dataProvider = "intervals1") - public void testTargetListAgainstIntervalList(String testName, String arguments) throws IOException { - final List md5 = Collections.emptyList(); - final File targetListFile = createTempFile("RTCTest", ".targets"); - final File intervalListFile = createTempFile("RTCTest", ".interval_list"); - - WalkerTest.WalkerTestSpec targetListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5); - WalkerTest.WalkerTestSpec intervalListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5); - - targetListSpec.setOutputFileLocation(targetListFile); - intervalListSpec.setOutputFileLocation(intervalListFile); - - executeTest(testName + " (compare target-list and interval-list output)", targetListSpec); - executeTest(testName + " (compare target-list and interval-list output)", intervalListSpec); - - final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference)); - final GenomeLocParser hg19GenomeLocParser = new GenomeLocParser(seq); - final List targetList = IntervalUtils.intervalFileToList(hg19GenomeLocParser, - targetListFile.getAbsolutePath()); - final List targetListResult = new ArrayList<>(); - for ( GenomeLoc target : targetList ) { - targetListResult.add(new Interval(target.getContig(), target.getStart(), target.getStop())); - } - - final List intervalListResult = IntervalList.fromFile(intervalListFile).getIntervals(); - - Assert.assertFalse(targetListResult.isEmpty()); - Assert.assertFalse(intervalListResult.isEmpty()); - Assert.assertEquals(targetListResult, intervalListResult); - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java deleted file mode 100644 index 4d2a628e4..000000000 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java +++ /dev/null @@ -1,85 +0,0 @@ -/* -* By downloading the PROGRAM you agree to the following terms of use: -* -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY -* -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. -*/ - -package org.broadinstitute.gatk.tools.walkers.indels; - -import org.broadinstitute.gatk.engine.walkers.WalkerTest; -import org.testng.annotations.Test; - -import java.util.ArrayList; - -public class RealignerTargetCreatorLargeScaleTest extends WalkerTest { - @Test( timeOut = 18000000 ) - public void testRealignerTargetCreator() { - - WalkerTestSpec spec1 = new WalkerTestSpec( - "-R " + hg18Reference + - " -T RealignerTargetCreator" + - " --known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + - " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + - " -L chr1:1-50,000,000" + - " -o /dev/null", - 0, - new ArrayList(0)); - executeTest("testRealignerTargetCreatorWholeGenome", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - "-R " + hg18Reference + - " -T RealignerTargetCreator" + - " --known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + - " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + - " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + - " -o /dev/null", - 0, - new ArrayList(0)); - executeTest("testRealignerTargetCreatorWholeExome", spec2); - } -} diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java index f6cc5399b..6a1aea7ba 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -88,7 +88,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-o %s" ), 2, - Arrays.asList("af979bcb353edda8dee2127605c71daf","3934b5de598024496a5de0ec35bde5b0") + Arrays.asList("af979bcb353edda8dee2127605c71daf","7ed46f6aa4565b5012acde17119a1a31") ); executeTest("testTrueNegativeMV", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java index 08be802f2..b113e0d08 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -81,7 +81,6 @@ public class PhasingUtilsUnitTest extends BaseTest { private ReferenceSequenceFile referenceFile; private Genotype genotype1; private Genotype genotype2; - private Genotype genotype2unphased; private String contig; private List alleleList1; private List alleleList2; @@ -94,9 +93,8 @@ public class PhasingUtilsUnitTest extends BaseTest { genomeLocParser = new GenomeLocParser(referenceFile); alleleList1 = Arrays.asList(Allele.create("T", true), Allele.create("C", false)); alleleList2 = Arrays.asList(Allele.create("G", true), Allele.create("A", false)); - genotype1 = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-1", "10-2"}).attribute("PQ", 100.0).alleles(alleleList1).phased(true).make(); - genotype2 = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-2", "10-1"}).attribute("PQ", 200.0).alleles(alleleList2).phased(true).make(); - genotype2unphased = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-2", "10-1"}).attribute("PQ", 200.0).alleles(alleleList2).phased(false).make(); + genotype1 = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-1", "10-2"}).attribute("PQ", 100.0).alleles(alleleList1).make(); + genotype2 = new GenotypeBuilder().name("sample").attribute("HP", new String[]{"10-2", "10-1"}).attribute("PQ", 200.0).alleles(alleleList2).make(); contig = new String("1"); vc1 = new VariantContextBuilder().chr(contig).id("id1").source("TC").start(start).stop(start).alleles(alleleList1).genotypes(genotype1).make(); vc2 = new VariantContextBuilder().chr(contig).id("id2").source("GA").start(start+1).stop(start+1).alleles(alleleList2).genotypes(genotype2).make(); @@ -186,7 +184,6 @@ public class PhasingUtilsUnitTest extends BaseTest { @Test public void TestAlleleSegregationIsKnown(){ Assert.assertTrue(PhasingUtils.alleleSegregationIsKnown(genotype1, genotype2)); - Assert.assertFalse(PhasingUtils.alleleSegregationIsKnown(genotype1, genotype2unphased)); } @Test diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java index 094163ea7..0638804d6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -70,7 +70,6 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { " --no_cmdline_in_header"; } - @Test public void test1() { WalkerTestSpec spec = new WalkerTestSpec( @@ -87,7 +86,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10) + " -L chr20:1232503-1332503", 1, - Arrays.asList("27c0e81c71f599685f6bdc433652645d")); + Arrays.asList("39d4f9b5650667491091ccee7c245b06")); executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec); } @@ -127,7 +126,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10) + " -L chr20:652810-681757", 1, - Arrays.asList("acfcca2d271c3403dc42a16e0494f11b")); + Arrays.asList("f06edaabb82af64f1465dd27b9c9948e")); executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec); } @@ -137,7 +136,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10) + " -L chr20:332341-802503", 1, - Arrays.asList("504e9af1f767db3d9da9bb6665daabcb")); + Arrays.asList("16ac184f0f8c81c9b4a6cbc235a58872")); executeTest("Use trio-phased VCF, adding read-backed phasing information in HP tag (as is now standard for RBP) [TEST SEVEN]", spec); } @@ -152,7 +151,40 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { " -o %s" + " --no_cmdline_in_header", 1, - Arrays.asList("d7797171d9ca4e173fab6b5af1e6d539")); + Arrays.asList("0b47205ebdf2cf752ad91ff49e82c401")); executeTest("Do not merge unphased SNPs", spec); } + + @Test + public void testMergeSNPsIfSameRead() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T ReadBackedPhasing" + + " -R " + b37KGReferenceWithDecoy + + " -I " + privateTestDir + "readBackedPhasing.bam" + + " --variant " + privateTestDir + "readBackedPhasing.vcf.gz" + + " -enableMergeToMNP -maxDistMNP 2 -L 1:1875000-1877000" + + " -o %s" + + " --no_cmdline_in_header", + 1, + Arrays.asList("1419d9292d6e5db6282204826cb53bf7")); + executeTest("Merge SNPs if on the same read", spec); + } + + @Test + public void testDontMergeSpanningDeletions() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T ReadBackedPhasing" + + " -R " + b37KGReferenceWithDecoy + + " -I " + privateTestDir + "phasing_test_with_span_del_1.bam" + + " -I " + privateTestDir + "phasing_test_with_span_del_2.bam" + + " -I " + privateTestDir + "phasing_test_with_span_del_3.bam" + + " -I " + privateTestDir + "phasing_test_with_span_del_4.bam" + + " --variant " + privateTestDir + "phasing_test_with_span_del.vcf" + + " -enableMergeToMNP" + + " -o %s" + + " --no_cmdline_in_header", + 1, + Arrays.asList("8a3cd58dd6b1d04ab8c699f4e328dff4")); + executeTest("Don't merge symbolic SPAN_DEL (*) alleles (into the nonexistent ** MNP).", spec); + } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java index 7e707479f..7e6e8f034 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/OverhangFixingManagerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java index afaaf7036..5386c2b16 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java index f5b4264dd..251de2f27 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java index 984e06eee..4a105aa96 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java index 247f3ca16..8840a03c2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/validation/ValidationSiteSelectorIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java index 88bd7a4cd..20cf0e29d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java index 11b34a0c0..d28b5f708 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalWalkerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -226,7 +226,7 @@ public class VariantEvalWalkerUnitTest extends BaseTest { // test pairs of strats new StratifiedEvalTestProvider(12, - Arrays.asList(4, 3, 2, 3), + Arrays.asList(3, 4, 3, 2), Arrays.asList(1, 2), Arrays.asList(3, 4)); return StratifiedEvalTestProvider.getTests(StratifiedEvalTestProvider.class); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java index a01355e65..b413af37a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java index e4b1dc4eb..44afa81fb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java index f5b92941e..3765b418e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManagerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java index 103d25b67..3abc6553b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 926fab004..7c716fef4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -196,8 +196,8 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf", "3ad7f55fb3b072f373cbce0b32b66df4", // tranches - "73489f9365e4884b2dd89477350a7fe0", // recal file - "0bd2067f831e5388b790e7bb7f45d98f"); // cut VCF + "051a3b8c15988ee4cd86ae918bec896b", // recal file + "93a6e7ab6cbd6ae24a5b2a6f0fd29d92"); // cut VCF @DataProvider(name = "VRBCFTest") public Object[][] createVRBCFTest() { @@ -346,6 +346,42 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { } } + @Test(enabled = true) + public void testApplyRecalibrationAlleleSpecificSNPmode() { + final String base = "-R " + b37KGReference + + " -T ApplyRecalibration" + + " -L 3:113005755-195507036" + + " -mode SNP -AS" + + " -ts_filter_level 99.7" + + " --no_cmdline_in_header" + + " -input " + privateTestDir + "VQSR.AStest.input.vcf" + + " -o %s" + + " -tranchesFile " + privateTestDir + "VQSR.AStest.snps.tranches" + + " -recalFile " + privateTestDir + "VQSR.AStest.snps.recal"; + + final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("dbcf0cb5c2a0eb2312e6ca7d4e3aeeda")); + final List outputFiles = executeTest("testApplyRecalibrationAlleleSpecificSNPmode", spec).getFirst(); + setPDFsForDeletion(outputFiles); + } + + @Test(enabled = true) + public void testApplyRecalibrationAlleleSpecificINDELmode() { + final String base = "-R " + b37KGReference + + " -T ApplyRecalibration" + + " -L 3:113005755-195507036" + + " -mode INDEL -AS" + + " -ts_filter_level 99.3" + + " --no_cmdline_in_header" + + " -input " + privateTestDir + "VQSR.AStest.postSNPinput.vcf" + + " -o %s" + + " -tranchesFile " + privateTestDir + "VQSR.AStest.indels.tranches" + + " -recalFile " + privateTestDir + "VQSR.AStest.indels.recal"; + + final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("38d4b8e89dbf8acb6a36dfa1bb55c54c")); + final List outputFiles = executeTest("testApplyRecalibrationAlleleSpecificINDELmode", spec).getFirst(); + setPDFsForDeletion(outputFiles); + } + private void setPDFsForDeletion( final List walkerOutputFiles ) { for ( final File outputFile : walkerOutputFiles ) { new File(outputFile.getAbsolutePath() + ".pdf").deleteOnExit(); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorModelOutputUnitTest.java similarity index 53% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorModelOutputUnitTest.java index c200701f3..56e515029 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorModelOutputUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -49,147 +49,166 @@ * 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. */ -package org.broadinstitute.gatk.engine.recalibration; +package org.broadinstitute.gatk.tools.walkers.variantrecalibration; +import static org.testng.Assert.*; -// the imports for unit testing. - - -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.QualityUtils; -import org.broadinstitute.gatk.utils.Utils; +import Jama.Matrix; +import org.apache.commons.lang.StringUtils; +import org.apache.log4j.Logger; +import org.broadinstitute.gatk.utils.report.GATKReport; +import org.broadinstitute.gatk.utils.report.GATKReportTable; import org.testng.Assert; -import org.testng.annotations.BeforeSuite; -import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.util.ArrayList; -import java.util.Arrays; import java.util.List; +import java.util.Random; - -public class QualQuantizerUnitTest extends BaseTest { - @BeforeSuite - public void before() { - - } - - // -------------------------------------------------------------------------------- - // - // merge case Provider - // - // -------------------------------------------------------------------------------- - - private class QualIntervalTestProvider extends TestDataProvider { - final QualQuantizer.QualInterval left, right; - int exError, exTotal, exQual; - double exErrorRate; - - private QualIntervalTestProvider(int leftE, int leftN, int rightE, int rightN, int exError, int exTotal) { - super(QualIntervalTestProvider.class); - - QualQuantizer qq = new QualQuantizer(0); - left = qq.new QualInterval(10, 10, leftN, leftE, 0); - right = qq.new QualInterval(11, 11, rightN, rightE, 0); - - this.exError = exError; - this.exTotal = exTotal; - this.exErrorRate = (leftE + rightE + 1) / (1.0 * (leftN + rightN + 1)); - this.exQual = QualityUtils.errorProbToQual(this.exErrorRate); - } - } - - @DataProvider(name = "QualIntervalTestProvider") - public Object[][] makeQualIntervalTestProvider() { - new QualIntervalTestProvider(10, 100, 10, 1000, 20, 1100); - new QualIntervalTestProvider(0, 100, 10, 900, 10, 1000); - new QualIntervalTestProvider(10, 900, 0, 100, 10, 1000); - new QualIntervalTestProvider(0, 0, 10, 100, 10, 100); - new QualIntervalTestProvider(1, 10, 9, 90, 10, 100); - new QualIntervalTestProvider(1, 10, 9, 100000, 10, 100010); - new QualIntervalTestProvider(1, 10, 9, 1000000, 10,1000010); - - return QualIntervalTestProvider.getTests(QualIntervalTestProvider.class); - } - - @Test(dataProvider = "QualIntervalTestProvider") - public void testQualInterval(QualIntervalTestProvider cfg) { - QualQuantizer.QualInterval merged = cfg.left.merge(cfg.right); - Assert.assertEquals(merged.nErrors, cfg.exError); - Assert.assertEquals(merged.nObservations, cfg.exTotal); - Assert.assertEquals(merged.getErrorRate(), cfg.exErrorRate); - Assert.assertEquals(merged.getQual(), cfg.exQual); - } +public class VariantRecalibratorModelOutputUnitTest { + protected final static Logger logger = Logger.getLogger(VariantRecalibratorModelOutputUnitTest.class); + private final boolean printTables = true; @Test - public void testMinInterestingQual() { - for ( int q = 0; q < 15; q++ ) { - for ( int minQual = 0; minQual <= 10; minQual ++ ) { - QualQuantizer qq = new QualQuantizer(minQual); - QualQuantizer.QualInterval left = qq.new QualInterval(q, q, 100, 10, 0); - QualQuantizer.QualInterval right = qq.new QualInterval(q+1, q+1, 1000, 100, 0); + public void testVQSRModelOutput() { + final int numAnnotations = 6; + final double shrinkage = 1.0; + final double dirichlet = 0.001; + final double priorCounts = 20.0; + final int numGoodGaussians = 2; + final int numBadGaussians = 1; + final double epsilon = 1e-6; - QualQuantizer.QualInterval merged = left.merge(right); - boolean shouldBeFree = q+1 <= minQual; - if ( shouldBeFree ) - Assert.assertEquals(merged.getPenalty(), 0.0); - else - Assert.assertTrue(merged.getPenalty() > 0.0); + Random rand = new Random(12878); + MultivariateGaussian goodGaussian1 = new MultivariateGaussian(numAnnotations); + goodGaussian1.initializeRandomMu(rand); + goodGaussian1.initializeRandomSigma(rand); + + MultivariateGaussian goodGaussian2 = new MultivariateGaussian(numAnnotations); + goodGaussian2.initializeRandomMu(rand); + goodGaussian2.initializeRandomSigma(rand); + + MultivariateGaussian badGaussian1 = new MultivariateGaussian(numAnnotations); + badGaussian1.initializeRandomMu(rand); + badGaussian1.initializeRandomSigma(rand); + + List goodGaussianList = new ArrayList<>(); + goodGaussianList.add(goodGaussian1); + goodGaussianList.add(goodGaussian2); + + List badGaussianList = new ArrayList<>(); + badGaussianList.add(badGaussian1); + + GaussianMixtureModel goodModel = new GaussianMixtureModel(goodGaussianList, shrinkage, dirichlet, priorCounts); + GaussianMixtureModel badModel = new GaussianMixtureModel(badGaussianList, shrinkage, dirichlet, priorCounts); + + if (printTables) { + System.out.println("Good model mean matrix:"); + System.out.println(vectorToString(goodGaussian1.mu)); + System.out.println(vectorToString(goodGaussian2.mu)); + System.out.println("\n\n"); + + System.out.println("Good model covariance matrices:"); + goodGaussian1.sigma.print(10, 3); + goodGaussian2.sigma.print(10, 3); + System.out.println("\n\n"); + + System.out.println("Bad model mean matrix:\n"); + System.out.println(vectorToString(badGaussian1.mu)); + System.out.println("\n\n"); + + System.out.println("Bad model covariance matrix:"); + badGaussian1.sigma.print(10, 3); + } + + VariantRecalibrator vqsr = new VariantRecalibrator(); + List annotationList = new ArrayList<>(); + annotationList.add("QD"); + annotationList.add("MQ"); + annotationList.add("FS"); + annotationList.add("SOR"); + annotationList.add("ReadPosRankSum"); + annotationList.add("MQRankSum"); + + + GATKReport report = vqsr.writeModelReport(goodModel, badModel, annotationList); + if(printTables) + report.print(System.out); + + //Check values for Gaussian means + GATKReportTable goodMus = report.getTable("PositiveModelMeans"); + for(int i = 0; i < annotationList.size(); i++) { + Assert.assertEquals(goodGaussian1.mu[i], (Double)goodMus.get(0,annotationList.get(i)), epsilon); + } + for(int i = 0; i < annotationList.size(); i++) { + Assert.assertEquals(goodGaussian2.mu[i], (Double)goodMus.get(1,annotationList.get(i)), epsilon); + } + + GATKReportTable badMus = report.getTable("NegativeModelMeans"); + for(int i = 0; i < annotationList.size(); i++) { + Assert.assertEquals(badGaussian1.mu[i], (Double)badMus.get(0,annotationList.get(i)), epsilon); + } + + //Check values for Gaussian covariances + GATKReportTable goodSigma = report.getTable("PositiveModelCovariances"); + for(int i = 0; i < annotationList.size(); i++) { + for(int j = 0; j < annotationList.size(); j++) { + Assert.assertEquals(goodGaussian1.sigma.get(i,j), (Double)goodSigma.get(i,annotationList.get(j)), epsilon); + } + } + + //add annotationList.size() to row indexes for second Gaussian because the matrices are concatenated by row in the report + for(int i = 0; i < annotationList.size(); i++) { + for(int j = 0; j < annotationList.size(); j++) { + Assert.assertEquals(goodGaussian2.sigma.get(i,j), (Double)goodSigma.get(annotationList.size()+i,annotationList.get(j)), epsilon); + } + } + + GATKReportTable badSigma = report.getTable("NegativeModelCovariances"); + for(int i = 0; i < annotationList.size(); i++) { + for(int j = 0; j < annotationList.size(); j++) { + Assert.assertEquals(badGaussian1.sigma.get(i,j), (Double)badSigma.get(i,annotationList.get(j)), epsilon); } } } + @Test + //This is tested separately to avoid setting up a VariantDataManager and populating it with fake data + public void testAnnotationNormalizationOutput() { + final VariantRecalibrator vqsr = new VariantRecalibrator(); + final List annotationList = new ArrayList<>(); + annotationList.add("QD"); + annotationList.add("FS"); + annotationList.add("ReadPosRankSum"); + annotationList.add("MQ"); + annotationList.add("MQRankSum"); + annotationList.add("SOR"); - // -------------------------------------------------------------------------------- - // - // High-level case Provider - // - // -------------------------------------------------------------------------------- + final double epsilon = 1e-6; - private class QuantizerTestProvider extends TestDataProvider { - final List nObservationsPerQual = new ArrayList(); - final int nLevels; - final List expectedMap; - - private QuantizerTestProvider(final List nObservationsPerQual, final int nLevels, final List expectedMap) { - super(QuantizerTestProvider.class); - - for ( int x : nObservationsPerQual ) - this.nObservationsPerQual.add((long)x); - this.nLevels = nLevels; - this.expectedMap = expectedMap; + double[] meanVector = {16.13, 2.45, 0.37, 59.08, 0.14, 0.91}; + final String columnName = "Mean"; + final String formatString = "%.3f"; + GATKReportTable vectorTable = vqsr.makeVectorTable("AnnotationMeans", "Mean for each annotation, used to normalize data", annotationList, meanVector, columnName, formatString); + for(int i = 0; i < annotationList.size(); i++) { + Assert.assertEquals(meanVector[i], (Double)vectorTable.get(i, columnName), epsilon); } - @Override - public String toString() { - return String.format("QQTest nLevels=%d nObs=[%s] map=[%s]", - nLevels, Utils.join(",", nObservationsPerQual), Utils.join(",", expectedMap)); + if (printTables) { + final GATKReport report = new GATKReport(); + report.addTable(vectorTable); + report.print(System.out); } } - @DataProvider(name = "QuantizerTestProvider") - public Object[][] makeQuantizerTestProvider() { - List allQ2 = Arrays.asList(0, 0, 1000, 0, 0); - - new QuantizerTestProvider(allQ2, 5, Arrays.asList(0, 1, 2, 3, 4)); - new QuantizerTestProvider(allQ2, 1, Arrays.asList(2, 2, 2, 2, 2)); - - new QuantizerTestProvider(Arrays.asList(0, 0, 1000, 0, 1000), 2, Arrays.asList(2, 2, 2, 2, 4)); - new QuantizerTestProvider(Arrays.asList(0, 0, 1000, 1, 1000), 2, Arrays.asList(2, 2, 2, 4, 4)); - new QuantizerTestProvider(Arrays.asList(0, 0, 1000, 10, 1000), 2, Arrays.asList(2, 2, 2, 2, 4)); - - return QuantizerTestProvider.getTests(QuantizerTestProvider.class); - } - - @Test(dataProvider = "QuantizerTestProvider", enabled = true) - public void testQuantizer(QuantizerTestProvider cfg) { - QualQuantizer qq = new QualQuantizer(cfg.nObservationsPerQual, cfg.nLevels, 0); - logger.warn("cfg: " + cfg); - for ( int i = 0; i < cfg.expectedMap.size(); i++) { - int expected = cfg.expectedMap.get(i); - int observed = qq.originalToQuantizedMap.get(i); - //logger.warn(String.format(" qq map: %s : %d => %d", i, expected, observed)); - Assert.assertEquals(observed, expected); + private String vectorToString(double[] meanVec) { + String returnString = ""; + for (int j = 0; j < meanVec.length; j++) { + returnString += String.format("%.3f", meanVec[j]); + if (j < meanVec.length-1) + returnString += ","; } + return returnString; } + } \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java index 346566720..9c2594ed0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -74,7 +74,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -L 20:10,000,000-10,001,432" + " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", 1, - Arrays.asList("3e60ca3e04fecf5d6004c08d6f7503ca")); + Arrays.asList("43fa27382e654081af69ea05bd26e281")); executeTest("testUsingDiscoveredAF", spec); } @@ -89,7 +89,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -L 20:10,000,000-10,001,432" + " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", 1, - Arrays.asList("1cca249ebc2599c7f24210d4f3204049")); + Arrays.asList("d63893f530fb749505ec685a5c57ff69")); executeTest("testMissingPriors", spec); } @@ -103,7 +103,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -V " + validationDataLocation + "NA12878.Jan2013.haplotypeCaller.subset.indels.vcf" + " -supporting " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", 1, - Arrays.asList("cc59ceb6dab620a353edf03ef14090f1")); + Arrays.asList("a5d7bcad5a2a194441d00eb6574b8300")); executeTest("testInputINDELs", spec); } @@ -117,7 +117,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -V " + CEUtrioTest + " -supporting " + CEUtrioPopPriorsTest, 1, - Arrays.asList("c7d35ce5f3675528fc484baa1c5df7b4")); + Arrays.asList("98bf63fd2ae3fa1cc42e66fa6b4f50f5")); executeTest("testFamilyPriors", spec); } @@ -131,7 +131,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -V " + getThreeMemberNonTrioTest + " -skipPop", 1, - Arrays.asList("c523b99da1f7e0c0ea4090b916ae7379")); + Arrays.asList("e71420099fcfc824f1cf92ff2010b69e")); executeTest("testFamilyPriors", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java index 080c8da02..97ba4fc07 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -100,7 +100,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", 1, - Arrays.asList("f3538bcaf27f5e8b036d4c1f8734e4c2")); + Arrays.asList("787aca81ad51cd40267f92f3309fa47e")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -112,7 +112,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", 1, - Arrays.asList("32cd060d6662bdc835f70a848d48fb0e")); + Arrays.asList("d52f018643ffed072f43dfd4d33ca082")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -190,7 +190,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { @Test public void testMD5s() throws Exception { final String cmd = baseTestString(" -L 1:69485-69791"); - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("82fa951ce741451267dbf30335e0f71d")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("021ec495e70044039d092ebd5ef4b82a")); spec.disableShadowBCF(); executeTest("testMD5s", spec); } @@ -198,7 +198,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { @Test public void testBasepairResolutionOutput() throws Exception { final String cmd = baseTestString(" -L 1:69485-69791 --convertToBasePairResolution"); - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e1bfa842d53f86d46b2166574c0c66c")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d5bc938a26cd197d9b1c80cb8dfefbba")); spec.disableShadowBCF(); executeTest("testBasepairResolutionOutput", spec); } @@ -206,7 +206,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { @Test public void testBreakBlocks() throws Exception { final String cmd = baseTestString(" -L 1:69485-69791 --breakBandsAtMultiplesOf 5"); - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("76d78f83c7db247ce12087d6118dc5df")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("31c2f26e6b172a957a3f504734df5eff")); spec.disableShadowBCF(); executeTest("testBreakBlocks", spec); } @@ -217,7 +217,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf", 1, - Arrays.asList("cb46cb8fd6506ab3e80bd50f9231643c")); + Arrays.asList("097160606e65547722a1726e031529ec")); spec.disableShadowBCF(); executeTest("testSpanningDeletions", spec); } @@ -228,7 +228,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.many.g.vcf", 1, - Arrays.asList("5aeb14d64b9103b62d053aeb6158e5de")); + Arrays.asList("f517c2d361defeaac245916c835811d5")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsForOneSample", spec); } @@ -239,7 +239,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.many.haploid.g.vcf", 1, - Arrays.asList("3fca32a67922bf30f72fe066fe7159fe")); + Arrays.asList("0a8d217b2833070dcaa3bbc1e7602b1c")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsForOneSampleHaploid", spec); } @@ -250,7 +250,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.many.tetraploid.g.vcf", 1, - Arrays.asList("6891eaaef2991d7f967c7876fd2e4f5c")); + Arrays.asList("3fd437ad1f9e18303fec517653a30b6d")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsForOneSampleTetraploid", spec); } @@ -259,7 +259,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { public void testWrongReferenceBaseBugFix() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input1.vcf" + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input2.vcf") + " -o %s --no_cmdline_in_header"); - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("224c3d6e06f7ce4bdb55411b2e376577")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("129879954e5b453d30326f100cbc2e83")); spec.disableShadowBCF(); executeTest("testWrongReferenceBaseBugFix",spec); @@ -268,7 +268,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { @Test public void testBasepairResolutionInput() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V " + privateTestDir + "gvcf.basepairResolution.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d3244d99e9423b45099a220f19fac516")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d5b4abe639081e6bf9c8970ca8405dbe")); spec.disableShadowBCF(); executeTest("testBasepairResolutionInput", spec); } @@ -277,8 +277,28 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("cbb2571eeb95e661acee8f9e1d1cbfbd")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("f6a7fa62c33de963c55262820effe44a")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } + + @Test + public void testASMateRankSumAnnotation() throws Exception { + final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest -V " + + privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.MateRankSum.chr20snippet.g.vcf"; + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("2c264ed0057c93276c647f55998c4f25")); + spec.disableShadowBCF(); + executeTest("testASMateRankSumAnnotation", spec); + } + + @Test + public void testASInsertSizeRankSumAnnotation() throws Exception { + final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V " + + privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.InsertSizeRankSum.chr20snippet.g.vcf"; + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("ff5ca958e81e406cfe010d5649b5c0d1")); + spec.disableShadowBCF(); + executeTest("testASInsertSizeRankSumAnnotation", spec); + } + + } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java index cc5bcbbff..eddf113ac 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -144,7 +144,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest { @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "9bdda937754e1407183406808f560723"); } // official project VCF files in tabix format @Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "6344953a82a422115bd647ec1d696b94"); } // official project VCF files in tabix format - @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "c4b995405872b22ded76c0a9e183c52d"); } + @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "51cf4543e46c8434e32c426f59507d1e"); } @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "f9d1d7e6246f0ce9e493357d5b320323"); } @@ -169,7 +169,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest { " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" + " -genotypeMergeOptions UNIQUIFY -L 1"), 1, - Arrays.asList("8f8ba6d671f67386883c11873df3cf95")); + Arrays.asList("8b75e835ed19c06c358a2185cd0e14db")); cvExecuteTest("threeWayWithRefs", spec, true); } @@ -186,10 +186,10 @@ public class CombineVariantsIntegrationTest extends WalkerTest { cvExecuteTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec, true); } - @Test public void complexTestFull() { combineComplexSites("", "3a702773e31674b14a1073d455f6f1ce"); } - @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "cabad0e328f1c967d44aaf2085da5dcf"); } - @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "31f6f62664cc5891e9a8e228dbb6278d"); } - @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "31f6f62664cc5891e9a8e228dbb6278d"); } + @Test public void complexTestFull() { combineComplexSites("", "80c3b7ba39c8a3f3511fc1ea61ecd4da"); } + @Test public void complexTestMinimal() { combineComplexSites(" -minimalVCF", "e7da95bbcf3890a4debbfa07cbd646e5"); } + @Test public void complexTestSitesOnly() { combineComplexSites(" -sites_only", "d7ee8da6ceee4dd1212122c2e9cab2a6"); } + @Test public void complexTestSitesOnlyMinimal() { combineComplexSites(" -sites_only -minimalVCF", "d7ee8da6ceee4dd1212122c2e9cab2a6"); } @Test public void combineDBSNPDuplicateSites() { @@ -207,7 +207,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest { + " -R " + b37KGReference + " -V " + privateTestDir + "combineVariantsLeavesRecordsUnfiltered.vcf", 1, - Arrays.asList("11aab642395645589e48edee1fb179e2")); + Arrays.asList("0f221847e76521250de1abcba535e49c")); cvExecuteTest("combineLeavesUnfilteredRecordsUnfiltered: ", spec, false); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java index 1df099b00..a1e4a60e6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java index f0b6d33da..729340392 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetricsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java index eb9f56899..84e668051 100755 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordanceIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java index bcaf889b8..b93f5f4a9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -71,7 +71,6 @@ import java.util.Collections; import java.util.List; public class GenotypeGVCFsIntegrationTest extends WalkerTest { - private static String baseTestString(String args, String ref) { return "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + ref + args; } @@ -85,7 +84,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference), 1, - Arrays.asList("beebc536d20d69a45c6f56fbb041c9bc")); + Arrays.asList("8d9788afd0de26bd9d9e55dd0e9fc3ed")); executeTest("testUpdatePGT", spec); } @@ -95,7 +94,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample -log " + logFileName, b37KGReference), 1, - Arrays.asList("527d513874a787821daf54b8fc8a33e3")); + Arrays.asList("5dd4698da963a423446bb1e183eb75aa")); executeTest("testUpdatePGTStrandAlleleCountsBySample", spec); File file = new File(logFileName); @@ -108,9 +107,9 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { baseTestString(" -V:sample1 " + privateTestDir + "combine.single.sample.pipeline.1.vcf" + " -V:sample2 " + privateTestDir + "combine.single.sample.pipeline.2.vcf" + " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + - " -L 20:10,000,000-20,000,000", b37KGReference), + " -L 20:10,000,000-11,000,000", b37KGReference), 1, - Arrays.asList("63bdb33fe44b6589adc5c36b0ea740b2")); + Arrays.asList("c9edd4ca8c2801c4681322087d82e781")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -122,7 +121,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, - Arrays.asList("3708b0d993a683e8c7421f60d7123cf4")); + Arrays.asList("64fa89f20ee25df21ad20ce4ada7e7ad")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -134,7 +133,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, - Arrays.asList("7d7a65ea549fcd30553766ad4333f9e2")); + Arrays.asList("b1d93f4cd93093c208be2c9842f38d12")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -146,7 +145,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference), 1, - Arrays.asList("8b338d065806f7c7eea67f56a1f6009e")); + Arrays.asList("c2f30f25ba4a84e38c04aa49b95694e8")); executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec); } @@ -159,7 +158,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-20,000,000", b37KGReference), 1, - Arrays.asList("2d4e6a3193c493514576a758e891b951")); + Arrays.asList("f48114bc6348cdc9dc4f0960f5dcf5f8")); executeTest("combineSingleSamplePipelineGVCFHierarchical", spec); } @@ -171,17 +170,28 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference), 1, - Arrays.asList("7693207e925359df331e64664c5b8763")); + Arrays.asList("f88841deb5c2ce4f3bbea1e914a13898")); executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec); } + @Test(enabled = true) + public void combineBPresGVCFs() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString(" -V " + privateTestDir + "NA12891.BPres.g.vcf" + + " -V " + privateTestDir + "NA12892.BPres.g.vcf" + + " -L 20:10433000-10436909", b37KGReference), + 1, + Arrays.asList("f342872f485e6978501facc78c354078")); + executeTest("combineBPresGVCFs", spec); + } + @Test(enabled = true) public void testJustOneSample() { WalkerTestSpec spec = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference + " -V " + privateTestDir + "gvcfExample1.vcf", 1, - Arrays.asList("84ad9c6e7582dbcc693deacdeff5984a")); + Arrays.asList("9ff344a5ab87a2c3b128e435e2e86db0")); executeTest("testJustOneSample", spec); } @@ -192,14 +202,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V " + privateTestDir + "gvcfExample1.vcf" + " -V " + privateTestDir + "gvcfExample2.vcf", 1, - Arrays.asList("54b76f721811c9c7958e849c40b8d4e2")); + Arrays.asList("0c07ed795562ea96eab427e63a970384")); executeTest("testSamplesWithDifferentLs", spec); } @Test(enabled = true) public void testNoPLsException() { // Test with input files with (1) 0/0 and (2) ./. - final String md5 = "276159213ddaaf82cd0e640cc7a77fc4"; + final String md5 = "2f3d71272fdac19ac861cc7159edfb08"; WalkerTestSpec spec1 = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference + " --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf", @@ -219,7 +229,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-nda"), 1, - Arrays.asList("3c9c84b78e7d3b358c8cb7e29a2d302b")); + Arrays.asList("ce064429e6cbcaa956d52ef22e102f2f")); executeTest("testNDA", spec); } @@ -228,7 +238,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-maxAltAlleles 1"), 1, - Arrays.asList("87ed70b8f910b662aa67e8ed1b2ed174")); + Arrays.asList("1f1c0605fc8a500c9646132e0d7420a0")); executeTest("testMaxAltAlleles", spec); } @@ -237,7 +247,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"), 1, - Arrays.asList("1d98fb542a39090db3a8f89ae232e1e5")); + Arrays.asList("0283e784ed49bc2dce32a26137c43409")); executeTest("testStandardConf", spec); } @@ -260,7 +270,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference), 1, - Arrays.asList("eeff965cd79c0b7085c7d4d7ecf82b68")); + Arrays.asList("34d76dc8dabc6a97e6d8f5365d7531e5")); spec.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC executeTest("testStrandAlleleCountsBySample", spec); } @@ -277,7 +287,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" + " --uniquifySamples", b37KGReference), 1, - Arrays.asList("b73f5bf5646695ca019d84d44c74c819")); + Arrays.asList("16d7374502fa3cf99863d15d31b5ef86")); executeTest("testUniquifiedSamples", spec); } @@ -449,7 +459,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { } - private static final String simpleSpanningDeletionsMD5 = "85c14341171548997e4503f7b5a9253f"; + private static final String simpleSpanningDeletionsMD5 = "4629c2f02ff58c111828269091cded82"; @Test(enabled = true) public void testSpanningDeletionsMD5() { @@ -479,7 +489,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf -V " + privateTestDir + "spanningDel.3.g.vcf", 1, - Arrays.asList("6c5761ffb7a0c5252f3f5048d52f500e")); + Arrays.asList("7fe5364565585d31a0bb6a9dfa4a01d4")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsMD5", spec); } @@ -490,7 +500,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.delOnly.g.vcf", 1, - Arrays.asList("c8414446dbac9a3639bfc2f347cc2c1d")); + Arrays.asList("057f9368f380bf3c12b539a749deac61")); spec.disableShadowBCF(); executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec); } @@ -501,7 +511,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.depr.delOnly.g.vcf", 1, - Arrays.asList("d1d8c3db65905b4ef79f960f9565ca94")); + Arrays.asList("e8f5186718050fe0784416e41425563f")); spec.disableShadowBCF(); executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec); } @@ -524,7 +534,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "ad-bug-input.vcf", 1, - Arrays.asList("a8dcb9024e3701449ec2a1fe75e0d057")); + Arrays.asList("5ed5cb6aac68aa8943dc45b8b90eb508")); spec.disableShadowBCF(); executeTest("testBadADPropagationHaploidBugTest", spec); } @@ -535,7 +545,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "261_S01_raw_variants_gvcf.vcf", 1, - Arrays.asList("01a9eee63801d46de8fcf1d6f80f8359")); + Arrays.asList("37eec6aedd26aa3430a15d90d7f8a011")); spec.disableShadowBCF(); executeTest("testSAC", spec); } @@ -546,7 +556,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "tetraploid-multisample-sac.g.vcf", 1, - Arrays.asList("8c79a16f6a524d49ff402b8c0b39b396")); + Arrays.asList("76532a74d4ba49f23362c149ad31a229")); spec.disableShadowBCF(); executeTest("testSACMultisampleTetraploid", spec); } @@ -557,20 +567,38 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" + " -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" + " -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames), - 1, - Arrays.asList("75f6402da0f6b8b4e69c847fe8b5179a")); + Arrays.asList("b7106be316e43ca04204b78038f65c9f")); executeTest("testSetZeroRGQsToNoCall", spec); } @Test - public void testAlleleSpecificAnnotations() { + public void testAlleleSpecificAnnotations() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("35daaea8dea591d35ca99854c8d36e5f")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("89712a9fe5b6db16be2257be2b0b4759")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } + @Test + public void testASMateRankSumAnnotation() { + final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest --disableDithering -V " + + privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.MateRankSum.chr20snippet.g.vcf"; + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e41a139600ab58a67910cdc60053726")); + spec.disableShadowBCF(); + executeTest("testASMateRankSumAnnotation", spec); + } + + @Test + public void testASInsertSizeRankSumAnnotation() { + final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + + privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.InsertSizeRankSum.chr20snippet.g.vcf"; + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b1334fbfbf21934aac1c1eda0b5062d5")); + spec.disableShadowBCF(); + executeTest("testASInsertSizeRankSumAnnotation", spec); + } + + @Test //make sure none of the assumptions about things being merged as lists break the single-sample case //This test file also doesn't have raw data, so test to make sure that doesn't make GenotypeGVCFs crash and burn @@ -578,7 +606,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations_oneSample() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b6026b2a2d2da39f181a4905b2225dad")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("7d86260e91fe74588e01339a2064b59c")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations_oneSample", spec); } @@ -588,16 +616,25 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations_elevenSamples() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "multiSamples.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("84b5723c9c8eeb5549aaceb4fd4053b5")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("a889fe6775575513e84905b4fa98f8b3")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations_elevenSamples", spec); } + @Test + public void testMonomorphicVCwithAlt() { + final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header --disableDithering -V " + + privateTestDir + "monomorphicGVCwithAlt.vcf"; + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("8bf329a40637623515972dcc0e09a49e")); + spec.disableShadowBCF(); + executeTest("testAlleleSpecificAnnotations", spec); + } + @Test public void testFractionInformativeReads() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("794cfec86a8bee1f6955766b5a98b950")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("b338bf1807791b23255b8cb1947c01b2")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java index 4b5d9979f..1bcbc50e3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -136,9 +136,8 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -split", 1, - Arrays.asList("534bea653d4a0e59e74f4107c1768558")); + Arrays.asList("58c09033814d41fab5da4c152eab7fa2")); executeTest("test left alignment with hard multiple alleles", spec); - } @Test @@ -146,8 +145,34 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header -split", 1, - Arrays.asList("189b8136ee62b54bf7b227e99c892440")); + Arrays.asList("6d22a6b78d24ee2329b91f27a91751cf")); executeTest("test left alignment with hard multiple alleles, don't trim", spec); + } + @Test + public void testLeftAlignmentWithMultialleliecGenotypes() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split", + 1, + Arrays.asList("0acb354a2c28e250ef2853c1e0a0fafb")); + executeTest("test left alignment of multiple alleles with genoptypes", spec); + } + + @Test + public void testLeftAlignmentWithMultialleliecGenotypesHetNoRef() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt-het-noref.vcf --no_cmdline_in_header -split", + 1, + Arrays.asList("a335913de938082061d6bbb863626ee2")); + executeTest("test left alignment of multiple alleles with genoptypes, including het-noref", spec); + } + + @Test + public void testLeftAlignmentWithMultialleliecGenotypesKeepOriginalAC() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split -keepOriginalAC", + 1, + Arrays.asList("67657ee509665fd0d7a2c9024981ba92")); + executeTest("test left alignment of multiple alleles with genoptypes, keep original AC", spec); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java index 440582438..2199e5823 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java index 9b78c08aa..c27392baa 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java index b7adf675d..925c48d1a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariantsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java index 64636d182..b434d97d3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -69,6 +69,8 @@ public class SelectVariantsIntegrationTest extends WalkerTest { private static final String INVERT_SELECTION_MD5 = "26d192b868746ab14133f145ae812e7c"; private static final String MAX_FILTERED_GT_SELECTION_MD5 = "f83ac0deb7a8b022d6d40a85627a71ec"; private static final String MIN_FILTERED_GT_SELECTION_MD5 = "346620b7a5d66dabf89d3f42d6e27db7"; + private static final String NO_CALL_FILTERING_KEEP_ONE = "6e2401190c5ada6a3bed2640c068f43b"; + private static final String NO_CALL_FILTERING_KEEP_TWO = "6bced1ab6a3d58f1fd905b7f601987a3"; @Test public void testDiscordanceNoSampleSpecified() { @@ -367,7 +369,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants --keepOriginalDP -R " + b37KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("ce5168e2eadee2550188892b1ea444be") + Arrays.asList("9ad02f0df308eecb0634b3cd386956e9") ); executeTest("testKeepOriginalDP--" + testFile, spec); @@ -393,7 +395,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("cc33eb41a821d9aebdfb99d309854db0") + Arrays.asList("c78a65b41edbdd386211042e8f65220b") ); executeTest("testNoGTs--" + testFile, spec); @@ -406,7 +408,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants -trimAlternates --variant " + testfile, 1, - Arrays.asList("b86340de516d6c37cc3a2eeb3bfb4821") + Arrays.asList("c963ca96d543ecccab8055295d2a4dab") ); executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec); } @@ -418,7 +420,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header " + "-sn SAMPLE-CC -sn SAMPLE-CT -sn SAMPLE-CA --excludeNonVariants --variant " + testfile, 1, - Arrays.asList("7807bb2bf8c70963f65a97f30c8deb39") + Arrays.asList("7f5484a74ab648608228eafea96f8ad3") ); executeTest("test multi allelic annotation ordering --" + testfile, spec); } @@ -469,19 +471,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest { final String testFile = privateTestDir + "forHardLeftAlignVariantsTest.vcf"; final String cmd = "-T SelectVariants -R " + b37KGReference + " -sn NA12878 -env -trimAlternates " + "-V " + testFile + " -o %s --no_cmdline_in_header"; - WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("354cd7aa25791465d0f4c7d53b81a3a3")); + WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("21d83006b012eeea84c6612976348d3c")); executeTest("testAlleleTrimming", spec); } @DataProvider(name="unusedAlleleTrimmingProvider") public Object[][] unusedAlleleTrimmingProvider() { return new Object[][] { - { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "354cd7aa25791465d0f4c7d53b81a3a3"}, - { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "5e81af1825aa207b0a352f5eeb5db700"}, - { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "339cca608ff18a355abc629bca448043"}, - { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "3e8e2ebbc576ceee717a7ce80e23dd35"}, - { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "8650d66b2199a4f8ce0acc660b2091cd"}, - { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "14538e17d5aca22c655c42e130f8cebc"} + { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "21d83006b012eeea84c6612976348d3c"}, + { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "8fc0c8a7de6bb579e1534b936f844090"}, + { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "595392b623b0869f1d87e46edf3de122"}, + { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "bba873b8eeeb4c01199140c37deb6f6b"}, + { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "93858f706dac876a8581f6b89bb85cc5"}, + { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "5d831401367eb8b0ab49ffa34e0dd278"} }; } @@ -653,7 +655,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 --variant " + testFile + " -ped " + pedFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("f7fe7cbc84b3f2dfadcc40e19eeeb1f9")); + Arrays.asList("c68779547b28dfef39792598df8a93e9")); executeTest("testMendelianViolationSelection--" + testFile, spec); } @@ -666,7 +668,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 -invMv --variant " + testFile + " -ped " + pedFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("865418a69ee57be4432f248c027e6aff")); + Arrays.asList("0ac6fda76228080bdb39c0e698440718")); executeTest("testInvertMendelianViolationSelection--" + testFile, spec); } @@ -730,12 +732,25 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants --setFilteredGtToNocall -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("7771f07a9997296852ab367fac2c7a6c") + Arrays.asList("410c6b7bb62fc43bb41eee627670f757") ); spec.disableShadowBCF(); executeTest("testSetFilteredGtoNocall--" + testfile, spec); } + + @Test + public void testSetFilteredGtoNocallUpdateInfo() { + String testfile = privateTestDir + "selectVariantsInfoField.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants --setFilteredGtToNocall --removeUnusedAlternates --excludeNonVariants -R " + b37KGReference + " --variant " + + testfile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("349136d92f915f8c7ba8a2f92e51d6b7")); + executeTest("testSetFilteredGtoNocallUpdateInfo", spec); + } + @Test public void testSACSimpleDiploid() { String testfile = privateTestDir + "261_S01_raw_variants_gvcf.vcf"; @@ -743,7 +758,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -trimAlternates", 1, - Arrays.asList("c9d297e7758bf5681270029401cc97c2")); + Arrays.asList("d3bb7ea37a7c9dce8b34bf2020961619")); spec.disableShadowBCF(); executeTest("testSACSimpleDiploid", spec); } @@ -755,7 +770,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates", 1, - Arrays.asList("7aecb079b16448f0377b6b03069b2994")); + Arrays.asList("67a92b4d4174ff41f6f88ddf5ab6e422")); spec.disableShadowBCF(); executeTest("testSACDiploid", spec); } @@ -771,4 +786,56 @@ public class SelectVariantsIntegrationTest extends WalkerTest { spec.disableShadowBCF(); executeTest("testSACNonDiploid", spec); } + + @Test + public void testMaxNoCall1() { + final String testfile = privateTestDir + "vcfexample.forNoCallFiltering.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + hg19Reference + " --variant " + testfile + " -o %s --no_cmdline_in_header --maxNOCALLnumber 1", + 1, + Arrays.asList(NO_CALL_FILTERING_KEEP_ONE)); + spec.disableShadowBCF(); + + executeTest("testMaxNoCall1", spec); + } + + @Test + public void testMaxNoCall0_25() { + final String testfile = privateTestDir + "vcfexample.forNoCallFiltering.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + hg19Reference + " --variant " + testfile + " -o %s --no_cmdline_in_header --maxNOCALLfraction 0.25", + 1, + Arrays.asList(NO_CALL_FILTERING_KEEP_ONE)); + spec.disableShadowBCF(); + + executeTest("testMaxNoCall0_25", spec); + } + + @Test + public void testMaxNoCall2() { + final String testfile = privateTestDir + "vcfexample.forNoCallFiltering.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + hg19Reference + " --variant " + testfile + " -o %s --no_cmdline_in_header --maxNOCALLnumber 2", + 1, + Arrays.asList(NO_CALL_FILTERING_KEEP_TWO)); + spec.disableShadowBCF(); + + executeTest("testMaxNoCall2", spec); + } + + @Test + public void testMaxNoCall0_5() { + final String testfile = privateTestDir + "vcfexample.forNoCallFiltering.vcf"; + + WalkerTestSpec spec = new WalkerTestSpec( + "-T SelectVariants -R " + hg19Reference + " --variant " + testfile + " -o %s --no_cmdline_in_header --maxNOCALLfraction 0.5", + 1, + Arrays.asList(NO_CALL_FILTERING_KEEP_TWO)); + spec.disableShadowBCF(); + + executeTest("testMaxNoCall0_5", spec); + } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java index a6b020e41..45677ffee 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -95,12 +95,12 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest { { // new tests on b37 using testdir VCF final String testfile = privateTestDir + "NA12878.hg19.example1.vcf"; final String args = "-select 'DP > 30' -V " + testfile; - new ParallelSelectTestProvider(b37KGReference, args, "b899cebdd30e6641437489b746301797", nt); + new ParallelSelectTestProvider(b37KGReference, args, "64f9258e9e3024b6361abbeeeefafee9", nt); } { // AD and PL decoding race condition final String testfile = privateTestDir + "race_condition.vcf"; final String args = "-env -trimAlternates -sn SAMPLE -L 1:1-10,000,000 -V " + testfile; - new ParallelSelectTestProvider(b37KGReference, args, "ace613ed2e4929f448d30d85110d6ced", nt); + new ParallelSelectTestProvider(b37KGReference, args, "f289f22aacf1a5638a9fb6b32c5cf6fb", nt); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java index aa61d2c7e..0aa2aedcc 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFStreamingIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java index 7d2f2d0c6..8d4ccac28 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariantsIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -51,16 +51,19 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; +import htsjdk.samtools.util.TestUtil; import org.apache.commons.io.FileUtils; import org.apache.log4j.Level; import org.broadinstitute.gatk.engine.walkers.WalkerTest; import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.io.IOUtils; import org.testng.Assert; import org.testng.annotations.Test; import java.io.File; import java.io.IOException; import java.util.Arrays; +import java.util.Collections; public class ValidateVariantsIntegrationTest extends WalkerTest { @@ -198,12 +201,12 @@ public class ValidateVariantsIntegrationTest extends WalkerTest { } @Test(description = "Checks out of order header contigs") - public void testOutOfOrderHeaderContigsError() { - + public void testOutOfOrderHeaderContigs() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString("complexEvents-outOfOrder.vcf", "ALL", DEFAULT_REGION, b37KGReference), - 0, UserException.LexicographicallySortedSequenceDictionary.class); - executeTest("test out of order header contigs error", spec); + 0, + Arrays.asList(EMPTY_MD5)); + executeTest("test out of order header contigs", spec); } @Test(description = "Fixes '''bug''' reported in story https://www.pivotaltracker.com/story/show/68725164") @@ -279,7 +282,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString("longAlleles-wrongLength.vcf", "ALL", "1", b37KGReference) + " --reference_window_stop 208 -U ALLOW_SEQ_DICT_INCOMPATIBILITY ", - 0, Arrays.asList(EMPTY_MD5)); + 0, Collections.singletonList(EMPTY_MD5)); executeTest("test to allow wrong header contig length, not checking dictionary incompatibility", spec); } @@ -288,7 +291,78 @@ public class ValidateVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString("longAlleles-wrongLength.vcf", "ALL", "1", b37KGReference) + " --reference_window_stop 208 -U ", - 0, Arrays.asList(EMPTY_MD5)); + 0, Collections.singletonList(EMPTY_MD5)); executeTest("test to allow wrong header contig length, no compatibility checks", spec); } + + @Test + public void testGoodGvcf() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("NA12891.AS.chr20snippet.g.vcf", "ALL", "20:10433000-10437000", b37KGReference) + " -gvcf --reference_window_stop 208 -U ", + 0, Collections.singletonList("d41d8cd98f00b204e9800998ecf8427e")); + executeTest("tests correct gvcf", spec); + } + + @Test + public void testGoodGvcfExcludingAlleles() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("NA12891.AS.chr20snippet.g.vcf", "-ALLELES", "20:10433000-10437000", b37KGReference) + " -gvcf --reference_window_stop 208 -U ", + 0, Collections.singletonList("d41d8cd98f00b204e9800998ecf8427e")); + executeTest("tests correct gvcf", spec); + } + + + @Test(expectedExceptions = RuntimeException.class ) + public void testBadGvcfMissingNON_REF() { + + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("NA12891.AS.chr20snippet.BAD_MISSING_NON_REF.g.vcf", "-ALLELES", "20:10433000-10437000", b37KGReference) + " -gvcf --reference_window_stop 208 -U ", + 0, Collections.singletonList(EMPTY_MD5)); + executeTest("tests capture of missing NON_REF allele", spec); + } + + @Test(expectedExceptions = RuntimeException.class ) + public void testBadGvcfRegions() { + + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("diploid-gvcf.bad-IncompleteRegion.vcf", "-ALLELES", "20:10433000-10437000", b37KGReference) + " -gvcf --reference_window_stop 208 -U ", + 0, Collections.singletonList(EMPTY_MD5)); + executeTest("tests capture of non-complete region", spec); + } + + @Test(expectedExceptions = RuntimeException.class ) + public void testNonOverlappingRegions() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("NA12891.AS.chr20snippet_BAD_INCOMPLETE_REGION.g.vcf", "-ALLELES", "Y:4966254-4967190", b37KGReference) + " -gvcf --reference_window_stop 208 -U ", + 0, Collections.singletonList(EMPTY_MD5)); + executeTest("tests capture of non-complete region", spec); + } + + @Test + public void testNonOverlappingRegionsBP_RESOLUTION() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("gvcf.basepairResolution.vcf", "-ALLELES", "20:10000000-10010000", b37KGReference) + " -gvcf --reference_window_stop 208 -U ", + 0, Collections.singletonList(EMPTY_MD5)); + executeTest("tests capture of non-complete region, on BP_RESOLUTION gvcf", spec); + } + @Test + public void testCorrectCreationOfBlocks() throws IOException { + final File tempDir = IOUtils.tempDir("RefBlocks", "test", new File(privateTestDir)); + tempDir.mkdir(); + tempDir.deleteOnExit(); + final File output = File.createTempFile("RefBlocks", ".g.vcf", tempDir); + String baseIntervals = " 1:1-100 -L 5:1-200 "; + String intervalString = " -L " + baseIntervals; + final WalkerTestSpec hc = new WalkerTestSpec("-T HaplotypeCaller " + intervalString + " -I " + privateTestDir + "NA12878.4.snippet.bam " + + " -R /humgen/1kg/reference/human_g1k_v37_decoy.fasta -ERC GVCF -o " + output, Collections.singletonList(EMPTY_MD5)); + executeTest("running hc", hc); + + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString(tempDir.getName() + "/" + output.getName(), "-ALLELES", baseIntervals, b37KGReference) + " -gvcf --reference_window_stop 208 -U ", + 0, Collections.singletonList(EMPTY_MD5)); + executeTest("testing the correct creation of reference blocks", spec); + + TestUtil.recursiveDelete(tempDir); + } + } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java index a2b1b3f8b..dabfa27d5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtils.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtils.java index 269527c4d..2f18281f1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtils.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtils.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtilsUnitTest.java index 2e1035209..924ae3385 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantUtilsUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java index dae526d31..49df08fdb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java index 61ef9991c..6381f1949 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java index 8d4474473..ed937c881 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTableIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * @@ -90,14 +90,14 @@ public class VariantsToTableIntegrationTest extends WalkerTest { @Test(enabled = true) public void testMultiAllelicOneRecord() { WalkerTestSpec spec = new WalkerTestSpec(variantsToTableMultiAllelicCmd(""), - Arrays.asList("0ff49c08690f61a38614606a090f23ea")); + Arrays.asList("b468589f4d2bf4c7d85a0584b77fc0fd")); executeTest("testMultiAllelicOneRecord", spec); } @Test(enabled = true) public void testMultiAllelicSplitRecords() { - WalkerTestSpec spec = new WalkerTestSpec(variantsToTableMultiAllelicCmd(" -SMA"), - Arrays.asList("17a0fc80409d2fc00ad2bbb94b3a346b")); + WalkerTestSpec spec = new WalkerTestSpec(variantsToTableMultiAllelicCmd(" -F TYPE -SMA"), + Arrays.asList("74b37874afff05d65cf7b0587b7168ec")); executeTest("testMultiAllelicSplitRecords", spec); } @@ -193,7 +193,7 @@ public class VariantsToTableIntegrationTest extends WalkerTest { " --moltenize -SMA" + " -o %s", 1, - Arrays.asList("c131e2c3cfb673c456cb160bda476101")); + Arrays.asList("84d103b54f6799424bf49c854831d059")); executeTest("testMoltenOutputWithMultipleAlleles", spec); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java index 81cc0f26e..71da7cf0c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java index 1509655cf..be669cca2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/ContigComparatorUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java index 49477f01d..03c135457 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/RandomDNA.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java index b7a76d1c8..a7d02e0ca 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/CountSetUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java index 36acb38e7..e1f2802ec 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IndexedSetUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java index d62c00a12..ffd236874 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/collections/IntMaxHeapUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java index d4056f927..2bad5d72d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java index e65fe4b27..7d81ab7ad 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java index 620b0f190..d6ebce21e 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java index e55b51a24..778e1aac7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java index 360955cb2..c31dcda2b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotypeUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java index 13972ae90..96f8ddf18 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAlleleUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java index 5fddfdd1d..95e4806fa 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java index 9f2f0f398..eb421ba3f 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/GVCFWriterUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java index 7b1f5c756..09f66aa22 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/gvcf/HomRefBlockUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java index 93a5393de..114214994 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java index 4393d134c..8bf949953 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/CnyPairHMMUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java index fe6042771..635f783cf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMEmpiricalBenchmark.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java index 3181b43c0..f8329fff2 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModelUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java index 21bd5670d..e50a0b28b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMSyntheticBenchmark.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java index aefd8dff2..8d4a835c4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMTestData.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java index 8cef47ea1..0ab6a9bcb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java index e499d6139..7375ad341 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java @@ -5,7 +5,7 @@ * SOFTWARE LICENSE AGREEMENT * FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 ("BROAD") and the LICENSEE and is effective at the date the downloading is completed ("EFFECTIVE DATE"). * * WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and * WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. @@ -21,11 +21,11 @@ * 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. * * 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. +* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system ("PHONE-HOME") which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE'S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. * * 4. OWNERSHIP OF INTELLECTUAL PROPERTY * LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. * LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. * diff --git a/protected/pom.xml b/protected/pom.xml index 82cbd8514..2bef5b158 100644 --- a/protected/pom.xml +++ b/protected/pom.xml @@ -5,7 +5,7 @@ org.broadinstitute.gatk gatk-root - 3.5 + 3.6-SNAPSHOT ../public/gatk-root diff --git a/public/VectorPairHMM/pom.xml b/public/VectorPairHMM/pom.xml index b2d2319bf..b0e75eb1d 100644 --- a/public/VectorPairHMM/pom.xml +++ b/public/VectorPairHMM/pom.xml @@ -5,7 +5,7 @@ org.broadinstitute.gatk gatk-root - 3.5 + 3.6-SNAPSHOT ../../public/gatk-root diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.java b/public/VectorPairHMM/src/main/c++/Sandbox.java index 99c91d23b..a1ecb21f9 100644 --- a/public/VectorPairHMM/src/main/c++/Sandbox.java +++ b/public/VectorPairHMM/src/main/c++/Sandbox.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml index bdd5dbdf2..9aa973f0a 100644 --- a/public/external-example/pom.xml +++ b/public/external-example/pom.xml @@ -9,7 +9,7 @@ External Example - 3.5 + 3.6-SNAPSHOT - 1.141 - 1.141 + 2.4.1 + 2.4.1 @@ -196,6 +196,11 @@ commons-math 2.2 + + org.apache.commons + commons-math3 + 3.5 + net.java.dev.jna jna @@ -368,7 +373,7 @@ org.apache.maven.plugins maven-shade-plugin - 2.1 + 2.4.3 org.apache.maven.plugins diff --git a/public/gatk-tools-public/pom.xml b/public/gatk-tools-public/pom.xml index ad14fa578..63332a3d0 100644 --- a/public/gatk-tools-public/pom.xml +++ b/public/gatk-tools-public/pom.xml @@ -5,7 +5,7 @@ org.broadinstitute.gatk gatk-aggregator - 3.5 + 3.6-SNAPSHOT ../.. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java index f11e01d20..b62f1717e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/CatVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java index ccb4be7f8..a8d06a603 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalance.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -49,18 +49,18 @@ import java.util.Map; /** * Allele balance across all samples * - *

    This is an experimental annotation that attempts to estimate whether the data supporting a variant call fits allelic ratio expectations, or whether there might be some bias in the data. Each sample will contribute its allelic read depth (from the AD annotation) to either ABHom or ABHet depending on its genotype call: ABHom if the call is homozygous (REF/REF or ALT/ALT), and ABHet if the call is heterozygous (REF/ALT). Additionally, reads that support something other than the genotyped alleles (called "non-alleles") will be counted in the OND tag, which represents the overall fraction of data that diverges from the diploid hypothesis.

    + *

    This is a set of experimental annotations that attempt to estimate whether the data supporting a variant call fits allelic ratio expectations, or whether there might be some bias in the data. ABHom is the proportion of reads from homozygous samples that support the call (REF or ALT depending on whether the call is hom-ref or hom-var). ABHet is the proportion of REF reads from heterozygous samples. OND represents the overall fraction of data that diverges from the diploid hypothesis, based on the number of reads that support something other than the genotyped alleles (called "non-alleles"). Note that each sample's contribution is weighted by its genotype quality so that individual mis-calls don't affect the overall ratio too much.

    *

    Calculations

    - *

    $$ ABHom = \frac{# ALT alleles}{total # alleles} $$
    - * $$ ABHet = \frac{# REF alleles}{# total alleles} $$
    - * $$ OND = \frac{# genotyped alleles}{# alleles + # non-alleles} $$ + *

    $$ ABHom = \frac{# REF or ALT reads from homozygous samples}{# REF + ALT reads from homozygous samples} $$
    + * $$ ABHet = \frac{# REF reads from heterozygous samples}{# REF + ALT reads from heterozygous samples} $$
    + * $$ OND = \frac{# reads from non-alleles}{# all reads} $$ *

    - *

    For ABHom, the value should be close to 1.00 because ideally, all the reads should support a single allele. For ABHet, the value should be close to 0.5, so half of the alleles support the ref allele and half of the alleles support the alt allele. Divergence from these expected ratios may indicate that there is some bias in favor of one allele. Note the caveats below regarding cancer and RNAseq analysis.

    + *

    For ABHom, the value should be close to 1.00 because ideally, all the reads should support a single allele. For ABHet, the value should be close to 0.5, so half of the reads support the ref allele and half of the reads support the alt allele. Divergence from these expected ratios may indicate that there is some bias in favor of one allele. Note the caveats below regarding cancer and RNAseq analysis.

    *

    Caveats

    *
      - *
    • This annotation will only work properly for biallelic variants where all samples are called heterozygous or homozygous.
      • + *
    • This annotation will only work properly for biallelic SNPs in diploid organisms where all samples are either called heterozygous or homozygous.
      • *
    • This annotation cannot currently be calculated for indels.
      • - *
    • tThe reasoning underlying this annotation only applies to germline variants in DNA sequencing data. In somatic/cancer analysis, divergent ratios are expected due to tumor heterogeneity. In RNAseq analysis, divergent ratios may indicate differential allele expression.
      • + *
    • The reasoning underlying this annotation only applies to germline variants in DNA sequencing data. In somatic/cancer analysis, divergent ratios are expected due to tumor heterogeneity and normal contamination. In RNAseq analysis, divergent ratios may indicate differential allele expression.
      • *
    • As stated above, this annotation is experimental and should be interpreted with caution as we cannot guarantee that it is appropriate. Basically, use it at your own risk.
      • *
    *

    Related annotations

    @@ -215,4 +215,4 @@ public class AlleleBalance extends InfoFieldAnnotation { GATKVCFConstants.ALLELE_BALANCE_HOM_KEY, GATKVCFConstants.NON_DIPLOID_RATIO_KEY); } -} \ No newline at end of file +} diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java index fb7300809..24913bfe9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleBalanceBySample.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -59,13 +59,13 @@ import java.util.Set; * *

    This is an experimental annotation that attempts to estimate whether the data supporting a heterozygous genotype call fits allelic ratio expectations, or whether there might be some bias in the data.

    *

    Calculation

    - *

    $$ AB = \frac{# ALT alleles}{total # alleles} $$

    - *

    Ideally, the value of AB should be close to 0.5, so half of the alleles support the ref allele and half of the alleles support the alt allele. Divergence from the expected ratio may indicate that there is some bias in favor of one allele. Note the caveats below regarding cancer and RNAseq analysis.

    + *

    $$ AB = \frac{# REF reads from heterozygous samples}{# REF + ALT reads from heterozygous samples} $$

    + *

    Ideally, the value of AB should be close to 0.5, so half of the reads support the REF allele and half of the reads support the ALT allele. Divergence from the expected ratio may indicate that there is some bias in favor of one allele. Note the caveats below regarding cancer and RNAseq analysis.

    *

    Caveats

    *
      - *
    • This annotation will only work properly for biallelic heterozygous calls.
      • + *
    • This annotation will only work properly for biallelic heterozygous calls in diploid organisms.
      • *
    • This annotation cannot currently be calculated for indels.
      • - *
    • The reasoning underlying this annotation only applies to germline variants in DNA sequencing data. In somatic/cancer analysis, divergent ratios are expected due to tumor heterogeneity. In RNAseq analysis, divergent ratios may indicate differential allele expression.
      • + *
    • The reasoning underlying this annotation only applies to germline variants in DNA sequencing data. In somatic/cancer analysis, divergent ratios are expected due to tumor heterogeneity and normal contamination. In RNAseq analysis, divergent ratios may indicate differential allele expression.
      • *
    • As stated above, this annotation is experimental and should be interpreted with caution as we cannot guarantee that it is appropriate. Basically, use it at your own risk.
      • *
    *

    Related annotations

    @@ -178,4 +178,4 @@ public class AlleleBalanceBySample extends GenotypeAnnotation implements Experim public List getKeyNames() { return Arrays.asList(GATKVCFConstants.ALLELE_BALANCE_KEY); } public List getDescriptions() { return Arrays.asList(GATKVCFHeaderLines.getFormatLine(getKeyNames().get(0))); } -} \ No newline at end of file +} diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java index df3944214..3e4be932a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AlleleSpecificAnnotationData.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java index 66ea8dff6..e13e9f1ed 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/BaseCounts.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java index a89859fa3..8702c3b0f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java index 747e0fc23..711bc560d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FractionInformativeReads.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -30,6 +30,7 @@ import htsjdk.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.BetaTestingAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.ReducibleAnnotation; import org.broadinstitute.gatk.utils.MathUtils; @@ -44,7 +45,7 @@ import java.util.List; import java.util.Map; /** - * The fraction of reads that were deemed "informative" by the HaplotypeCaller over the entire cohort + * The fraction of reads deemed informative over the entire cohort * *

    The FractionInformativeReads annotation produces a single fraction for each site: sum(AD)/sum(DP). The sum in the numerator * is over all the samples in the cohort and all the alleles in each sample. The sum in the denominator is over all the samples. @@ -52,7 +53,7 @@ import java.util.Map; * *

    Caveats

    *
      - *
    • This annotation is generated by HaplotypeCaller or GenotypeGVCFs (it will not work when called from VariantAnnotator).
      • + *
    • This annotation can be generated by HaplotypeCaller, MuTect2 or GenotypeGVCFs (it will not work when called from VariantAnnotator).
      • *
    * *

    Related annotations

    @@ -61,7 +62,7 @@ import java.util.Map; *
*/ -public class FractionInformativeReads extends InfoFieldAnnotation implements ReducibleAnnotation { +public class FractionInformativeReads extends InfoFieldAnnotation implements ReducibleAnnotation, BetaTestingAnnotation { @Override public String getRawKeyName() { return null; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java index 34c58683f..27a98d825 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/LowMQ.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java index be3b40194..372ae5e34 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/MappingQualityZeroBySample.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java index b4cafa8f7..015e466d2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/NBaseCount.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java index 0c18bb187..bf998078d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ReducibleAnnotationData.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java index ceb353bdc..836140bd5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEff.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java index adb2c4ab4..d558b289f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtil.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java index ca386e8d8..1063f1ed6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java index bddc020c9..40360262a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -163,7 +163,7 @@ public class VariantAnnotatorEngine { final Map, String> overlapBindings = new LinkedHashMap<>(); for ( final RodBinding b : walker.getCompRodBindings()) if ( b.isBound() ) overlapBindings.put(b, b.getName()); - if ( dbSNPBinding != null && ! overlapBindings.keySet().contains(VCFConstants.DBSNP_KEY) ) + if ( dbSNPBinding != null && ! overlapBindings.values().contains(VCFConstants.DBSNP_KEY) ) overlapBindings.put(dbSNPBinding, VCFConstants.DBSNP_KEY); // add overlap detection with DBSNP by default variantOverlapAnnotator = new VariantOverlapAnnotator(dbSNPBinding, overlapBindings, engine.getGenomeLocParser()); @@ -357,9 +357,9 @@ public class VariantAnnotatorEngine { final Map annotationsFromCurrentType = currentASannotation.finalizeRawData(vc, originalVC); if ( annotationsFromCurrentType != null ) { infoAnnotations.putAll(annotationsFromCurrentType); - //clean up raw annotation data after annotations are finalized - infoAnnotations.remove(currentASannotation.getRawKeyName()); } + //clean up raw annotation data after annotations are finalized + infoAnnotations.remove(currentASannotation.getRawKeyName()); } // generate a new annotated VC diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java index 8fd0abe05..667cb846b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantOverlapAnnotator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java index 55c3e47cc..2589c6a0d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AS_StandardAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java index ee818ea34..91de64ce8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java index bb488679b..a9f7d3990 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationHelpUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java index 985774f51..07894c693 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java index 40a94cf70..a6ac476ad 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java index 363da058e..c65422a2f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotatorCompatible.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/BetaTestingAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/BetaTestingAnnotation.java new file mode 100644 index 000000000..2a7887021 --- /dev/null +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/BetaTestingAnnotation.java @@ -0,0 +1,32 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.annotator.interfaces; + +/** + * Annotations implementing this interface are not guaranteed to persist between GATK versions + */ +public interface BetaTestingAnnotation { +} diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java index 87954d221..1ad22b316 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ExperimentalAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java index 590c6b9c1..5cc4c55ad 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java index cc91cda52..b60d76718 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java index 25d2d8f41..225d556be 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/ReducibleAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java index c489d66bc..eb670d4d7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/RodRequiringAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java index 70d7c9f25..86b1f5a45 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java index 72eecaa36..38578ab6a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardSomaticAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java index 13fe48b66..b96a0d10e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/StandardUGAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java index 4bb9b28aa..ae7a5c516 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java index cc9a7d7b9..e911c34b2 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/WorkInProgressAnnotation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java index bf2eddccb..a69cd1e3c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLoci.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java index 1951a43c1..7e3079b65 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLoci.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java index 6f0e5507f..f222380dc 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java index 96144ce13..942fadcd6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -106,7 +106,7 @@ import java.util.*; // todo -- alter logarithmic scaling to spread out bins more // todo -- allow for user to set linear binning (default is logarithmic) // todo -- formatting --> do something special for end bins in getQuantile(int[] foo), this gets mushed into the end+-1 bins for now -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class}, gotoDev = HelpConstants.MC) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class}) @By(DataSource.REFERENCE) @PartitionBy(PartitionType.NONE) @Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE) @@ -433,7 +433,7 @@ public class DepthOfCoverage extends LocusWalker 0 ) { + if ( !statsByInterval.isEmpty() ) { for(DoCOutputType.Partition partition: partitionTypes) { if ( checkType(statsByInterval.get(0).getSecond().getCoverageByAggregationType(partition) ,partition) ) { printIntervalStats(statsByInterval, @@ -523,14 +523,16 @@ public class DepthOfCoverage extends LocusWalker geneNamesToStats = new HashMap(); // allows indirect updating of objects in list for ( Pair targetStats : statsByTarget ) { - String gene = getGeneName(targetStats.first,refseqIterator); - if ( geneNamesToStats.keySet().contains(gene) ) { - logger.debug("Merging "+geneNamesToStats.get(gene).toString()+" and "+targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample).toString()); - geneNamesToStats.get(gene).merge(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample)); - } else { - DepthOfCoverageStats merger = new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample)); - geneNamesToStats.put(gene,merger); - statsByGene.add(new Pair(gene,merger)); + List genes = getGeneNames(targetStats.first,refseqIterator); + for (String gene : genes) { + if ( geneNamesToStats.keySet().contains(gene) ) { + logger.debug("Merging "+geneNamesToStats.get(gene).toString()+" and "+targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample).toString()); + geneNamesToStats.get(gene).merge(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample)); + } else { + DepthOfCoverageStats merger = new DepthOfCoverageStats(targetStats.second.getCoverageByAggregationType(DoCOutputType.Partition.sample)); + geneNamesToStats.put(gene,merger); + statsByGene.add(new Pair(gene,merger)); + } } } @@ -542,27 +544,30 @@ public class DepthOfCoverage extends LocusWalker getGeneNames(GenomeLoc target, LocationAwareSeekableRODIterator refseqIterator) { logger.debug("Examining "+target.toString()); - if (refseqIterator == null) { return "UNKNOWN"; } + + List unknown = Arrays.asList("UNKNOWN"); + + if (refseqIterator == null) { return unknown; } RODRecordList annotationList = refseqIterator.seekForward(target); logger.debug("Annotation list is " + (annotationList == null ? "null" : annotationList.getName())); - if (annotationList == null) { return "UNKNOWN"; } + if (annotationList == null) { return unknown; } + List geneNames = new ArrayList(); for(GATKFeature rec : annotationList) { if ( ((RefSeqFeature)rec.getUnderlyingObject()).overlapsExonP(target) ) { logger.debug("We do overlap "+ rec.getUnderlyingObject().toString()); - return ((RefSeqFeature)rec.getUnderlyingObject()).getGeneName(); + geneNames.add(((RefSeqFeature)rec.getUnderlyingObject()).getGeneName()); + } else { + logger.debug("No overlap"); } - logger.debug("No overlap"); } - return "UNKNOWN"; - + if (geneNames.isEmpty()) { geneNames = unknown; } + + return geneNames; + } private LocationAwareSeekableRODIterator initializeRefSeq() { @@ -972,7 +985,7 @@ public class DepthOfCoverage extends LocusWalkerThis is a very simple implementation of a Bayesian genotyper that outputs a text based call format. It was developed + * solely to serve as a toy example in the original GATK publication, and should NOT be used in actual analysis work.

* * @author aaron */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_TOY, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} ) public class GATKPaperGenotyper extends LocusWalker implements TreeReducible { public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java index 5be2e8933..70354081f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaAlternateReferenceMaker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java index 4eb8f3e23..52090b456 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaReferenceMaker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java index 062297beb..7c0e04089 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaSequence.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java index 01d26c04e..35226f3a1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/fasta/FastaStats.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java index c0de7b9d7..dacc6fd65 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/ClusteredSnps.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java index e48c8f45b..901991cb6 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContext.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java index e47d54b6a..915825aa8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/FiltrationContextWindow.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java index 3c61235e3..fb975c37b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -45,6 +45,7 @@ import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; import htsjdk.variant.variantcontext.*; import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import java.util.*; @@ -53,9 +54,13 @@ import java.util.*; * Filter variant calls based on INFO and FORMAT annotations * *

- * This tool is designed for hard-filtering variant calls based on certain criteria. - * Records are hard-filtered by changing the value in the FILTER field to something other than PASS. Filtered records - * will be preserved in the output unless their removal is requested in the command line.

+ * This tool is designed for hard-filtering variant calls based on certain criteria. Records are hard-filtered + * by changing the value in the FILTER field to something other than PASS. Filtered records will be preserved + * in the output unless their removal is requested in the command line.

+ * + *

The most common way of specifying filtering criteria is by using JEXL queries. See the + * article on JEXL expressions in the + * documentation Guide for detailed information and examples.

* *

Input

*

@@ -75,13 +80,21 @@ import java.util.*; * -o output.vcf \ * --variant input.vcf \ * --filterExpression "AB < 0.2 || MQ0 > 50" \ - * --filterName "Nov09filters" \ - * --mask mask.vcf \ - * --maskName InDel + * --filterName "SomeFilterName" * + * + *

Caveat

+ *

when you run VariantFiltration with a command that includes multiple logical parts, each part of the command is applied + * individually to the original form of the VCF record. Say you ran a VF command that includes three parts: one applies + * some genotype filters, another applies setFilterGtToNoCall (which changes sample genotypes to ./. whenever a sample has a + * genotype-level FT annotation), and yet another one filters sites based on whether any samples have a no-call there. You might + * think that such a command would allow you to filter sites based on sample-level annotations in one go. However, that would only + * work if the parts of the command were applied internally in series (like a pipeline) but that's not the case; they are applied + * in parallel to the same original record. So unfortunately, to achieve the desired result, these filters should be applied as + * separate commands.

* */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VAREVAL, extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=-50,stop=50)) public class VariantFiltration extends RodWalker { @@ -229,6 +242,13 @@ public class VariantFiltration extends RodWalker { Set hInfo = new HashSet(); hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames)); + // need AC, AN and AF since output if set filtered genotypes to no-call + if ( setFilteredGenotypesToNocall ) { + hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY)); + hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY)); + hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY)); + } + if ( clusterWindow > 0 ) hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters")); @@ -390,6 +410,18 @@ public class VariantFiltration extends RodWalker { if ( !genotypeFilterExps.isEmpty() || setFilteredGenotypesToNocall ) { GenotypesContext genotypes = GenotypesContext.create(vc.getGenotypes().size()); + // + // recompute AC, AN and AF if filtered genotypes are set to no-call + // + // occurrences of alternate alleles over all genotypes + final Map calledAltAlleles = new LinkedHashMap(vc.getNAlleles()-1); + for ( final Allele altAllele : vc.getAlternateAlleles() ) { + calledAltAlleles.put(altAllele, 0); + } + + int calledAlleles = 0; + boolean haveFilteredNoCallAlleles = false; + // for each genotype, check filters then create a new object for ( final Genotype g : vc.getGenotypes() ) { if ( g.isCalled() ) { @@ -403,16 +435,23 @@ public class VariantFiltration extends RodWalker { } // if sample is filtered and --setFilteredGtToNocall, set genotype to non-call - if ( !filters.isEmpty() && setFilteredGenotypesToNocall ) + if ( !filters.isEmpty() && setFilteredGenotypesToNocall ) { + haveFilteredNoCallAlleles = true; genotypes.add(new GenotypeBuilder(g).filters(filters).alleles(diploidNoCallAlleles).make()); - else + } + else { genotypes.add(new GenotypeBuilder(g).filters(filters).make()); + calledAlleles = GATKVariantContextUtils.incrementChromosomeCountsInfo(calledAltAlleles, calledAlleles, g); + } } else { genotypes.add(g); } } builder.genotypes(genotypes); + // if filtered genotypes are set to no-call, output recomputed AC, AN, AF + if ( haveFilteredNoCallAlleles ) + GATKVariantContextUtils.updateChromosomeCountsInfo(calledAltAlleles, calledAlleles, builder); } // make a new variant context based on filters diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java index 96586c030..1a7a47eee 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCMappingQualityFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java index ac15e7439..1c1e71f1d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDoclet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java index 8e3881cdb..79db163ba 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help/WalkerDocumentationHandler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java similarity index 65% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java index 10c118c31..766371358 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManager.java @@ -1,52 +1,26 @@ /* -* By downloading the PROGRAM you agree to the following terms of use: +* Copyright 2012-2016 Broad Institute, Inc. * -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. * -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package org.broadinstitute.gatk.tools.walkers.indels; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java similarity index 88% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java index 050d174ca..31e29fdcb 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealigner.java @@ -1,52 +1,26 @@ /* -* By downloading the PROGRAM you agree to the following terms of use: +* Copyright 2012-2016 Broad Institute, Inc. * -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. * -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package org.broadinstitute.gatk.tools.walkers.indels; @@ -101,10 +75,11 @@ import java.util.*; * it is impossible to place reads on the reference genome such at mismatches are minimized across all reads. Consequently, even when some reads are * correctly mapped with indels, reads covering the indel near just the start or end of the read are often incorrectly mapped with respect the true indel, * also requiring realignment. Local realignment serves to transform regions with misalignments due to indels into clean reads containing a consensus - * indel suitable for standard variant discovery approaches. Unlike most mappers, this walker uses the full alignment context to determine whether an - * appropriate alternate reference (i.e. indel) exists. Following local realignment, the GATK tool Unified Genotyper can be used to sensitively and - * specifically identify indels. + * indel suitable for standard variant discovery approaches. *

+ *

Note that indel realignment is no longer necessary for variant discovery if you plan to use a variant caller that performs a haplotype assembly + * step, such as HaplotypeCaller or MuTect2. However it is still required when using legacy callers such as UnifiedGenotyper or the original MuTect.

+ * *

There are 2 steps to the realignment process:

*
    *
  1. Determining (small) suspicious intervals which are likely in need of realignment (see the RealignerTargetCreator tool)
    2. @@ -145,7 +120,7 @@ import java.util.*; * * @author ebanks */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class}) @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = ReadTransformer.ApplicationTime.ON_OUTPUT) public class IndelRealigner extends ReadWalker { diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java new file mode 100644 index 000000000..58202f059 --- /dev/null +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/LeftAlignIndels.java @@ -0,0 +1,116 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import htsjdk.samtools.Cigar; +import htsjdk.samtools.SAMRecord; +import org.broadinstitute.gatk.utils.commandline.Output; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.sam.GATKSAMFileWriter; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.engine.walkers.ReadWalker; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.sam.AlignmentUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; + + +/** + * Left-align indels within reads in a bam file + * + *

    This tool left-aligns any indels within read cigars in order to standardize representation when there are multiple valid + * representations possible (i.e. where the same indel can be placed at multiple positions and still represent the same haplotype). + * The standard convention is to place an indel at the left-most position possible, but this is not always followed, so + * this tool can be used to correct the representation of indels.

    + * + *

    Note

    + *

    This is only really needed when calling variants with legacy locus-based tools such as UnifiedGenotyper. With more + * sophisticated tools (like HaplotypeCaller) that involve reconstructing haplotypes (eg through haplotype assembly), the problem + * of multiple valid representations is handled internally and does not need to be corrected explicitly.

    + * + *

    Input

    + *

    + * A bam file with mapped reads. + *

    + * + *

    Output

    + *

    + * A bam file in which indels have been left-aligned where appropriate. + *

    + * + *

    Usage example

    + * 
    + * java -jar GenomeAnalysisTK.jar \
+ *   -R reference.fasta \
+ *   -T LeftAlignIndels \
+ *   -I reads.bam \
+ *   -o output_with_leftaligned_indels.bam
+ *
    + * + */ +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_DATA, extraDocs = {CommandLineGATK.class} ) +public class LeftAlignIndels extends ReadWalker { + + @Output(required=false, doc="Output bam") + protected GATKSAMFileWriter writer = null; + + public void initialize() {} + + private void emit(final SAMRecord read) { + if ( writer != null ) + writer.addAlignment(read); + } + + public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) { + // we can not deal with screwy records + if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) { + emit(read); + return 0; + } + + // move existing indels (for 1 indel reads only) to leftmost position within identical sequence + int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read); + if ( numBlocks == 2 ) { + Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0, true); + newCigar = IndelRealigner.reclipCigar(newCigar, read); + read.setCigar(newCigar); + } + + emit(read); + return 1; + } + + public Integer reduceInit() { + return 0; + } + + public Integer reduce(Integer value, Integer sum) { + return sum + value; + } + + public void onTraversalDone(Integer result) {} +} \ No newline at end of file diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java new file mode 100644 index 000000000..a7eae01e1 --- /dev/null +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBin.java @@ -0,0 +1,102 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import com.google.java.contract.Requires; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.HasGenomeLocation; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; + +import java.util.ArrayList; +import java.util.List; + +/** +* User: carneiro +* Date: 2/16/13 +* Time: 11:15 PM +*/ +class ReadBin implements HasGenomeLocation { + + private final ArrayList reads = new ArrayList(); + private byte[] reference = null; + private GenomeLoc loc = null; + private final GenomeLocParser parser; + private final int referencePadding; + + public ReadBin(final GenomeLocParser parser, final int referencePadding) { + this.parser = parser; + this.referencePadding = referencePadding; + } + + // Return false if we can't process this read bin because the reads are not correctly overlapping. + // This can happen if e.g. there's a large known indel with no overlapping reads. + public void add(GATKSAMRecord read) { + + final int readStart = read.getSoftStart(); + final int readStop = read.getSoftEnd(); + if ( loc == null ) + loc = parser.createGenomeLoc(read.getReferenceName(), readStart, Math.max(readStop, readStart)); // in case it's all an insertion + else if ( readStop > loc.getStop() ) + loc = parser.createGenomeLoc(loc.getContig(), loc.getStart(), readStop); + + reads.add(read); + } + + public List getReads() { + return reads; + } + + @Requires("referenceReader.isUppercasingBases()") + public byte[] getReference(CachingIndexedFastaSequenceFile referenceReader) { + // set up the reference if we haven't done so yet + if ( reference == null ) { + // first, pad the reference to handle deletions in narrow windows (e.g. those with only 1 read) + int padLeft = Math.max(loc.getStart()- referencePadding, 1); + int padRight = Math.min(loc.getStop()+ referencePadding, referenceReader.getSequenceDictionary().getSequence(loc.getContig()).getSequenceLength()); + loc = parser.createGenomeLoc(loc.getContig(), loc.getContigIndex(), padLeft, padRight); + reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases(); + } + + return reference; + } + + public GenomeLoc getLocation() { + return loc; + } + + public int size() { + return reads.size(); + } + + public void clear() { + reads.clear(); + reference = null; + loc = null; + } + +} diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java similarity index 65% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java index a5354831a..6d4e86252 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreator.java @@ -1,52 +1,26 @@ /* -* By downloading the PROGRAM you agree to the following terms of use: +* Copyright 2012-2016 Broad Institute, Inc. * -* BROAD INSTITUTE -* SOFTWARE LICENSE AGREEMENT -* FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: * -* This Agreement is made between the Broad Institute, Inc. with a principal address at 415 Main Street, Cambridge, MA 02142 (“BROAD”) and the LICENSEE and is effective at the date the downloading is completed (“EFFECTIVE DATE”). +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. * -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and -* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions. -* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows: -* -* 1. DEFINITIONS -* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk on the EFFECTIVE DATE. -* -* 2. LICENSE -* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to BROAD promptly upon their creation. -* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement. -* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement. -* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. PHONE-HOME FEATURE -* LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. -* -* 4. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012-2015 Broad Institute, Inc. -* Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 5. INDEMNIFICATION -* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement. -* -* 6. NO REPRESENTATIONS OR WARRANTIES -* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME. -* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. -* -* 7. ASSIGNMENT -* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void. -* -* 8. MISCELLANEOUS -* 8.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries. -* 8.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes. -* 8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. -* 8.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt. -* 8.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter. -* 8.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement. -* 8.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles. +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package org.broadinstitute.gatk.tools.walkers.indels; @@ -95,9 +69,10 @@ import java.util.TreeSet; * it is impossible to place reads on the reference genome such that mismatches are minimized across all reads. Consequently, even when some reads are * correctly mapped with indels, reads covering the indel near just the start or end of the read are often incorrectly mapped with respect the true indel, * also requiring realignment. Local realignment serves to transform regions with misalignments due to indels into clean reads containing a consensus - * indel suitable for standard variant discovery approaches. Unlike most mappers, this tool uses the full alignment context to determine whether an - * appropriate alternate reference (i.e. indel) exists. + * indel suitable for standard variant discovery approaches. *

    + *

    Note that indel realignment is no longer necessary for variant discovery if you plan to use a variant caller that performs a haplotype assembly + * step, such as HaplotypeCaller or MuTect2. However it is still required when using legacy callers such as UnifiedGenotyper or the original MuTect.

    *

    There are 2 steps to the realignment process:

    *
      *
    1. Determining (small) suspicious intervals which are likely in need of realignment (RealignerTargetCreator)
      2. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java index 53c155f0b..7ca62f75a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java index d38543c5b..4b2f88e81 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileup.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java index e0d2a3cd4..b309802ea 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountBases.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java index 21f04271c..0aa3ab45a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountIntervals.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java index 004906c46..8657aec96 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountLoci.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java index a8291418f..ac0f4034b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountMales.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java index 78f194f9e..3dbfb486f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODs.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java index 8934fce68..fc08cff19 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountRODsByRef.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java index 20d60a19f..37c68a614 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadEvents.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java index 17aa5bc69..387d1c6a0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountReads.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java index 942e7c372..f004ae0fb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/CountTerminusEvent.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java index 579f43fa3..9a36e6ed1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/DocumentationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java index 030c964e8..ff85c08d3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ErrorThrowing.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java index fee78877c..5e81b5479 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStat.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java index cd2c33630..2c00f06b0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/Pileup.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java index 7873af930..6783a2857 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/PrintRODs.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java index 93493544d..49983241d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/QCRef.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -63,7 +63,7 @@ import java.io.PrintStream; * * */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_REFUTILS, extraDocs = {CommandLineGATK.class} ) public class QCRef extends RefWalker { @Output public PrintStream out; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java index 1517ae73b..176ba38b5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/ReadClippingStats.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java index 1043675cc..518b4d8c7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/qc/RodSystemValidation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java index f8b46b62d..f0eaeb448 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReads.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java index 6aede1b75..eb1cf18c0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReads.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -195,7 +195,7 @@ public class PrintReads extends ReadWalker impleme //Add the program record (if appropriate) and set up the writer final boolean preSorted = true; - if (toolkit.getArguments().BQSR_RECAL_FILE != null && !NO_PG_TAG ) { + if (!NO_PG_TAG ) { NWaySAMFileWriter.setupWriter(out, toolkit, outputHeader, preSorted, this, PROGRAM_RECORD_NAME); } else { out.writeHeader(outputHeader); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java index 029d8b88a..9a671e760 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java index 1e151adb4..db0bfa087 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -90,7 +90,7 @@ import java.util.List; * *

      Caveat

      *
        - *
      • This tool will only process biallelic sites. If your callset contains multiallelic sites, they will be ignored. + *
      • This tool will only process biallelic SNP sites. If your callset contains multiallelic sites, they will be ignored. * Optionally, you can subset your callset to just biallelic variants using e.g. * SelectVariants * with the option "-restrictAllelesTo BIALLELIC".
        • @@ -110,48 +110,46 @@ public class ASEReadCounter extends LocusWalker { /** * If this argument is enabled, loci with total depth lower than this threshold after all filters have been applied - * will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold. + * will be skipped. This can be set to -1 by default to disable the evaluation and ignore this threshold. */ - @Argument(fullName = "minDepthOfNonFilteredBase", shortName = "minDepth", doc = "Minimum number of bases that pass filters", required = false, minValue = 0, maxValue = Integer.MAX_VALUE) + @Argument(fullName = "minDepthOfNonFilteredBase", shortName = "minDepth", doc = "Minimum number of bases that pass filters", required = false, minValue = -1, maxValue = Integer.MAX_VALUE) public int minDepthOfNonFilteredBases = -1; /** * If this argument is enabled, reads with mapping quality values lower than this threshold will not be counted. - * This is set to -1 by default to disable the evaluation and ignore this threshold. + * This can be set to -1 by default to disable the evaluation and ignore this threshold. */ - @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum read mapping quality", required = false, minValue = 0, maxValue = Integer.MAX_VALUE) + @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum read mapping quality", required = false, minValue = -1, maxValue = Integer.MAX_VALUE) public int minMappingQuality = 0; /** * If this argument is enabled, bases with quality scores lower than this threshold will not be counted. - * This is set to -1 by default to disable the evaluation and ignore this threshold. + * This can be set to -1 by default to disable the evaluation and ignore this threshold. */ - @Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum base quality", required = false, minValue = 0, maxValue = Byte.MAX_VALUE) + @Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum base quality", required = false, minValue = -1, maxValue = Byte.MAX_VALUE) public byte minBaseQuality = 0; /** - * These options modify how the tool deals with overlapping read pairs. - * COUNT_READS - Count all reads independently, even if they are from the same fragment. - * COUNT_FRAGMENTS - Count all fragments, even if the reads that compose the fragment are not consistent at that base. - * COUNT_FRAGMENTS_REQUIRE_SAME_BASE - Count all fragments, but only if the reads that compose the fragment are consistent at that base (default). + * These options modify how the tool deals with overlapping read pairs. The default value is COUNT_FRAGMENTS_REQUIRE_SAME_BASE. */ @Argument(fullName = "countOverlapReadsType", shortName = "overlap", doc = "Handling of overlapping reads from the same fragment", required = false) public CoverageUtils.CountPileupType countType = CoverageUtils.CountPileupType.COUNT_FRAGMENTS_REQUIRE_SAME_BASE; /** - * Available options are csv, table, rtable. By default, the format is an r-readable table. + * Available options are csv, table, rtable. By default, the format is rtable (an r-readable table). */ @Argument(fullName = "outputFormat", doc = "Format of the output file, can be CSV, TABLE, RTABLE", required = false) public OUTPUT_FORMAT outputFormat = OUTPUT_FORMAT.RTABLE; + // Hiding these argument pending reevaluation (currently don't seem to work and aren't tested) /** * Consider a spanning deletion as contributing to coverage. Also enables deletion counts in per-base output. */ - @Advanced + @Hidden @Argument(fullName = "includeDeletions", shortName = "dels", doc = "Include information on deletions", required = false) public boolean includeDeletions = false; - @Advanced + @Hidden @Argument(fullName = "ignoreDeletionSites", doc = "Ignore sites consisting only of deletions", required = false) public boolean ignoreDeletionSites = false; @@ -202,7 +200,7 @@ public class ASEReadCounter extends LocusWalker { final List VCs = tracker.getValues(sites, context.getLocation()); if(VCs != null && VCs.size() > 1) throw new UserException("More then one variant context at position: "+contig+":"+position); - if(VCs == null || VCs.size() == 0) + if(VCs == null || VCs.isEmpty()) return null; final VariantContext vc = VCs.get(0); @@ -211,7 +209,11 @@ public class ASEReadCounter extends LocusWalker { return null; } + if ( vc.getNAlleles() == 1 || vc.getAlternateAllele(0).getBases().length == 0 ) + throw new UserException("The file of variant sites must contain heterozygous sites and cannot be a GVCF file containing alleles."); + final char altAllele = (char)vc.getAlternateAllele(0).getBases()[0]; + final String siteID = vc.getID(); final ReadBackedPileup pileup = filterPileup(context.getBasePileup(), countType, includeReadsWithDeletionAtLoci()); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java index 1617f4f39..1e97c388a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEval.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -29,7 +29,6 @@ import com.google.java.contract.Requires; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.util.IntervalTree; import htsjdk.samtools.SAMSequenceRecord; -import oracle.jrockit.jfr.StringConstantPool; import org.apache.log4j.Logger; import htsjdk.tribble.Feature; import org.broadinstitute.gatk.engine.samples.Trio; @@ -139,7 +138,7 @@ import java.util.*; * command line, to rapidly ascertain whether it will work or not.

        * */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VAREVAL, extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=-50, stop=50)) @PartitionBy(PartitionType.NONE) public class VariantEval extends RodWalker implements TreeReducible { @@ -755,4 +754,4 @@ public class VariantEval extends RodWalker implements TreeRedu public boolean ignoreAC0Sites() { return ! keepSitesWithAC0; } -} \ No newline at end of file +} diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java index aef7d8b35..313a2cd7d 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalReportWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java index 1e634b718..1758b6acb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CompOverlap.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java index 2ab63c51b..7727611ce 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/CountVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java index 21164ce36..0a00bf856 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java index 878d6fcbe..fb902516a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/IndelSummary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 29d81ce96..cd419a3e1 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java index ea7394461..1fbe7d513 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MetricsCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java index a45dfbcdc..e46fba144 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/MultiallelicSummary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java index f9c67e872..519794804 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java index 9ee366c06..929b79202 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/StandardEval.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index ef91df2ee..ec62fbde9 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index b60ed8445..2b8a10a8e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java index 74b280f0c..42db6023c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/ValidationReport.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java index f1144a097..e1e767797 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantEvaluator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java index a34ddeb4c..1b180d648 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/VariantSummary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java index 2ab005ae2..38363f7f4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleCount.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java index d52ea8f41..352ee7494 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/AlleleFrequency.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java index 72006196b..3c273de56 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CompRod.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java index 0645fd53f..4ac99d11f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Contig.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java index f4c31a5d1..0a02efede 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/CpG.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java index 1e8368f91..e26651885 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Degeneracy.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java index 429396835..5222e756a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/DynamicStratification.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java index dddb20197..5e07ad1b0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/EvalRod.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java index e4acb9ea1..948c1f4fd 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Family.java @@ -1,6 +1,6 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. -* +* Copyright 2012-2016 Broad Institute, Inc. +* * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation * files (the "Software"), to deal in the Software without @@ -9,10 +9,10 @@ * copies of the Software, and to permit persons to whom the * Software is furnished to do so, subject to the following * conditions: -* +* * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. -* +* * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java index ac9b9e497..4178aed6a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Filter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java index 89ffe8691..d9b8dc33e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/FunctionalClass.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java index 48efe1ee4..64df04145 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IndelSize.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java index 57ba0e7bb..7514ead14 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/IntervalStratification.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java index 7a1106241..c9c4f5f6e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/JexlExpression.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java index 1faf818f1..3e783a661 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Novelty.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java index 9430d9faa..b6c81698c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/OneBPIndel.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java index 9a9313cca..fd18c6737 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/RequiredStratification.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java index c052dcaa5..3c03ca4db 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/Sample.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java index a09feae98..62ce8bd8c 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/SnpEffPositionModifier.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java index de9388a5f..888867630 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/StandardStratification.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java index 7349ccbfa..635ad50f4 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/TandemRepeat.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java index 5b4e6c089..7a246337e 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantStratifier.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java index bc017db56..4dd4fcadf 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/VariantType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java index 4d3dcae43..2c7daaad7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNode.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java index 305f65c94..995f65310 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratNodeIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java index c9398a15b..c5ccb19b7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/StratificationManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java index f206a30ab..5aeef7b5a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/stratifications/manager/Stratifier.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java index 035fabaa4..9ed84f4a8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Analysis.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java index d5f70a9a5..99cd79b14 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/AnalysisModuleScanner.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java index ac02b4d09..cf602ebe7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/DataPoint.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java index f18c381aa..2516bcbe5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/EvaluationContext.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java index f7a156673..9e2126c46 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/Molten.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java index 3b1c1424a..52b52813f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/SortableJexlVCMatchExp.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java index 15198dd53..74b03414f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/util/VariantEvalUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java index 330a723c4..d1a743cf8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VQSRCalibrationCurve.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java index 090124882..8a11da65a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -72,9 +72,9 @@ import java.util.*; *
      * *

      By default, the input sets will be named variants, variants2, variants3, and so on. You can override this by - * providing an explicit name tag for each input, using the syntax " -V:format,name". Each input tagged in this + * providing an explicit name tag for each input, using the syntax " -V:name,format". Each input tagged in this * way will be labeled as such in the output (i.e., set=name rather than set=variants2). For example, you could specify - * a set of control samples as " -V:vcf,control my_control_samples.vcf", and the resulting VCF records would contain + * a set of control samples as " -V:control,vcf my_control_samples.vcf", and the resulting VCF records would contain * the annotation "set=control" in the INFO field. It is strongly recommended to provide explicit names in this way * when a rod priority list is provided.

      * @@ -123,8 +123,8 @@ import java.util.*; * *

      Caveats

      *
        - *
      • This tool is not intended to manipulate GVCFS! To combine GVCF files output by HaplotypeCaller, use CombineGVCFs.
        • - *
      • To join intermediate VCFs produced by running jobs in parallel by interval (e.g. by chromosome), use CatVariants.
        • + *
      • This tool is not intended to manipulate GVCFS! To combine GVCF files output for different samples by HaplotypeCaller, use CombineGVCFs.
        • + *
      • To join intermediate VCFs produced by running jobs in parallel by interval (e.g. by chromosome) from the same sample, use CatVariants.
        • *
      * *

      Additional notes

      diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java index 5019662f4..5361abc3f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ConcordanceMetrics.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java index 4ac6b9b0d..ccac49b24 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeConcordance.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -204,7 +204,7 @@ import java.util.*; * * */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VAREVAL, extraDocs = {CommandLineGATK.class} ) public class GenotypeConcordance extends RodWalker>,ConcordanceMetrics> { /** diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java index 0ba7e1013..c169a2844 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -44,6 +44,9 @@ import org.broadinstitute.gatk.engine.walkers.Window; import org.broadinstitute.gatk.engine.SampleUtils; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.variant.ChromosomeCountConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines; import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; @@ -118,7 +121,7 @@ import java.util.*; * --splitMultiallelics * * - *

      Split multiallelics into biallics, left align but don't trim alleles

      + *

      Split multiallelics into biallics, left align but don't trim alleles, and store the original AC, AF, and AN values

      * 
        * java -jar GenomeAnalysisTK.jar \
  *   -T LeftAlignAndTrimVariants \
@@ -127,6 +130,7 @@ import java.util.*;
  *   -o output.vcf \
  *   --splitMultiallelics \
  *   --dontTrimAlleles
+ *   --keepOriginalAC
  *
      * */ @@ -153,6 +157,14 @@ public class LeftAlignAndTrimVariants extends RodWalker { @Argument(fullName="splitMultiallelics", shortName="split", doc="Split multiallelic records and left-align individual alleles", required=false) protected boolean splitMultiallelics = false; + /** + * When subsetting a callset, this tool recalculates the AC, AF, and AN values corresponding to the contents of the + * subset. If this flag is enabled, the original values of those annotations will be stored in new annotations called + * AC_Orig, AF_Orig, and AN_Orig. + */ + @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Store the original AC, AF, and AN values after subsetting", required=false) + private boolean keepOriginalChrCounts = false; + @Output(doc="File to which variants should be written") protected VariantContextWriter baseWriter = null; @@ -165,11 +177,21 @@ public class LeftAlignAndTrimVariants extends RodWalker { private int referenceWindowStop; public void initialize() { - String trackName = variantCollection.variants.getName(); - Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)); - Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); + final String trackName = variantCollection.variants.getName(); + final Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)); + final Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); + + final Set headerLines = new HashSet<>(); + headerLines.addAll(vcfHeaders.get(trackName).getMetaDataInSortedOrder()) ; + if ( splitMultiallelics ) + headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions)); + + if (keepOriginalChrCounts) { + headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AC_KEY)); + headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AF_KEY)); + headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AN_KEY)); + } - Set headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder(); baseWriter.writeHeader(new VCFHeader(headerLines, samples)); writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, MAX_INDEL_LENGTH); @@ -187,7 +209,8 @@ public class LeftAlignAndTrimVariants extends RodWalker { for ( final VariantContext vc : VCs ) { // split first into biallelics, and optionally don't trim alleles to minimal representation if (splitMultiallelics) { - final List vcList = GATKVariantContextUtils.splitVariantContextToBiallelics(vc); + final List vcList = GATKVariantContextUtils.splitVariantContextToBiallelics(vc, false, + GATKVariantContextUtils.GenotypeAssignmentMethod.BEST_MATCH_TO_ORIGINAL, keepOriginalChrCounts); for (final VariantContext biallelicVC: vcList) { changedSites += trimAlignWrite(biallelicVC, ref, vcList.size()); } @@ -226,7 +249,7 @@ public class LeftAlignAndTrimVariants extends RodWalker { // ignore if the reference length is greater than the reference window stop before and after expansion if ( refLength > MAX_INDEL_LENGTH && refLength > referenceWindowStop ) { - logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d", + logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --reference_window_stop >= %d", REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getChr(), vc.getStart(), refLength)); return 0; } @@ -237,10 +260,6 @@ public class LeftAlignAndTrimVariants extends RodWalker { // align the VC final Pair result = alignAndWrite(v, ref); - // strip out PLs and AD if we've subsetted the alleles - if ( numBiallelics > 1 ) - result.first = new VariantContextBuilder(result.first).genotypes(GATKVariantContextUtils.stripPLsAndAD(result.first.getGenotypes())).make(); - // write out new VC writer.add(result.first); @@ -301,7 +320,6 @@ public class LeftAlignAndTrimVariants extends RodWalker { if ( !newCigar.equals(originalCigar) && newCigar.numCigarElements() > 1 ) { int difference = originalIndex - newCigar.getCigarElement(0).getLength(); VariantContext newVC = new VariantContextBuilder(vc).start(vc.getStart()-difference).stop(vc.getEnd()-difference).make(); - //System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + vc.getChr()+":"+(vc.getStart()-difference)); final int indelIndex = originalIndex-difference; final byte[] newBases = new byte[indelLength + 1]; @@ -323,7 +341,7 @@ public class LeftAlignAndTrimVariants extends RodWalker { * @param ref Ref bases * @param indexOfRef Index in ref where to create indel * @param indelLength Indel length - * @return + * @return Haplotype, containing the reference and the indel */ @Requires({"vc != null","ref != null", "indexOfRef +indelLength < ref.length", "vc.getNAlleles() == 2"}) @Ensures("result != null") diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java index 41962bbcc..ce737178a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RandomlySplitVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java index e95cbf379..28bce4803 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectHeaders.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java index abd53f9f0..f177b7393 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -309,9 +309,11 @@ import java.util.*; @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) public class SelectVariants extends RodWalker implements TreeReducible { static final int MAX_FILTERED_GENOTYPES_DEFAULT_VALUE = Integer.MAX_VALUE; - static final int MIN_FILTERED_GENOTYPES_DEFAULT_VALUE = 0; static final double MAX_FRACTION_FILTERED_GENOTYPES_DEFAULT_VALUE = 1.0; + static final int MIN_FILTERED_GENOTYPES_DEFAULT_VALUE = 0; static final double MIN_FRACTION_FILTERED_GENOTYPES_DEFAULT_VALUE = 0.0; + private static final int MAX_NOCALL_NUMBER_DEFAULT_VALUE = Integer.MAX_VALUE; + private static final double MAX_NOCALL_FRACTION_DEFAULT_VALUE = 1.0; @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); @@ -564,6 +566,18 @@ public class SelectVariants extends RodWalker implements TreeR @Argument(fullName="minFractionFilteredGenotypes", required=false, doc="Maximum fraction of samples filtered at the genotype level") private double minFractionFilteredGenotypes = MIN_FRACTION_FILTERED_GENOTYPES_DEFAULT_VALUE; + /** + * If this argument is provided, select sites where at most the given number of samples have no-call genotypes. + */ + @Argument(fullName="maxNOCALLnumber", required=false, doc="Maximum number of samples with no-call genotypes") + private int maxNOCALLnumber = MAX_NOCALL_NUMBER_DEFAULT_VALUE; + + /** + * If this argument is provided, select sites where at most the given fraction of samples have no-call genotypes. + */ + @Argument(fullName="maxNOCALLfraction", required=false, doc="Maximum fraction of samples with no-call genotypes") + private double maxNOCALLfraction = MAX_NOCALL_FRACTION_DEFAULT_VALUE; + /** * If this argument is provided, set filtered genotypes to no-call (./.). */ @@ -650,7 +664,7 @@ public class SelectVariants extends RodWalker implements TreeR "Samples entered on command line (through -sf or -sn) that are not present in the VCF.", "A list of these samples:", Utils.join(",", commandLineUniqueSamples), - "To ignore these samples, run with --allowNonOverlappingCommandLineSamples")); + "To ignore these samples, run with --ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES")); } } @@ -694,6 +708,13 @@ public class SelectVariants extends RodWalker implements TreeR Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); headerLines.add(new VCFHeaderLine("source", "SelectVariants")); + // need AC, AN and AF since output if set filtered genotypes to no-call + if (setFilteredGenotypesToNocall) { + headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY)); + headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY)); + headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY)); + } + if (keepOriginalChrCounts) { headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AC_KEY)); headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AF_KEY)); @@ -815,7 +836,7 @@ public class SelectVariants extends RodWalker implements TreeR if (containsIndelLargerOrSmallerThan(vc, maxIndelSize, minIndelSize)) continue; - if ( needNumFilteredGenotypes()) { + if ( considerFilteredGenotypes()) { int numFilteredSamples = numFilteredGenotypes(vc); double fractionFilteredGenotypes = samples.isEmpty() ? 0.0 : numFilteredSamples / samples.size(); if (numFilteredSamples > maxFilteredGenotypes || numFilteredSamples < minFilteredGenotypes || @@ -823,6 +844,13 @@ public class SelectVariants extends RodWalker implements TreeR continue; } + if (considerNoCallGenotypes()) { + final int numNoCallSamples = numNoCallGenotypes(vc); + final double fractionNoCallGenotypes = samples.isEmpty() ? 0.0 : ((double) numNoCallSamples) / samples.size(); + if (numNoCallSamples > maxNOCALLnumber || fractionNoCallGenotypes > maxNOCALLfraction) + continue; + } + VariantContext sub = subsetRecord(vc, preserveAlleles, removeUnusedAlternates); VariantContext filteredGenotypeToNocall = setFilteredGenotypeToNocall(sub, setFilteredGenotypesToNocall); @@ -877,6 +905,25 @@ public class SelectVariants extends RodWalker implements TreeR return false; } + /** + * Find the number of no-call genotypes + * + * @param vc the variant context + * @return number of no-call genotypes + */ + private int numNoCallGenotypes(final VariantContext vc) { + if (vc == null) + return 0; + + int numFiltered = 0; + for ( final Genotype g : vc.getGenotypes() ) { + if ( g.isNoCall() ) + numFiltered++; + } + + return numFiltered; + } + /** * Find the number of filtered samples * @@ -1077,14 +1124,35 @@ public class SelectVariants extends RodWalker implements TreeR final VariantContextBuilder builder = new VariantContextBuilder(vc); final GenotypesContext genotypes = GenotypesContext.create(vc.getGenotypes().size()); + // + // recompute AC, AN and AF if filtered genotypes are set to no-call + // + // occurrences of alternate alleles over all genotypes + final Map calledAltAlleles = new LinkedHashMap(vc.getNAlleles()-1); + for ( final Allele altAllele : vc.getAlternateAlleles() ) { + calledAltAlleles.put(altAllele, 0); + } + int calledAlleles = 0; + boolean haveFilteredNoCallAlleles = false; for ( final Genotype g : vc.getGenotypes() ) { - if ( g.isCalled() && g.isFiltered() ) + if ( g.isCalled() && g.isFiltered() ) { + haveFilteredNoCallAlleles = true; genotypes.add(new GenotypeBuilder(g).alleles(diploidNoCallAlleles).make()); - else + } + else { + // increment the number called alleles and called alternate alleles + calledAlleles = GATKVariantContextUtils.incrementChromosomeCountsInfo(calledAltAlleles, calledAlleles, g); genotypes.add(g); + } } - return builder.genotypes(genotypes).make(); + builder.genotypes(genotypes); + + // if filtered genotypes are set to no-call, output recomputed AC, AN, AF + if ( haveFilteredNoCallAlleles ) + GATKVariantContextUtils.updateChromosomeCountsInfo(calledAltAlleles, calledAlleles, builder); + + return builder.make(); } /* * Add annotations to the new VC @@ -1183,14 +1251,24 @@ public class SelectVariants extends RodWalker implements TreeR } /** - * Need the number of filtered genotypes samples? + * Should the number of filtered genotypes be considered for filtering? * * @return true if any of the filtered genotype samples arguments is used (not the default value), false otherwise */ - private boolean needNumFilteredGenotypes(){ + private boolean considerFilteredGenotypes(){ return maxFilteredGenotypes != MAX_FILTERED_GENOTYPES_DEFAULT_VALUE || minFilteredGenotypes != MIN_FILTERED_GENOTYPES_DEFAULT_VALUE || maxFractionFilteredGenotypes != MAX_FRACTION_FILTERED_GENOTYPES_DEFAULT_VALUE || minFractionFilteredGenotypes != MIN_FRACTION_FILTERED_GENOTYPES_DEFAULT_VALUE; } -} \ No newline at end of file + + /** + * Should the number of no-call genotypes be considered for filtering? + * + * @return true if any of the filtered genotype samples arguments is used (not the default value), false otherwise + * + */ + private boolean considerNoCallGenotypes(){ + return maxNOCALLnumber != MAX_NOCALL_NUMBER_DEFAULT_VALUE || maxNOCALLfraction != MAX_NOCALL_FRACTION_DEFAULT_VALUE; + } +} diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java index a5b710acc..ce9e84c0f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -26,23 +26,26 @@ package org.broadinstitute.gatk.tools.walkers.variantutils; import htsjdk.tribble.TribbleException; -import org.broadinstitute.gatk.utils.commandline.Argument; -import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; -import org.broadinstitute.gatk.engine.CommandLineGATK; -import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; -import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.gatk.utils.contexts.AlignmentContext; -import org.broadinstitute.gatk.utils.contexts.ReferenceContext; -import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; -import org.broadinstitute.gatk.engine.walkers.Reference; -import org.broadinstitute.gatk.engine.walkers.RodWalker; -import org.broadinstitute.gatk.engine.walkers.Window; -import org.broadinstitute.gatk.utils.exceptions.UserException; -import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; -import org.broadinstitute.gatk.utils.help.HelpConstants; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFConstants; +import org.broadinstitute.gatk.engine.CommandLineGATK; +import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection; +import org.broadinstitute.gatk.engine.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.gatk.engine.walkers.Reference; +import org.broadinstitute.gatk.engine.walkers.RodWalker; +import org.broadinstitute.gatk.engine.walkers.Window; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocSortedSet; +import org.broadinstitute.gatk.utils.commandline.Argument; +import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; +import org.broadinstitute.gatk.utils.contexts.AlignmentContext; +import org.broadinstitute.gatk.utils.contexts.ReferenceContext; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature; +import org.broadinstitute.gatk.utils.help.HelpConstants; +import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker; +import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; import java.io.File; import java.util.*; @@ -120,9 +123,9 @@ import java.util.*; * * */ -@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VALIDATION, extraDocs = {CommandLineGATK.class} ) +@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VAREVAL, extraDocs = {CommandLineGATK.class} ) @Reference(window=@Window(start=0,stop=100)) -public class ValidateVariants extends RodWalker { +public class ValidateVariants extends RodWalker { // Log message for a reference allele that is too long protected static final String REFERENCE_ALLELE_TOO_LONG_MSG = "Reference allele is too long"; @@ -184,12 +187,21 @@ public class ValidateVariants extends RodWalker { /** * By default, even filtered records are validated. */ - @Argument(fullName = "doNotValidateFilteredRecords", shortName = "doNotValidateFilteredRecords", doc = "skip validation on filtered records", required = false) + @Argument(fullName = "doNotValidateFilteredRecords", shortName = "doNotValidateFilteredRecords", doc = "skip validation on filtered records", required = false, exclusiveOf = "VALIDATE_GVCF") protected Boolean DO_NOT_VALIDATE_FILTERED = false; @Argument(fullName = "warnOnErrors", shortName = "warnOnErrors", doc = "just emit warnings on errors instead of terminating the run at the first instance", required = false) protected Boolean WARN_ON_ERROR = false; + /** + * Validate this file as a gvcf. In particular, every variant must include a allele, and that + * every base in the territory under consideration is covered by a variant (or a reference block). + * If you specifed intervals (using -L or -XL) to restrict analysis to a subset of genomic regions, + * those intervals will need to be covered in a valid gvcf. + */ + @Argument(fullName = "validateGVCF", shortName = "gvcf", doc = "Validate this file as a GVCF", required = false, exclusiveOf = "DO_NOT_VALIDATE_FILTERED") + protected Boolean VALIDATE_GVCF = false; + private long numErrors = 0; private File file = null; @@ -208,29 +220,60 @@ public class ValidateVariants extends RodWalker { referenceWindowStop = getToolkit().getArguments().reference_window_stop; } - public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { if ( tracker == null ) - return 0; + return null; + + int lastVcEnd = -1; Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation()); - for ( VariantContext vc : VCs ) - validate(vc, tracker, ref); + if (VALIDATE_GVCF && VCs.size() > 1) { + logger.error("GVCF validation can only be performed one file at a time. Validation results are invalid."); + } + for ( VariantContext vc : VCs ) { + validate(vc, tracker, ref, VALIDATE_GVCF); + lastVcEnd = vc.getEnd(); + } - return VCs.size(); + return GenomeLoc.setStop(ref.getLocus(), lastVcEnd); } - public Integer reduceInit() { return 0; } + @Override + public GenomeLocSortedSet reduce(GenomeLoc value, GenomeLocSortedSet sum) { + sum.add(value, true); + return sum; + } - public Integer reduce(Integer value, Integer sum) { return sum+value; } + @Override + public GenomeLocSortedSet reduceInit() { + return new GenomeLocSortedSet(getToolkit().getGenomeLocParser()); + } - public void onTraversalDone(Integer result) { - if ( numErrors == 0 ) - System.out.println("Successfully validated the input file. Checked " + result + " records with no failures."); + @Override + public void onTraversalDone(GenomeLocSortedSet result) { + if (VALIDATE_GVCF) { + final GenomeLocSortedSet uncoveredIntervals = getToolkit().getIntervals().subtractRegions(result); + if (uncoveredIntervals.coveredSize() > 0) { + final UserException e = new UserException.FailsStrictValidation(file, "A GVCF must cover the entire region. Found " + uncoveredIntervals.coveredSize() + + " loci with no VariantContext covering it. The first uncovered segment is:" + + uncoveredIntervals.iterator().next()); + + if (WARN_ON_ERROR) { + numErrors++; + logger.warn("***** " + e.getMessage() + " *****"); + } else { + throw e; + } + } + } + + if (numErrors == 0) + System.out.println("Successfully validated the input file. Checked " + result.size() + " records with no failures."); else System.out.println("Found " + numErrors + " records with failures."); } - private void validate(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref) { + private void validate(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, boolean gvcf) { if ( DO_NOT_VALIDATE_FILTERED && vc.isFiltered() ) return; @@ -240,8 +283,8 @@ public class ValidateVariants extends RodWalker { // reference length is greater than the reference window stop before and after expansion if ( refLength > 100 && refLength > referenceWindowStop ) { - logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d", - REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getChr(), vc.getStart(), refLength)); + logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --reference_window_stop >= %d", + REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getContig(), vc.getStart(), refLength)); return; } @@ -252,7 +295,7 @@ public class ValidateVariants extends RodWalker { // get the RS IDs Set rsIDs = null; if ( tracker.hasValues(dbsnp.dbsnp) ) { - rsIDs = new HashSet(); + rsIDs = new HashSet<>(); for ( VariantContext rsID : tracker.getValues(dbsnp.dbsnp, ref.getLocus()) ) rsIDs.addAll(Arrays.asList(rsID.getID().split(VCFConstants.ID_FIELD_SEPARATOR))); } @@ -260,6 +303,10 @@ public class ValidateVariants extends RodWalker { try { for (final ValidationType t : validationTypes) applyValidationType(vc, reportedRefAllele, observedRefAllele, rsIDs, t); + + if (gvcf) { + ValidateGVCFVariant(vc); + } } catch (TribbleException e) { if ( WARN_ON_ERROR ) { numErrors++; @@ -279,6 +326,13 @@ public class ValidateVariants extends RodWalker { * @return never {@code null} but perhaps an empty set. */ private Collection calculateValidationTypesToApply(final List excludeTypes) { + + if (VALIDATE_GVCF && !excludeTypes.contains(ValidationType.ALLELES)) { + // Note: in a future version allele validation might be OK for GVCFs, if that happens + // this will be more complicated. + logger.warn("GVCF format is currently incompatible with allele validation. Not validating Alleles."); + excludeTypes.add(ValidationType.ALLELES); + } if (excludeTypes.isEmpty()) return Collections.singleton(ValidationType.ALL); final Set excludeTypeSet = new LinkedHashSet<>(excludeTypes); @@ -295,6 +349,13 @@ public class ValidateVariants extends RodWalker { } } + private void ValidateGVCFVariant(final VariantContext vc) { + if (!vc.hasAllele(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE)) { + throw new TribbleException.InternalCodecException(String.format("In a GVCF all records must contain a %s allele. Offending record: %s", + GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE_NAME, vc.toStringWithoutGenotypes())); + } + } + private void applyValidationType(VariantContext vc, Allele reportedRefAllele, Allele observedRefAllele, Set rsIDs, ValidationType t) { switch( t ) { case ALL: diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java index a75491d67..7a316cbb5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToAllelicPrimitives.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java index 10f463727..57c0fe7ff 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java index a2651ef29..ef4546181 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -295,6 +295,8 @@ public class VariantsToTable extends RodWalker { if ( splitMultiAllelic && field.equals("ALT") ) { // we need to special case the ALT field when splitting out multi-allelic records addFieldValue(splitAltAlleles(vc), records); + } else if (splitMultiAllelic && field.equals("TYPE")) { + addFieldValue(splitAlleleTypes(vc), records); } else if ( getters.containsKey(field) ) { addFieldValue(getters.get(field).get(vc), records); } else if ( vc.hasAttribute(field) ) { @@ -461,4 +463,23 @@ public class VariantsToTable extends RodWalker { return vc.getAlternateAlleles(); } + + private static Object splitAlleleTypes(VariantContext vc) { + final int numAltAlleles = vc.getAlternateAlleles().size(); + if (numAltAlleles == 1) + return vc.getType().toString(); + List altAlleles = vc.getAlternateAlleles(); + List alleleTypes = new ArrayList<>(numAltAlleles); + for (Allele allele : altAlleles) { + if (allele.length() == vc.getReference().length()) { + if ( allele.length() == 1 ) + alleleTypes.add("SNP"); + else + alleleTypes.add("MNP"); + } + else + alleleTypes.add("INDEL"); + } + return alleleTypes; + } } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java index 051137009..3bf2c11b5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCF.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java index 9e6ad827f..40a571b8c 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/CatVariantsIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -92,14 +92,14 @@ public class CatVariantsIntegrationTest { final File catVariantsTempList2 = BaseTest.createTempListFile("CatVariantsTest2", CatVariantsVcf2.getAbsolutePath()); new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest", ".vcf"), "c055705e0606f4fe89d339d416c182e1"); - new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest", ".bcf"), "2a82e959b3b07b461d64bd5ed7298aa3"); + new CatVariantsTestProvider(CatVariantsBcf1, CatVariantsBcf2, BaseTest.createTempFile("CatVariantsTest", ".bcf"), "b7085b466ee49ba0857c6ff6ffe32bf3"); for (String extension1 : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) { for (String extension2 : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) { final File file1 = new File(CatVariantsDir, "CatVariantsTest1.vcf" + extension1); final File file2 = new File(CatVariantsDir, "CatVariantsTest2.vcf" + extension2); new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf"), "c055705e0606f4fe89d339d416c182e1"); - new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".bcf"), "2a82e959b3b07b461d64bd5ed7298aa3"); + new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".bcf"), "820124f0ef22324e070ee21c91a633a4"); new CatVariantsTestProvider(file1, file2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "3beb2c58fb795fcdc485de9868eda576"); } new CatVariantsTestProvider(CatVariantsVcf1, CatVariantsVcf2, BaseTest.createTempFile("CatVariantsTest.", ".vcf" + extension1), "3beb2c58fb795fcdc485de9868eda576"); diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java index f26f6a90a..540f350ab 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -34,6 +34,7 @@ public class BAQIntegrationTest extends WalkerTest { private final static String baseCommand = "-T PrintReads -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" + " -o %s" + + " --no_pg_tag " + " -L 1:10,000,000-10,100,000"; // -------------------------------------------------------------------------------------------------------------- diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java index 4e11d0df3..f1746cb6d 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java index 521f4c237..a79555139 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/CompressedDataListUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java index 15279a0ad..5460291bc 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/SnpEffUtilUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java index 3ac2a3d44..1889f6f4d 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java index e24564a4b..e9140c7cd 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java index 1f5e398fe..c78cd38d1 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageB36IntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java index f25ac3a94..d064328c0 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -86,23 +86,23 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { // now add the expected files that get generated spec.addAuxFile("0f9603eb1ca4a26828e82d8c8f4991f6", baseOutputFile); spec.addAuxFile("51e6c09a307654f43811af35238fb179", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts")); - spec.addAuxFile("520720a88ae7608257af51bc41c06b87", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions")); + spec.addAuxFile("3bf1d7247ea68d1afb35c2032c68dbdf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions")); spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics")); - spec.addAuxFile("6958004a8156f3f267caa6b04cf90f5f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); - spec.addAuxFile("ebbfc9b9f4e12ac989c127061948c565", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); - spec.addAuxFile("e003bef6762833a5cebca25d94194616", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); + spec.addAuxFile("681dcbedcf7ca14bb44134abd1d8da3f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); + spec.addAuxFile("0f58e7f0909b84897fea5daebd9d2948", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); + spec.addAuxFile("2832e48c12b1d8811ccd319a8ffb8dc1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); spec.addAuxFile("a836b92ac17b8ff9788e2aaa9116b5d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts")); - spec.addAuxFile("0732b6d2db9c94b0fcf18ca1f19772a8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions")); + spec.addAuxFile("22fee04ffca7fa489ae2e66309de12e4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions")); spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics")); - spec.addAuxFile("3522f7380554b926c71a7258250c1d63", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); - spec.addAuxFile("2cd9d8c5e37584edd62ca6938659cf59", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); - spec.addAuxFile("78fdd35a63a7a4c6b3a043b946b04730", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); + spec.addAuxFile("2de22ad840bf40621e51316728a32fe9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); + spec.addAuxFile("6c84a067016c63e8c2face2de800acc7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); + spec.addAuxFile("2629883b99428f51e2d90d820b45504a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); spec.addAuxFile("6909d50a7da337cd294828b32b945eb8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); - spec.addAuxFile("aa00e3652dd518ccbae2caa00171835b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); + spec.addAuxFile("f6e52c5659f53afdcfc69c25272b9e99", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); - spec.addAuxFile("0ce5ebfa46b081820d013bdbbfe42d34", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); - spec.addAuxFile("c7c5bad6c6818995c634f350aa66fde9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); - spec.addAuxFile("949c9ce745753cd98f337600d3931d09", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); + spec.addAuxFile("c2fb3a31d02df03c35afbe7f2284ad66", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); + spec.addAuxFile("d1b3d08c6e9565a1dab727d089085761", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); + spec.addAuxFile("c0fadfcfd88cec81ba0d57b33bdec277", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); execute("testBaseOutputNoFiltering",spec); } @@ -119,7 +119,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { spec.setOutputFileLocation(baseOutputFile); spec.addAuxFile("6ccd7d8970ba98cb95fe41636a070c1c",baseOutputFile); - spec.addAuxFile("4429d33ce8836c09ba2b5ddfae2f998e",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); + spec.addAuxFile("fcaac186b7ccd10f3a6cb89ea49dcc1e",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); execute("testNoCoverageDueToFiltering",spec); } @@ -164,7 +164,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { spec.addAuxFile("a148e50f9db207adfd5d5f0f29eb54d8", baseOutputFile); spec.addAuxFile("7ccd5193a3c035d1cc856cbc89e3daf4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); spec.addAuxFile("2efe59c20721ce61bc5b334a26d11720", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); - spec.addAuxFile("9194cec953e0fe0b84a681f9bb63ffbe", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_gene_summary")); + spec.addAuxFile("3dd61151e758c1f3c4bd1150b6577b45", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_gene_summary")); spec.addAuxFile("cf62d95ec1f459fbbe35370c3f0ca481", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); spec.addAuxFile("b4fcb739b7f9e309e38a7d5e7e4ebb9f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); spec.addAuxFile("6bf63f9c62071e850c6f0b6356fb63eb", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); @@ -211,4 +211,48 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { File file = new File(logFileName); Assert.assertTrue(FileUtils.readFileToString(file).contains(DepthOfCoverage.incompatibleArgsMsg())); } + + @Test + public void testSampleGeneSummaryHeaderFix(){ + final String[] intervals = {privateTestDir+"intervals.list"}; + final String[] bams = {privateTestDir+"U145055CM2013D16882_snippet.bam", privateTestDir+"U145055PF2013D20189_snippet.bam", privateTestDir+"ControleMan1_snippet.bam"}; + String cmd = buildRootCmd(b37KGReference, new ArrayList(Arrays.asList(bams)), new ArrayList(Arrays.asList(intervals))) + + " -geneList "+privateTestDir+"ENSG00000186092.rod"; + + WalkerTestSpec spec = new WalkerTestSpec(cmd, 0, new ArrayList()); + + File baseOutputFile = WalkerTest.createTempFile("depthOfCoverageSampleGeneSummaryHeaderFix", ".tmp"); + spec.setOutputFileLocation(baseOutputFile); + + spec.addAuxFile("0b698e9d6c28479c378bf64182100e11", baseOutputFile); + spec.addAuxFile("97a782ce07fc487d0945b60f66721048", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); + spec.addAuxFile("02cd919ef71d8bcfb1c1622b7a683033", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); + spec.addAuxFile("799d8ff6a12d3109f985953ce91ab17c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_gene_summary")); + spec.addAuxFile("c9624eaa0a800da0b457daa752f7ed92", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); + spec.addAuxFile("34ac6759bff2d34890a30a44f8887336", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); + spec.addAuxFile("166b97db63a95c3ceb44d790d98a6fc1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); + spec.addAuxFile("77e03df80132408c6c773cdb1f835e83", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); + + execute("testSampleGeneSummaryHeaderFix", spec); + } + + @Test(expectedExceptions = RuntimeException.class) + public void testMissingSAMHeaderReadGroup() { + final String[] intervals = {"chr1:200-300"}; + final String[] bams = {privateTestDir + "exampleBAMNoRG.bam"}; + + final String cmd = buildRootCmd(exampleFASTA,new ArrayList<>(Arrays.asList(bams)),new ArrayList<>(Arrays.asList(intervals))); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 0, new ArrayList()); + execute("testMissingSAMHeaderReadGroup", spec); + } + + @Test(expectedExceptions = RuntimeException.class) + public void testMissingSAMHeaderReadGroupSample() { + final String[] intervals = {"chr1:200-300"}; + final String[] bams = {privateTestDir + "exampleBAMNoSM.bam"}; + + final String cmd = buildRootCmd(exampleFASTA,new ArrayList<>(Arrays.asList(bams)),new ArrayList<>(Arrays.asList(intervals))); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 0, new ArrayList()); + execute("testMissingSAMHeaderReadGroupSample", spec); + } } diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java index 92b3d862f..15020f8f0 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/diffengine/DiffObjectsIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java index 4d3223f30..1e9a1dc81 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java new file mode 100644 index 000000000..7be6c1ca8 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ConstrainedMateFixingManagerUnitTest.java @@ -0,0 +1,172 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.ProgressLoggerInterface; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +import java.util.ArrayList; +import java.util.List; + + +public class ConstrainedMateFixingManagerUnitTest extends BaseTest { + + private static SAMFileHeader header; + private static GenomeLocParser genomeLocParser; + + @BeforeClass + public void beforeClass() { + header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, 10000); + genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); + } + + @Test + public void testSecondaryAlignmentsDoNotInterfere() { + final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false); + final GATKSAMRecord read1 = properReads.get(0); + read1.setAlignmentStart(8); // move the read + read1.setFlags(99); // first in proper pair, mate negative strand + + final GATKSAMRecord read2Primary = properReads.get(1); + read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment + + Assert.assertEquals(read1.getInferredInsertSize(), 21); + + final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); + read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand + + final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 1000, 1000, 1000); + manager.addRead(read1, true, false); + manager.addRead(read2NonPrimary, false, false); + manager.addRead(read2Primary, false, false); + + Assert.assertEquals(manager.getNReadsInQueue(), 3); + + for ( final SAMRecord read : manager.getReadsInQueueForTesting() ) { + if ( read.getFirstOfPairFlag() ) { + Assert.assertEquals(read.getFlags(), 99); + Assert.assertEquals(read.getInferredInsertSize(), 23); + } else if ( read.getNotPrimaryAlignmentFlag() ) { + Assert.assertEquals(read.getFlags(), 393); + Assert.assertEquals(read.getInferredInsertSize(), -21); + } else { + Assert.assertEquals(read.getFlags(), 147); + Assert.assertEquals(read.getInferredInsertSize(), -23); + } + } + } + + @Test + public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() { + final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false); + final GATKSAMRecord read1 = properReads.get(0); + read1.setFlags(99); // first in proper pair, mate negative strand + + final GATKSAMRecord read2Primary = properReads.get(1); + read2Primary.setFlags(147); // second in pair, mate unmapped, not primary alignment + read2Primary.setAlignmentStart(1596); // move the read + + final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary); + read2NonPrimary.setReadName("foo"); + read2NonPrimary.setFlags(393); // second in proper pair, on reverse strand + read2NonPrimary.setAlignmentStart(451); + read2NonPrimary.setMateAlignmentStart(451); + + final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000); + manager.addRead(read2NonPrimary, false, false); + manager.addRead(read1, false, false); + + for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ ) + manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false); + + Assert.assertTrue(manager.forMateMatching.containsKey("foo")); + } + + @Test + public void testSupplementaryAlignmentsDoNotCauseBadMateFixing() { + final List properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 1000, 2000, true, false); + final GATKSAMRecord read1 = properReads.get(0); + read1.setFlags(99); // first in pair, negative strand + + final GATKSAMRecord read2 = properReads.get(1); + read2.setFlags(161); // second in pair, mate negative strand + + final GATKSAMRecord read2Supp = new GATKSAMRecord(read2); + read2Supp.setReadName("foo"); + read2Supp.setFlags(2209); // second in pair, mate negative strand, supplementary + read2Supp.setAlignmentStart(100); + read2Supp.setMateAlignmentStart(1000); + + final DummyWriter writer = new DummyWriter(); + final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(writer, genomeLocParser, 10000, 200, 10000); + manager.addRead(read2Supp, false, false); + manager.addRead(read1, false, false); + manager.addRead(read2, false, false); + manager.close(); // "write" the reads to our dummy writer + + // check to make sure that none of the mate locations were changed, which is the problem brought to us by a user + for ( final SAMRecord read : writer.reads ) { + final int start = read.getAlignmentStart(); + switch (start) { + case 100: + Assert.assertEquals(read.getMateAlignmentStart(), 1000); + break; + case 1000: + Assert.assertEquals(read.getMateAlignmentStart(), 2000); + break; + case 2000: + Assert.assertEquals(read.getMateAlignmentStart(), 1000); + break; + default: + Assert.assertTrue(false, "We saw a read located at the wrong position"); + } + } + } + + private class DummyWriter implements SAMFileWriter { + + public List reads; + + public DummyWriter() { reads = new ArrayList<>(10); } + + public void addAlignment(final SAMRecord alignment) { reads.add(alignment);} + + public SAMFileHeader getFileHeader() { return null; } + + public void setProgressLogger(final ProgressLoggerInterface progress) {} + + public void close() {} + } +} \ No newline at end of file diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java new file mode 100644 index 000000000..81b2c457c --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerIntegrationTest.java @@ -0,0 +1,161 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.testng.annotations.Test; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.Map; + +public class IndelRealignerIntegrationTest extends WalkerTest { + + private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.fixmates.bam"; + private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals"; + private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf"; + private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 "; + private static final String baseCommand = baseCommandPrefix + "-o %s "; + private static final String base_md5 = "ab7407d2299d9ba73449cea376eeb9c4"; + private static final String base_md5_with_SW_or_VCF = "fa57bd96b83038ac6a70e58e11bf5364"; + + @Test + public void testDefaults() { + + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommand, + 1, + Arrays.asList(base_md5)); + executeTest("test realigner defaults", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + baseCommand + "-known " + knownIndels, + 1, + Arrays.asList(base_md5_with_SW_or_VCF)); + executeTest("test realigner defaults with VCF", spec2); + } + + @Test + public void testKnownsOnly() { + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels, + 1, + Arrays.asList("c42b6f3e1270e43cce2b6f75b6a38f30")); + executeTest("realigner known indels only from VCF", spec1); + } + + @Test + public void testUseSW() { + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommand + "--consensusDeterminationModel USE_SW -known " + knownIndels, + 1, + Arrays.asList(base_md5_with_SW_or_VCF)); + executeTest("realigner use SW from VCF", spec1); + } + + @Test + public void testLods() { + HashMap e = new HashMap(); + e.put("-LOD 60", base_md5); + e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "0c4597e48b4e194de32ebe494704ea6b" ); + + for ( Map.Entry entry : e.entrySet() ) { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + baseCommand + entry.getKey(), + 1, + Arrays.asList(entry.getValue())); + executeTest(String.format("realigner [%s]", entry.getKey()), spec); + } + } + + @Test + public void testLongRun() { + WalkerTestSpec spec = new WalkerTestSpec( + "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s", + 1, + Arrays.asList("19e6859b9ef09c7e0a79a19626908b17")); + executeTest("realigner long run", spec); + } + + @Test + public void testNoTags() { + WalkerTestSpec spec = new WalkerTestSpec( + baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW", + 1, + Arrays.asList("8f5684359d7b26acaacfa657ef395a0c")); + executeTest("realigner no output tags", spec); + } + + @Test + public void testStats() { + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommandPrefix + "-stats %s -o /dev/null", + 1, + Arrays.asList("7ed8d4eed635613fd031598a5c9ef5a3")); + executeTest("realigner stats", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + baseCommandPrefix + "-LOD 60 -stats %s -o /dev/null", + 1, + Arrays.asList("e8b02bfc5debec55fe936a38c59463cc")); + executeTest("realigner stats", spec2); + } + + @Test + public void testMaxReadsInMemory() { + HashMap e = new HashMap(); + e.put("--maxReadsInMemory 10000", "236c64f2da0047534b44444d9d699378"); + e.put( "--maxReadsInMemory 40000", base_md5 ); + + for ( Map.Entry entry : e.entrySet() ) { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + baseCommand + entry.getKey(), + 1, + Arrays.asList(entry.getValue())); + executeTest(String.format("realigner [%s]", entry.getKey()), spec); + } + } + + @Test + public void testNWayOut() { + WalkerTestSpec spec1 = new WalkerTestSpec( + baseCommandPrefix + " -nWayOut .clean.bam ", + 1, + Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")); + executeTest("test realigner nWayOut", spec1); + } + + @Test + public void testBadCigarStringDoesNotFail() { + // Just making sure the test runs without an error, don't care about the MD5 value + WalkerTestSpec spec = new WalkerTestSpec( + "-T IndelRealigner -R " + b37KGReference + " -I " + privateTestDir + "Realigner.error.bam -L 19:5787200-5787300 -targetIntervals 19:5787205-5787300 -o %s", + 1, + Arrays.asList("")); + executeTest("test bad cigar string does not fail", spec); + } +} diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java new file mode 100644 index 000000000..649644712 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerLargeScaleTest.java @@ -0,0 +1,82 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.testng.annotations.Test; + +import java.util.ArrayList; + +public class IndelRealignerLargeScaleTest extends WalkerTest { + @Test( timeOut = 18000000 ) + public void testHighCoverage() { + WalkerTestSpec spec = new WalkerTestSpec( + + "-R " + b36KGReference + + " -T IndelRealigner" + + " -I " + validationDataLocation + "indelRealignerTest.pilot1.veryHighCoverage.bam" + + " -L 20:49,500-55,500" + + " -o /dev/null" + + " -targetIntervals " + validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals", + 0, + new ArrayList(0)); + executeTest("testIndelRealignerHighCoverage", spec); + } + + @Test( timeOut = 18000000 ) + public void testRealigner() { + WalkerTestSpec spec1 = new WalkerTestSpec( + + "-R " + hg18Reference + + " -T IndelRealigner" + + " -LOD 5" + + " -maxConsensuses 100" + + " -greedy 100" + + " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -o /dev/null" + + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + + " -L chr1:1-5,650,000" + + " -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals", + 0, + new ArrayList(0)); + executeTest("testIndelRealignerWholeGenome", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + "-R " + hg18Reference + + " -T IndelRealigner" + + " -LOD 5" + + " -maxConsensuses 100" + + " -greedy 100" + + " -known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -o /dev/null" + + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + + " -L chr1:1-150,000,000" + + " -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals", + 0, + new ArrayList(0)); + executeTest("testIndelRealignerWholeExome", spec2); + } +} diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java new file mode 100644 index 000000000..801db5269 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/IndelRealignerUnitTest.java @@ -0,0 +1,61 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileNotFoundException; + +public class IndelRealignerUnitTest extends BaseTest { + + private SAMFileHeader header; + + @BeforeClass + public void setup() throws FileNotFoundException { + final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); + } + + @Test + public void realignAtContigBorderTest() { + final int contigEnd = header.getSequence(0).getSequenceLength(); + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "goodRead", 0, contigEnd - 1, 2); + read.setCigarString("2M"); + Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), false); + read.setCigarString("1M1D1M"); + Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), true); + } + +} diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java new file mode 100644 index 000000000..d843374d2 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/ReadBinUnitTest.java @@ -0,0 +1,91 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; +import org.broadinstitute.gatk.utils.sam.ReadUtils; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +/** + * User: carneiro + * Date: 2/16/13 + * Time: 11:48 PM + */ +public class ReadBinUnitTest { + private GenomeLocParser parser; + private ReadBin readBin; + + private final int readLength = 100; // all reads will have the same size + private final int referencePadding = 10; // standard reference padding + + @BeforeClass + public void init() { + parser = new GenomeLocParser(ArtificialSAMUtils.createArtificialSamHeader().getSequenceDictionary()); + readBin = new ReadBin(parser, referencePadding); + } + + @DataProvider(name = "reads") + public Object[][] reads() { + + return new Object[][]{ + {"20S80M", 80}, + {"80M20S", 1}, + {"20S60M20S", 50}, + {"50I", 60}, + {"100M", 500} + }; + } + + /** + * Tests the GenomeLoc variable in the ReadBin after adding arbitrary reads + * + * @param cigarString the read's cigar string + * @param alignmentStart the read's alignment start + */ + @Test(enabled = true, dataProvider = "reads") + public void testAddingReads(String cigarString, int alignmentStart) { + final GATKSAMRecord read = createReadAndAddToBin(cigarString, alignmentStart); + final GenomeLoc readLoc = parser.createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getSoftStart(), Math.max(read.getSoftStart(), read.getSoftEnd())); + Assert.assertEquals(readBin.getLocation(), readLoc); + readBin.clear(); + } + + public GATKSAMRecord createReadAndAddToBin(String cigarString, int alignmentStart) { + final GATKSAMRecord read = ReadUtils.createRandomRead(readLength); + read.setCigarString(cigarString); + read.setAlignmentStart(alignmentStart); + readBin.add(read); + return read; + } +} + + diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java new file mode 100644 index 000000000..e4b7485d2 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorIntegrationTest.java @@ -0,0 +1,133 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.util.Interval; +import htsjdk.samtools.util.IntervalList; +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.BaseTest; +import org.broadinstitute.gatk.utils.GenomeLoc; +import org.broadinstitute.gatk.utils.GenomeLocParser; +import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.gatk.utils.interval.IntervalUtils; +import org.testng.Assert; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +public class RealignerTargetCreatorIntegrationTest extends WalkerTest { + + @DataProvider(name = "intervals1") + public Object[][] intervals1() { + String arguments = "-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000"; + return new Object[][]{ + {"test standard nt=1", arguments}, + {"test standard nt=4", "-nt 4 " + arguments} + }; + } + + @DataProvider(name = "intervals2") + public Object[][] intervals2() { + String arguments = "-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000"; + return new Object[][]{ + {"test with dbsnp nt=1", arguments}, + {"test with dbsnp nt=4", "-nt 4 " + arguments} + }; + } + + @Test(dataProvider = "intervals1") + public void testIntervals1(String testName, String arguments) { + String md5 = "3f0b63a393104d0c4158c7d1538153b8"; + + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5)); + executeTest(testName, spec); + } + + @Test(dataProvider = "intervals2") + public void testIntervals2(String testName, String arguments) { + String md5 = "d073237694175c75d37bd4f40b8c64db"; + + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(arguments + " -o %s", 1, Arrays.asList(md5)); + executeTest(testName, spec); + } + + @Test + public void testKnownsOnly() { + WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( + "-T RealignerTargetCreator -R " + b36KGReference + " --known " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -L " + privateTestDir + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -o %s", + 1, + Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96")); + executeTest("test rods only", spec3); + } + + @Test() + public void testBadCigarStringDoesNotFail() { + // Just making sure the test runs without an error, don't care about the MD5 value + WalkerTestSpec spec = new WalkerTestSpec( + "-T RealignerTargetCreator -R " + b37KGReference + " -I " + privateTestDir + "Realigner.error.bam -L 19:5787200-5787300 -o %s", + 1, + Arrays.asList("")); + executeTest("test bad cigar string string does not fail", spec); + } + + @Test(dataProvider = "intervals1") + public void testTargetListAgainstIntervalList(String testName, String arguments) throws IOException { + final List md5 = Collections.emptyList(); + final File targetListFile = createTempFile("RTCTest", ".targets"); + final File intervalListFile = createTempFile("RTCTest", ".interval_list"); + + WalkerTest.WalkerTestSpec targetListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5); + WalkerTest.WalkerTestSpec intervalListSpec = new WalkerTest.WalkerTestSpec(arguments, 1, md5); + + targetListSpec.setOutputFileLocation(targetListFile); + intervalListSpec.setOutputFileLocation(intervalListFile); + + executeTest(testName + " (compare target-list and interval-list output)", targetListSpec); + executeTest(testName + " (compare target-list and interval-list output)", intervalListSpec); + + final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference)); + final GenomeLocParser hg19GenomeLocParser = new GenomeLocParser(seq); + final List targetList = IntervalUtils.intervalFileToList(hg19GenomeLocParser, + targetListFile.getAbsolutePath()); + final List targetListResult = new ArrayList<>(); + for ( GenomeLoc target : targetList ) { + targetListResult.add(new Interval(target.getContig(), target.getStart(), target.getStop())); + } + + final List intervalListResult = IntervalList.fromFile(intervalListFile).getIntervals(); + + Assert.assertFalse(targetListResult.isEmpty()); + Assert.assertFalse(intervalListResult.isEmpty()); + Assert.assertEquals(targetListResult, intervalListResult); + } +} diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java new file mode 100644 index 000000000..8b90ef419 --- /dev/null +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/indels/RealignerTargetCreatorLargeScaleTest.java @@ -0,0 +1,59 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.tools.walkers.indels; + +import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.testng.annotations.Test; + +import java.util.ArrayList; + +public class RealignerTargetCreatorLargeScaleTest extends WalkerTest { + @Test( timeOut = 18000000 ) + public void testRealignerTargetCreator() { + + WalkerTestSpec spec1 = new WalkerTestSpec( + "-R " + hg18Reference + + " -T RealignerTargetCreator" + + " --known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + + " -L chr1:1-50,000,000" + + " -o /dev/null", + 0, + new ArrayList(0)); + executeTest("testRealignerTargetCreatorWholeGenome", spec1); + + WalkerTestSpec spec2 = new WalkerTestSpec( + "-R " + hg18Reference + + " -T RealignerTargetCreator" + + " --known " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + + " -o /dev/null", + 0, + new ArrayList(0)); + executeTest("testRealignerTargetCreatorWholeExome", spec2); + } +} diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java index 2648ed81e..fb15c598d 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CheckPileupIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java index 889646017..dcd424f65 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/CountReadsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java index f29cb80e8..f98cc4466 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/DictionaryConsistencyIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java index e86c3301f..bc762de3d 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/FlagStatIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java index a64efaf26..a52059bb5 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -40,7 +40,7 @@ public class PileupWalkerIntegrationTest extends WalkerTest { String gatk_args = "-T Pileup -I " + validationDataLocation + "FHS_Pileup_Test.bam " + "-R " + hg18Reference + " -L chr15:46,347,148 -o %s"; - String expected_md5 = "526c93b0fa660d6b953b57103e59fe98"; + String expected_md5 = "22211a5da34a45b3b6045dbcbce8fede"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5)); executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec); } @@ -115,7 +115,7 @@ public class PileupWalkerIntegrationTest extends WalkerTest { + "-R " + hg18Reference + " -outputInsertLength" + " -L chr15:46,347,148 -o %s"; - String expected_md5 = "53ced173768f3d4d90b8a8206e72eae5"; + String expected_md5 = "cae23b79598b23feec665704f5578897"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5)); executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases (with insert length)", spec); } diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java index 53acd511c..17cc7c367 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -56,9 +56,9 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "ec4cf54ed50a6baf69dbf98782c19aeb"); } @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "a9cf540e4ed2514061248a878e09a09c"); } - @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "906871df304dd966682e5798d59fc86b"); } + @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "906871df304dd966682e5798d59fc86b"); } - @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "b41995fea04034ca0427c4a71504ef83"); } + @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "b41995fea04034ca0427c4a71504ef83"); } @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); } @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "195b8bdfc0186fdca742764aa9b06363"); } diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java index cc436e1f9..8f848aa01 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -66,7 +66,7 @@ public class PrintReadsIntegrationTest extends WalkerTest { // See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance() {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "0b58c903f54e8543a8b2ce1439aa769b")}, {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "5b1154cc81dba6bcfe76188e4df8d79c")}, - {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "e9caf8a0e6ec947cdcbdfc48a4292eb5")}, + {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "a84efdc3d4a8d6329b5f0b494dd280d2")}, {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")}, {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")}, {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "", "e212d1799ae797e781b17e630656a9a1")}, diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java index 5d1b6c056..c374e9de7 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsLargeScaleTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java index c0aec4329..3b88a8e08 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java index 87589a50c..a316dffe7 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java index d656abae7..62318967c 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/ASEReadCounterIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -26,6 +26,7 @@ package org.broadinstitute.gatk.tools.walkers.rnaseq; import org.broadinstitute.gatk.engine.walkers.WalkerTest; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.testng.annotations.Test; import java.util.Arrays; @@ -100,6 +101,14 @@ public class ASEReadCounterIntegrationTest extends WalkerTest { executeTest("test high mq with no read passing", spec); } + @Test + public void testASEReadCounterNonRef() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + "-T ASEReadCounter -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -sites "+privateTestDir +"NA12878.chr20_2444518_2637800.RNAseq.NonRef.vcf -U ALLOW_N_CIGAR_READS", 0, + UserException.class); + executeTest("test sites VCF file", spec); + } + diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java index df61b7c9a..f31b2cdf3 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java index 9e893a09f..d7ba67fd0 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -55,7 +55,7 @@ public class VCFIntegrationTest extends WalkerTest { @Test(enabled = true) public void testReadingAndWritingWitHNoChanges() { - String md5ofInputVCF = "3dc9ac85f2c0541df9bc57b4d81f480b"; + String md5ofInputVCF = "a492a97a8d18ace8eeef02a6fe5f179b"; String testVCF = privateTestDir + "vcf4.1.example.vcf"; String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; diff --git a/public/gatk-utils/pom.xml b/public/gatk-utils/pom.xml index 75884d774..7b7c7f102 100644 --- a/public/gatk-utils/pom.xml +++ b/public/gatk-utils/pom.xml @@ -5,7 +5,7 @@ org.broadinstitute.gatk gatk-aggregator - 3.5 + 3.6-SNAPSHOT ../.. @@ -66,6 +66,10 @@ org.apache.commons commons-math + + org.apache.commons + commons-math3 + net.java.dev.jna jna diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java index be38c06cb..b3b773d96 100644 --- a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java +++ b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java index d9698c38d..8ead6a56c 100644 --- a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java +++ b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKBin.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java index 1a10819a8..34aed5a82 100644 --- a/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java +++ b/public/gatk-utils/src/main/java/htsjdk/samtools/GATKChunk.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java b/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java index f861ccbbe..aba557b98 100644 --- a/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java +++ b/public/gatk-utils/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java index e77ff641a..59f29080b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/AutoFormattingTime.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java index f0ed568ab..3cf5e0873 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BaseUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java index 20b602642..d0863f479 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/BitSetUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java index a069415df..e0917d28f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ContigComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java index 53613ca2a..00097db21 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/DeprecatedToolChecks.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -58,6 +58,7 @@ public class DeprecatedToolChecks { deprecatedGATKWalkers.put("LiftOverVariants","3.5 (use Picard LiftoverVCF instead; see documentation for usage)"); deprecatedGATKWalkers.put("FilterLiftedVariants","3.5 (use Picard LiftoverVCF instead; see documentation for usage)"); deprecatedGATKWalkers.put("ListAnnotations","3.5 (this tool was impractical; see the online documentation instead)"); + deprecatedGATKWalkers.put("GenotypeAndValidate","3.6 (this tool was old and untested -- no direct replacement)"); } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java index d41072adb..c64d5798f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLoc.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -540,7 +540,7 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome * * @return a newly allocated GenomeLoc as loc but with start == start */ - public GenomeLoc setStart(GenomeLoc loc, int start) { + public static GenomeLoc setStart(GenomeLoc loc, int start) { return new GenomeLoc(loc.getContig(), loc.getContigIndex(), start, loc.getStop()); } @@ -554,7 +554,7 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome * * @return a newly allocated GenomeLoc as loc but with stop == stop */ - public GenomeLoc setStop(GenomeLoc loc, int stop) { + public static GenomeLoc setStop(GenomeLoc loc, int stop) { return new GenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start, stop); } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java index 9cac5d536..d6d5b02e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -28,15 +28,18 @@ package org.broadinstitute.gatk.utils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import com.google.java.contract.ThrowEnsures; -import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.samtools.SAMRecord; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; -import org.apache.log4j.Logger; +import htsjdk.samtools.reference.ReferenceSequenceFile; import htsjdk.tribble.Feature; +import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + /** * Factory class for creating GenomeLocs */ @@ -105,6 +108,7 @@ public final class GenomeLocParser { this(seqDict, ValidationLevel.STANDARD); } + static public String AMBIGUOUS_CONTIG_WARNINIG = "Ambiguous contig prefix!"; /** * Create a genome loc parser based on seqDict with the specified level of validation * @param seqDict the sequence dictionary to use when creating genome locs @@ -126,6 +130,24 @@ public final class GenomeLocParser { logger.debug(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength())); } } + + final Pattern numericEnding = Pattern.compile(".*:[0-9][0-9,]*(\\+|-[0-9][0-9,]*)?$"); + for(final SAMSequenceRecord contig1: this.getContigs().getSequences()) { + final String name1 = contig1.getSequenceName(); + for (final SAMSequenceRecord contig2 : this.getContigs().getSequences()) { + if (contig1 == contig2) continue; + final String name2 = contig2.getSequenceName(); + + final Matcher numericMatcher = numericEnding.matcher(name1); + if (name1.startsWith(name2) && numericMatcher.matches()) { + logger.warn(AMBIGUOUS_CONTIG_WARNINIG); + logger.warn("Contig name" + name1 + " has a prefix that is also the name of another contig (" + + name1 + + "), and has an ending that looks like a genomic position. The contigs in this reference may not parse reliably." + + " In addition, the existence of a colon (:) in the contig name is not compliant with the VCF specifications (1.4.1.1)."); + } + } + } } /** @@ -350,7 +372,7 @@ public final class GenomeLocParser { @Requires("str != null") @Ensures("result != null") public GenomeLoc parseGenomeLoc(final String str) { - // 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000' + // 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000' or 'chr2:500+' //System.out.printf("Parsing location '%s'%n", str); String contig = null; @@ -358,15 +380,15 @@ public final class GenomeLocParser { int stop = -1; final int colonIndex = str.lastIndexOf(":"); - if(colonIndex == -1) { - contig = str.substring(0, str.length()); // chr1 + if (colonIndex == -1 || contigIsInDictionary(str) ) { + contig = str; // chr1 stop = Integer.MAX_VALUE; } else { contig = str.substring(0, colonIndex); final int dashIndex = str.indexOf('-', colonIndex); try { - if(dashIndex == -1) { - if(str.charAt(str.length() - 1) == '+') { + if (dashIndex == -1) { + if (str.charAt(str.length() - 1) == '+') { start = parsePosition(str.substring(colonIndex + 1, str.length() - 1)); // chr:1+ stop = Integer.MAX_VALUE; } else { @@ -377,7 +399,7 @@ public final class GenomeLocParser { start = parsePosition(str.substring(colonIndex + 1, dashIndex)); // chr1:1-1 stop = parsePosition(str.substring(dashIndex + 1)); } - } catch(Exception e) { + } catch (Exception e) { throw new UserException("Failed to parse Genome Location string: " + str, e); } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java index 6e777df29..dcb9476f8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/GenomeLocSortedSet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java index d0309193f..6d9647f02 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HasGenomeLocation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java index b158794ad..fa84259df 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/HeapSizeMonitor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java index 83003d24a..a9d767285 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/IndelUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java index ed985c418..243ad95d9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/LRUCache.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java index b2c2d1a5a..df7e396e8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequenceDictionary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java index a768a1c55..f16178d26 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -25,483 +25,541 @@ package org.broadinstitute.gatk.utils; -import cern.jet.math.Arithmetic; -import cern.jet.random.Normal; -import com.google.java.contract.Ensures; -import com.google.java.contract.Requires; -import org.apache.commons.math.MathException; -import org.apache.commons.math.distribution.NormalDistribution; -import org.apache.commons.math.distribution.NormalDistributionImpl; -import org.broadinstitute.gatk.utils.collections.Pair; -import org.broadinstitute.gatk.utils.exceptions.GATKException; +import htsjdk.samtools.util.Histogram; +import org.apache.commons.math3.distribution.NormalDistribution; +import org.apache.log4j.Logger; -import java.io.Serializable; -import java.util.Comparator; -import java.util.TreeSet; + +import java.util.*; +import java.util.concurrent.ConcurrentHashMap; /** - * Created by IntelliJ IDEA. - * User: chartl + * Imported with changes from Picard private. + * + * @author Tim Fennell */ public class MannWhitneyU { - private static Normal STANDARD_NORMAL = new Normal(0.0,1.0,null); - private static NormalDistribution APACHE_NORMAL = new NormalDistributionImpl(0.0,1.0,1e-2); - private static double LNSQRT2PI = Math.log(Math.sqrt(2.0*Math.PI)); + protected static Logger logger = Logger.getLogger(MannWhitneyU.class); - private TreeSet> observations; - private int sizeSet1; - private int sizeSet2; - private ExactMode exactMode; + private static final class Rank implements Comparable { + final double value; + float rank; + final int series; - public MannWhitneyU(ExactMode mode, boolean dither) { - if ( dither ) - observations = new TreeSet>(new DitheringComparator()); - else - observations = new TreeSet>(new NumberedPairComparator()); - sizeSet1 = 0; - sizeSet2 = 0; - exactMode = mode; - } - - public MannWhitneyU() { - this(ExactMode.POINT,true); - } - - public MannWhitneyU(boolean dither) { - this(ExactMode.POINT,dither); - } - - public MannWhitneyU(ExactMode mode) { - this(mode,true); - } - - /** - * Add an observation into the observation tree - * @param n: the observation (a number) - * @param set: whether the observation comes from set 1 or set 2 - */ - public void add(Number n, USet set) { - observations.add(new Pair(n,set)); - if ( set == USet.SET1 ) { - ++sizeSet1; - } else { - ++sizeSet2; - } - } - - public Pair getR1R2() { - long u1 = calculateOneSidedU(observations,MannWhitneyU.USet.SET1); - long n1 = sizeSet1*(sizeSet1+1)/2; - long r1 = u1 + n1; - long n2 = sizeSet2*(sizeSet2+1)/2; - long u2 = n1*n2-u1; - long r2 = u2 + n2; - - return new Pair(r1,r2); - } - - /** - * Runs the one-sided test under the hypothesis that the data in set "lessThanOther" stochastically - * dominates the other set - * @param lessThanOther - either Set1 or Set2 - * @return - u-based z-approximation, and p-value associated with the test (p-value is exact for small n,m) - */ - @Requires({"lessThanOther != null"}) - @Ensures({"validateObservations(observations) || Double.isNaN(result.getFirst())","result != null", "! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"}) - public Pair runOneSidedTest(USet lessThanOther) { - long u = calculateOneSidedU(observations, lessThanOther); - int n = lessThanOther == USet.SET1 ? sizeSet1 : sizeSet2; - int m = lessThanOther == USet.SET1 ? sizeSet2 : sizeSet1; - if ( n == 0 || m == 0 ) { - // test is uninformative as one or both sets have no observations - return new Pair(Double.NaN,Double.NaN); + private Rank(double value, float rank, int series) { + this.value = value; + this.rank = rank; + this.series = series; } - // the null hypothesis is that {N} is stochastically less than {M}, so U has counted - // occurrences of {M}s before {N}s. We would expect that this should be less than (n*m+1)/2 under - // the null hypothesis, so we want to integrate from K=0 to K=U for cumulative cases. Always. - return calculateP(n, m, u, false, exactMode); - } - - /** - * Runs the standard two-sided test, - * returns the u-based z-approximate and p values. - * @return a pair holding the u and p-value. - */ - @Ensures({"result != null", "! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"}) - //@Requires({"validateObservations(observations)"}) - public Pair runTwoSidedTest() { - Pair uPair = calculateTwoSidedU(observations); - long u = uPair.first; - int n = uPair.second == USet.SET1 ? sizeSet1 : sizeSet2; - int m = uPair.second == USet.SET1 ? sizeSet2 : sizeSet1; - if ( n == 0 || m == 0 ) { - // test is uninformative as one or both sets have no observations - return new Pair(Double.NaN,Double.NaN); - } - return calculateP(n, m, u, true, exactMode); - } - - /** - * Given a u statistic, calculate the p-value associated with it, dispatching to approximations where appropriate - * @param n - The number of entries in the stochastically smaller (dominant) set - * @param m - The number of entries in the stochastically larger (dominated) set - * @param u - the Mann-Whitney U value - * @param twoSided - is the test twosided - * @return the (possibly approximate) p-value associated with the MWU test, and the (possibly approximate) z-value associated with it - * todo -- there must be an approximation for small m and large n - */ - @Requires({"m > 0","n > 0"}) - @Ensures({"result != null", "! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"}) - protected static Pair calculateP(int n, int m, long u, boolean twoSided, ExactMode exactMode) { - Pair zandP; - if ( n > 8 && m > 8 ) { - // large m and n - normal approx - zandP = calculatePNormalApproximation(n,m,u, twoSided); - } else if ( n > 5 && m > 7 ) { - // large m, small n - sum uniform approx - // todo -- find the appropriate regimes where this approximation is actually better enough to merit slowness - // pval = calculatePUniformApproximation(n,m,u); - zandP = calculatePNormalApproximation(n, m, u, twoSided); - } else if ( n > 8 || m > 8 ) { - zandP = calculatePFromTable(n, m, u, twoSided); - } else { - // small m and n - full approx - zandP = calculatePRecursively(n,m,u,twoSided,exactMode); + @Override + public int compareTo(Rank that) { + return (int) (this.value - that.value); } - return zandP; - } - - public static Pair calculatePFromTable(int n, int m, long u, boolean twoSided) { - // todo -- actually use a table for: - // todo - n large, m small - return calculatePNormalApproximation(n,m,u, twoSided); - } - - /** - * Uses a normal approximation to the U statistic in order to return a cdf p-value. See Mann, Whitney [1947] - * @param n - The number of entries in the stochastically smaller (dominant) set - * @param m - The number of entries in the stochastically larger (dominated) set - * @param u - the Mann-Whitney U value - * @param twoSided - whether the test should be two sided - * @return p-value associated with the normal approximation - */ - @Requires({"m > 0","n > 0"}) - @Ensures({"result != null", "! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"}) - public static Pair calculatePNormalApproximation(int n,int m,long u, boolean twoSided) { - double z = getZApprox(n,m,u); - if ( twoSided ) { - return new Pair(z,2.0*(z < 0 ? STANDARD_NORMAL.cdf(z) : 1.0-STANDARD_NORMAL.cdf(z))); - } else { - return new Pair(z,STANDARD_NORMAL.cdf(z)); + @Override + public String toString() { + return "Rank{" + + "value=" + value + + ", rank=" + rank + + ", series=" + series + + '}'; } } /** - * Calculates the Z-score approximation of the u-statistic - * @param n - The number of entries in the stochastically smaller (dominant) set - * @param m - The number of entries in the stochastically larger (dominated) set - * @param u - the Mann-Whitney U value - * @return the asymptotic z-approximation corresponding to the MWU p-value for n < m + * The results of performing a rank sum test. */ - @Requires({"m > 0","n > 0"}) - @Ensures({"! Double.isNaN(result)", "! Double.isInfinite(result)"}) - private static double getZApprox(int n, int m, long u) { - double mean = ( ((long)m)*n+1.0)/2; - double var = (((long) n)*m*(n+m+1.0))/12; - double z = ( u - mean )/Math.sqrt(var); - return z; + public static class Result { + private final double u; + private final double z; + private final double p; + private final double medianShift; + + public Result(double u, double z, double p, double medianShift) { + this.u = u; + this.z = z; + this.p = p; + this.medianShift = medianShift; + } + + public double getU() { + return u; + } + + public double getZ() { + return z; + } + + public double getP() { + return p; + } + + public double getMedianShift() { + return medianShift; + } } /** - * Uses a sum-of-uniform-0-1 random variable approximation to the U statistic in order to return an approximate - * p-value. See Buckle, Kraft, van Eeden [1969] (approx) and Billingsly [1995] or Stephens, MA [1966, biometrika] (sum of uniform CDF) - * @param n - The number of entries in the stochastically smaller (dominant) set - * @param m - The number of entries in the stochastically larger (dominated) set - * @param u - mann-whitney u value - * @return p-value according to sum of uniform approx - * todo -- this is currently not called due to not having a good characterization of where it is significantly more accurate than the - * todo -- normal approxmation (e.g. enough to merit the runtime hit) + * The values of U1, U2 and the transformed number of ties needed for the calculation of sigma + * in the normal approximation. */ - public static double calculatePUniformApproximation(int n, int m, long u) { - long R = u + (n*(n+1))/2; - double a = Math.sqrt(m*(n+m+1)); - double b = (n/2.0)*(1-Math.sqrt((n+m+1)/m)); - double z = b + ((double)R)/a; - if ( z < 0 ) { return 1.0; } - else if ( z > n ) { return 0.0; } - else { - if ( z > ((double) n) /2 ) { - return 1.0-1/(Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); - } else { - return 1/(Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); + public static class TestStatistic { + private final double u1; + private final double u2; + private final double trueU; + private final double numOfTiesTransformed; + + public TestStatistic(double u1, double u2, double numOfTiesTransformed) { + this.u1 = u1; + this.u2 = u2; + this.numOfTiesTransformed = numOfTiesTransformed; + this.trueU = Double.NaN; + } + + public TestStatistic(double trueU, double numOfTiesTransformed) { + this.trueU = trueU; + this.numOfTiesTransformed = numOfTiesTransformed; + this.u1 = Double.NaN; + this.u2 = Double.NaN; + } + + public double getU1() { + return u1; + } + + public double getU2() { + return u2; + } + + public double getTies() { + return numOfTiesTransformed; + } + + public double getTrueU() { + return trueU; + } + } + + /** + * The ranked data in one list and a list of the number of ties. + */ + public static class RankedData { + private final Rank[] rank; + private final ArrayList numOfTies; + + public RankedData(Rank[] rank, ArrayList numOfTies) { + this.rank = rank; + this.numOfTies = numOfTies; + } + + public Rank[] getRank() { + return rank; + } + + public ArrayList getNumOfTies() { + return numOfTies; + } + } + + /** + * Key for the map from Integer[] to set of all permutations of that array. + */ + private static class Key { + final Integer[] listToPermute; + + private Key(Integer[] listToPermute) { + this.listToPermute = listToPermute; + } + + @Override + public boolean equals(Object o) { + if (o == null || getClass() != o.getClass()) return false; + + Key that = (Key) o; + return (Arrays.deepEquals(this.listToPermute, that.listToPermute)); + } + + @Override + public int hashCode() { + int result = 17; + for (Integer i : listToPermute) { + result = 31 * result + listToPermute[i]; } + return result; } } + // Constructs a normal distribution; this needs to be a standard normal in order to get a Z-score in the exact case + private static final double NORMAL_MEAN = 0; + private static final double NORMAL_SD = 1; + private static final NormalDistribution NORMAL = new NormalDistribution(NORMAL_MEAN, NORMAL_SD); + /** - * Helper function for the sum of n uniform random variables - * @param z - value at which to compute the (un-normalized) cdf - * @param m - a cutoff integer (defined by m <= z < m + 1) - * @param n - the number of uniform random variables - * @param k - holder variable for the recursion (alternatively, the index of the term in the sequence) - * @return the (un-normalized) cdf for the sum of n random variables + * A map of an Integer[] of the labels to the set of all possible permutations of those labels. */ - private static double uniformSumHelper(double z, int m, int n, int k) { - if ( k > m ) { return 0; } - int coef = (k % 2 == 0) ? 1 : -1; - return coef*Arithmetic.binomial(n,k)*Math.pow(z-k,n) + uniformSumHelper(z,m,n,k+1); + private static Map>> PERMUTATIONS = new ConcurrentHashMap>>(); + + /** + * The minimum length for both data series in order to use a normal distribution + * to calculate Z and p. If both series are shorter than this value then a permutation test + * will be used. + */ + private int minimumNormalN = 10; + + /** + * Sets the minimum number of values in each data series to use the normal distribution approximation. + */ + public void setMinimumSeriesLengthForNormalApproximation(final int n) { + this.minimumNormalN = n; } /** - * Calculates the U-statistic associated with a two-sided test (e.g. the RV from which one set is drawn - * stochastically dominates the RV from which the other set is drawn); two-sidedness is accounted for - * later on simply by multiplying the p-value by 2. - * - * Recall: If X stochastically dominates Y, the test is for occurrences of Y before X, so the lower value of u is chosen - * @param observed - the observed data - * @return the minimum of the U counts (set1 dominates 2, set 2 dominates 1) + * A variable that indicates if the test is one sided or two sided and if it's one sided + * which group is the dominator in the null hypothesis. */ - @Requires({"observed != null", "observed.size() > 0"}) - @Ensures({"result != null","result.first > 0"}) - public static Pair calculateTwoSidedU(TreeSet> observed) { - int set1SeenSoFar = 0; - int set2SeenSoFar = 0; - long uSet1DomSet2 = 0; - long uSet2DomSet1 = 0; - USet previous = null; - for ( Pair dataPoint : observed ) { + public enum TestType { + FIRST_DOMINATES, + SECOND_DOMINATES, + TWO_SIDED + } - if ( dataPoint.second == USet.SET1 ) { - ++set1SeenSoFar; - } else { - ++set2SeenSoFar; - } + public RankedData calculateRank(final double[] series1, final double[] series2) { + Arrays.sort(series1); + Arrays.sort(series2); - if ( previous != null ) { - if ( dataPoint.second == USet.SET1 ) { - uSet2DomSet1 += set2SeenSoFar; + // Make a merged ranks array + final Rank[] ranks = new Rank[series1.length + series2.length]; + { + int i = 0, j = 0, r = 0; + while (r < ranks.length) { + if (i >= series1.length) { + ranks[r++] = new Rank(series2[j++], r, 2); + } else if (j >= series2.length) { + ranks[r++] = new Rank(series1[i++], r, 1); + } else if (series1[i] <= series2[j]) { + ranks[r++] = new Rank(series1[i++], r, 1); } else { - uSet1DomSet2 += set1SeenSoFar; + ranks[r++] = new Rank(series2[j++], r, 2); } } - - previous = dataPoint.second; } - return uSet1DomSet2 < uSet2DomSet1 ? new Pair(uSet1DomSet2,USet.SET1) : new Pair(uSet2DomSet1,USet.SET2); + ArrayList numOfTies = new ArrayList<>(); + + // Now sort out any tie bands + for (int i = 0; i < ranks.length; ) { + float rank = ranks[i].rank; + int count = 1; + + for (int j = i + 1; j < ranks.length && ranks[j].value == ranks[i].value; ++j) { + rank += ranks[j].rank; + ++count; + } + + if (count > 1) { + rank /= count; + for (int j = i; j < i + count; ++j) { + ranks[j].rank = rank; + } + numOfTies.add(count); + } + + // Skip forward the right number of items + i += count; + } + + return new RankedData(ranks, numOfTies); } /** - * Calculates the U-statistic associated with the one-sided hypothesis that "dominator" stochastically dominates - * the other U-set. Note that if S1 dominates S2, we want to count the occurrences of points in S2 coming before points in S1. - * @param observed - the observed data points, tagged by each set - * @param dominator - the set that is hypothesized to be stochastically dominating - * @return the u-statistic associated with the hypothesis that dominator stochastically dominates the other set + * Rank both groups together and return a TestStatistic object that includes U1, U2 and number of ties for sigma */ - @Requires({"observed != null","dominator != null","observed.size() > 0"}) - @Ensures({"result >= 0"}) - public static long calculateOneSidedU(TreeSet> observed,USet dominator) { - long otherBeforeDominator = 0l; - int otherSeenSoFar = 0; - for ( Pair dataPoint : observed ) { - if ( dataPoint.second != dominator ) { - ++otherSeenSoFar; - } else { - otherBeforeDominator += otherSeenSoFar; + public TestStatistic calculateU1andU2(final double[] series1, final double[] series2) { + RankedData ranked = calculateRank(series1, series2); + Rank[] ranks = ranked.getRank(); + ArrayList numOfTies = ranked.getNumOfTies(); + + //Calculate number of ties transformed for formula for Sigma to calculate Z-score + ArrayList transformedTies = new ArrayList<>(); + for (int count : numOfTies) { + //If every single datapoint is tied then we want to return a p-value of .5 and + //the formula for sigma that includes the number of ties breaks down. Setting + //the number of ties to 0 in this case gets the desired result in the normal + //approximation case. + if (count != ranks.length) { + transformedTies.add((count * count * count) - count); } } - return otherBeforeDominator; + double numOfTiesForSigma = 0.0; + for (int count : transformedTies) { + numOfTiesForSigma += count; + } + + // Calculate R1 and R2 and U. + float r1 = 0, r2 = 0; + for (Rank rank : ranks) { + if (rank.series == 1) r1 += rank.rank; + else r2 += rank.rank; + } + + double n1 = series1.length; + double n2 = series2.length; + double u1 = r1 - ((n1 * (n1 + 1)) / 2); + double u2 = r2 - ((n2 * (n2 + 1)) / 2); + + TestStatistic result = new TestStatistic(u1, u2, numOfTiesForSigma); + return result; } /** - * The Mann-Whitney U statistic follows a recursive equation (that enumerates the proportion of possible - * binary strings of "n" zeros, and "m" ones, where a one precedes a zero "u" times). This accessor - * calls into that recursive calculation. - * @param n: number of set-one entries (hypothesis: set one is stochastically less than set two) - * @param m: number of set-two entries - * @param u: number of set-two entries that precede set-one entries (e.g. 0,1,0,1,0 -> 3 ) - * @param twoSided: whether the test is two sided or not. The recursive formula is symmetric, multiply by two for two-sidedness. - * @param mode: whether the mode is a point probability, or a cumulative distribution - * @return the probability under the hypothesis that all sequences are equally likely of finding a set-two entry preceding a set-one entry "u" times. + * Calculates the rank-sum test statisic U (sometimes W) from two sets of input data for a one-sided test + * with an int indicating which group is the dominator. Returns a test statistic object with trueU and number of + * ties for sigma. */ - @Requires({"m > 0","n > 0","u >= 0"}) - @Ensures({"result != null","! Double.isInfinite(result.getFirst())", "! Double.isInfinite(result.getSecond())"}) - public static Pair calculatePRecursively(int n, int m, long u, boolean twoSided, ExactMode mode) { - if ( m > 8 && n > 5 ) { throw new GATKException(String.format("Please use the appropriate (normal or sum of uniform) approximation. Values n: %d, m: %d",n,m)); } - double p = mode == ExactMode.POINT ? cpr(n,m,u) : cumulativeCPR(n,m,u); - //p *= twoSided ? 2.0 : 1.0; + public TestStatistic calculateOneSidedU(final double[] series1, final double[] series2, final TestType whichSeriesDominates) { + TestStatistic stat = calculateU1andU2(series1, series2); + TestStatistic result; + if (whichSeriesDominates == TestType.FIRST_DOMINATES) { + result = new TestStatistic(stat.getU1(), stat.getTies()); + } else { + result = new TestStatistic(stat.getU2(), stat.getTies()); + } + return result; + } + + /** + * Calculates the two-sided rank-sum test statisic U (sometimes W) from two sets of input data. + * Returns a test statistic object with trueU and number of ties for sigma. + */ + public TestStatistic calculateTwoSidedU(final double[] series1, final double[] series2) { + TestStatistic u1AndU2 = calculateU1andU2(series1, series2); + double u = Math.min(u1AndU2.getU1(), u1AndU2.getU2()); + TestStatistic result = new TestStatistic(u, u1AndU2.getTies()); + return result; + } + + /** + * Calculates the Z score (i.e. standard deviations from the mean) of the rank sum + * test statistics given input data of lengths n1 and n2 respectively, as well as the number of ties, for normal + * approximation only. + */ + public double calculateZ(final double u, final int n1, final int n2, final double nties, final TestType whichSide) { + double m = (n1 * n2) / 2d; + + //Adds a continuity correction + double correction; + if (whichSide == TestType.TWO_SIDED) { + correction = (u - m) >= 0 ? .5 : -.5; + } else { + correction = whichSide == TestType.FIRST_DOMINATES ? -.5 : .5; + } + + //If all the data is tied, the number of ties for sigma is set to 0. In order to get a p-value of .5 we need to + //remove the continuity correction. + if (nties == 0) { + correction = 0; + } + + double sigma = Math.sqrt((n1 * n2 / 12d) * ((n1 + n2 + 1) - nties / ((n1 + n2) * (n1 + n2 - 1)))); + return (u - m - correction) / sigma; + } + + /** + * Finds or calculates the median value of a sorted array of double. + */ + public double median(final double[] data) { + final int len = data.length; + final int mid = len / 2; + if (data.length % 2 == 0) { + return (data[mid] + data[mid - 1]) / 2d; + } else { + return data[mid]; + } + } + + + /** + * Constructs a new rank sum test with the given data. + * + * @param series1 group 1 data + * @param series2 group 2 data + * @param whichSide indicator of two sided test, 0 for two sided, 1 for series1 as dominator, 2 for series2 as dominator + * @return Result including U statistic, Z score, p-value, and difference in medians. + */ + public Result test(final double[] series1, final double[] series2, final TestType whichSide) { + final int n1 = series1.length; + final int n2 = series2.length; + + //If one of the groups is empty we return NaN + if (n1 == 0 || n2 == 0) { + return new Result(Float.NaN, Float.NaN, Float.NaN, Float.NaN); + } + + double u; + double nties; + + if (whichSide == TestType.TWO_SIDED) { + TestStatistic result = calculateTwoSidedU(series1, series2); + u = result.getTrueU(); + nties = result.getTies(); + } else { + TestStatistic result = calculateOneSidedU(series1, series2, whichSide); + u = result.getTrueU(); + nties = result.getTies(); + } + double z; - try { + double p; - if ( mode == ExactMode.CUMULATIVE ) { - z = APACHE_NORMAL.inverseCumulativeProbability(p); - } else { - double sd = Math.sqrt((1.0+1.0/(1+n+m))*(n*m)*(1.0+n+m)/12); // biased variance empirically better fit to distribution then asymptotic variance - //System.out.printf("SD is %f and Max is %f and prob is %f%n",sd,1.0/Math.sqrt(sd*sd*2.0*Math.PI),p); - if ( p > 1.0/Math.sqrt(sd*sd*2.0*Math.PI) ) { // possible for p-value to be outside the range of the normal. Happens at the mean, so z is 0. - z = 0.0; - } else { - if ( u >= n*m/2 ) { - z = Math.sqrt(-2.0*(Math.log(sd)+Math.log(p)+LNSQRT2PI)); - } else { - z = -Math.sqrt(-2.0*(Math.log(sd)+Math.log(p)+LNSQRT2PI)); - } + if (n1 >= this.minimumNormalN || n2 >= this.minimumNormalN) { + z = calculateZ(u, n1, n2, nties, whichSide); + p = 2 * NORMAL.cumulativeProbability(NORMAL_MEAN + z * NORMAL_SD); + if (whichSide != TestType.TWO_SIDED) { + p = p / 2; + } + } else { + // TODO -- This exact test is only implemented for the one sided test, but we currently don't call the two sided version + if (whichSide != TestType.FIRST_DOMINATES) { + logger.warn("An exact two-sided MannWhitneyU test was called. Only the one-sided exact test is implemented, use the approximation instead by setting minimumNormalN to 0."); + } + p = permutationTest(series1, series2, u); + z = NORMAL.inverseCumulativeProbability(p); + } + + return new Result(u, z, p, Math.abs(median(series1) - median(series2))); + } + + private void swap(Integer[] arr, int i, int j) { + int temp = arr[i]; + arr[i] = arr[j]; + arr[j] = temp; + } + + /** + * Uses a method that generates permutations in lexicographic order. (https://en.wikipedia.org/wiki/Permutation#Generation_in_lexicographic_order) + * @param temp Sorted list of elements to be permuted. + * @param allPermutations Empty set that will hold all possible permutations. + */ + private void calculatePermutations(Integer[] temp, Set> allPermutations) { + allPermutations.add(new ArrayList<>(Arrays.asList(temp))); + while (true) { + int k = -1; + for (int i = temp.length - 2; i >= 0; i--) { + if (temp[i] < temp[i + 1]) { + k = i; + break; } } - } catch (MathException me) { - throw new GATKException("A math exception occurred in inverting the probability",me); + if (k == -1) { + break; + } + + int l = -1; + for (int i = temp.length - 1; i >= k + 1; i--) { + if (temp[k] < temp[i]) { + l = i; + break; + } + } + + swap(temp, k, l); + + int end = temp.length - 1; + for (int begin = k + 1; begin < end; begin++) { + swap(temp, begin, end); + end--; + } + allPermutations.add(new ArrayList<>(Arrays.asList(temp))); } - - return new Pair(z,(twoSided ? 2.0*p : p)); } /** - * Hook into CPR with sufficient warning (for testing purposes) - * calls into that recursive calculation. - * @param n: number of set-one entries (hypothesis: set one is stochastically less than set two) - * @param m: number of set-two entries - * @param u: number of set-two entries that precede set-one entries (e.g. 0,1,0,1,0 -> 3 ) - * @return same as cpr + * Checks to see if the permutations have already been computed before creating them from scratch. + * @param listToPermute List of tags in numerical order to be permuted + * @param numOfPermutations The number of permutations this list will have (n1+n2 choose n1) + * @return Set of all possible permutations for the given list. */ - protected static double calculatePRecursivelyDoNotCheckValuesEvenThoughItIsSlow(int n, int m, long u) { - return cpr(n,m,u); + Set> getPermutations(final Integer[] listToPermute, int numOfPermutations) { + Key key = new Key(listToPermute); + Set> permutations = PERMUTATIONS.get(key); + if (permutations == null) { + permutations = new HashSet<>(numOfPermutations); + calculatePermutations(listToPermute, permutations); + PERMUTATIONS.put(key, permutations); + } + return permutations; } /** - * For testing + * Creates histogram of test statistics from a permutation test. * - * @param n: number of set-one entries (hypothesis: set one is stochastically less than set two) - * @param m: number of set-two entries - * @param u: number of set-two entries that precede set-one entries (e.g. 0,1,0,1,0 -> 3 ) + * @param series1 Data from group 1 + * @param series2 Data from group 2 + * @param testStatU Test statistic U from observed data + * @return P-value based on histogram with u calculated for every possible permutation of group tag. */ - protected static long countSequences(int n, int m, long u) { - if ( u < 0 ) { return 0; } - if ( m == 0 || n == 0 ) { return u == 0 ? 1 : 0; } + public double permutationTest(final double[] series1, final double[] series2, final double testStatU) { + final Histogram histo = new Histogram(); + final int n1 = series1.length; + final int n2 = series2.length; - return countSequences(n-1,m,u-m) + countSequences(n,m-1,u); - } + RankedData rankedGroups = calculateRank(series1, series2); + Rank[] ranks = rankedGroups.getRank(); - /** - * : just a shorter name for calculatePRecursively. See Mann, Whitney, [1947] - * @param n: number of set-1 entries - * @param m: number of set-2 entries - * @param u: number of times a set-2 entry as preceded a set-1 entry - * @return recursive p-value - */ - private static double cpr(int n, int m, long u) { - if ( u < 0 ) { - return 0.0; - } - if ( m == 0 || n == 0 ) { - // there are entries in set 1 or set 2, so no set-2 entry can precede a set-1 entry; thus u must be zero. - // note that this exists only for edification, as when we reach this point, the coefficient on this term is zero anyway - return ( u == 0 ) ? 1.0 : 0.0; - } + Integer[] firstPermutation = new Integer[n1 + n2]; - - return (((double)n)/(n+m))*cpr(n-1,m,u-m) + (((double)m)/(n+m))*cpr(n,m-1,u); - } - - private static double cumulativeCPR(int n, int m, long u ) { - // from above: - // the null hypothesis is that {N} is stochastically less than {M}, so U has counted - // occurrences of {M}s before {N}s. We would expect that this should be less than (n*m+1)/2 under - // the null hypothesis, so we want to integrate from K=0 to K=U for cumulative cases. Always. - double p = 0.0; - // optimization using symmetry, use the least amount of sums possible - long uSym = ( u <= n*m/2 ) ? u : ((long)n)*m-u; - for ( long uu = 0; uu < uSym; uu++ ) { - p += cpr(n,m,uu); - } - // correct by 1.0-p if the optimization above was used (e.g. 1-right tail = left tail) - return (u <= n*m/2) ? p : 1.0-p; - } - - /** - * hook into the data tree, for testing purposes only - * @return observations - */ - protected TreeSet> getObservations() { - return observations; - } - - /** - * hook into the set sizes, for testing purposes only - * @return size set 1, size set 2 - */ - protected Pair getSetSizes() { - return new Pair(sizeSet1,sizeSet2); - } - - /** - * Validates that observations are in the correct format for a MWU test -- this is only called by the contracts API during testing - * @param tree - the collection of labeled observations - * @return true iff the tree set is valid (no INFs or NaNs, at least one data point in each set) - */ - protected static boolean validateObservations(TreeSet> tree) { - boolean seen1 = false; - boolean seen2 = false; - boolean seenInvalid = false; - for ( Pair p : tree) { - if ( ! seen1 && p.getSecond() == USet.SET1 ) { - seen1 = true; + for (int i = 0; i < firstPermutation.length; i++) { + if (i < n1) { + firstPermutation[i] = 0; + } else { + firstPermutation[i] = 1; } + } - if ( ! seen2 && p.getSecond() == USet.SET2 ) { - seen2 = true; - } - - if ( Double.isNaN(p.getFirst().doubleValue()) || Double.isInfinite(p.getFirst().doubleValue())) { - seenInvalid = true; + final int numOfPerms = (int) MathUtils.binomialCoefficient(n1 + n2, n2); + Set> allPermutations = getPermutations(firstPermutation, numOfPerms); + + double[] newSeries1 = new double[n1]; + double[] newSeries2 = new double[n2]; + + //iterate over all permutations + for (List currPerm : allPermutations) { + int series1End = 0; + int series2End = 0; + for (int i = 0; i < currPerm.size(); i++) { + int grouping = currPerm.get(i); + if (grouping == 0) { + newSeries1[series1End] = ranks[i].rank; + series1End++; + } else { + newSeries2[series2End] = ranks[i].rank; + series2End++; + } } + assert (series1End == n1); + assert (series2End == n2); + double newU = MathUtils.sum(newSeries1) - ((n1 * (n1 + 1)) / 2.0); + histo.increment(newU); } - return ! seenInvalid && seen1 && seen2; - } + /** + * In order to deal with edge cases where the observed value is also the most extreme value, we are taking half + * of the count in the observed bin plus everything more extreme (in the FIRST_DOMINATES case the smaller bins) + * and dividing by the total count of everything in the histogram. Just using getCumulativeDistribution() gives + * a p-value of 1 in the most extreme case which doesn't result in a usable z-score. + */ + double sumOfAllSmallerBins = histo.get(testStatU).getValue() / 2.0; - /** - * A comparator class which uses dithering on tie-breaking to ensure that the internal treeset drops no values - * and to ensure that rank ties are broken at random. - */ - private static class DitheringComparator implements Comparator>, Serializable { - - public DitheringComparator() {} - - @Override - public boolean equals(Object other) { return false; } - - @Override - public int compare(Pair left, Pair right) { - double comp = Double.compare(left.first.doubleValue(),right.first.doubleValue()); - if ( comp > 0 ) { return 1; } - if ( comp < 0 ) { return -1; } - return Utils.getRandomGenerator().nextBoolean() ? -1 : 1; + for (final Histogram.Bin bin : histo.values()) { + if (bin.getId() < testStatU) sumOfAllSmallerBins += bin.getValue(); } + + return sumOfAllSmallerBins / histo.getCount(); } - /** - * A comparator that reaches into the pair and compares numbers without tie-braking. - */ - private static class NumberedPairComparator implements Comparator>, Serializable { - - public NumberedPairComparator() {} - - @Override - public boolean equals(Object other) { return false; } - - @Override - public int compare(Pair left, Pair right ) { - return Double.compare(left.first.doubleValue(),right.first.doubleValue()); - } - } - - public enum USet { SET1, SET2 } - public enum ExactMode { POINT, CUMULATIVE } - } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java index fb8e8d987..1bbb4c0c9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -315,11 +315,11 @@ public class MathUtils { return maxValue + (sum != 1.0 ? Math.log10(sum) : 0.0); } - public static double sumLog10(final double[] log10values) { + public static double sumLog10(final double ... log10values) { return Math.pow(10.0, log10sumLog10(log10values)); } - public static double log10sumLog10(final double[] log10values) { + public static double log10sumLog10(final double ... log10values) { return log10sumLog10(log10values, 0); } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java index 948332209..6639818c4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Median.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java index 3dfe13c19..a90b0d02b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MultiThreadedErrorTracker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java index 1b3af7066..55800c4f9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/NGSPlatform.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java index f2a8340b7..b06b83017 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/PathUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java index d67e5abc9..30aafde72 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/QualityUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java index 1ee279843..fda03c95f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java index 53ad3aca8..b493a7f26 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptExecutorException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java index 56f80e3e2..d9c05b2ae 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RScriptLibrary.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java index 982cfa371..2b3ad5f42 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/R/RUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java index 71d87409f..ef5004fa5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -111,6 +111,7 @@ public class SequenceDictionaryUtils { * @param dict2 the sequence dictionary dict2 * @param isReadsToReferenceComparison true if one of the dictionaries comes from a reads data source (eg., a BAM), * and the other from a reference data source + * @param enableContigOrderCheck enable checking the dictionary contig order * @param intervals the user-specified genomic intervals: only required when isReadsToReferenceComparison is true, * otherwise can be null */ @@ -121,9 +122,10 @@ public class SequenceDictionaryUtils { final String name2, final SAMSequenceDictionary dict2, final boolean isReadsToReferenceComparison, - final GenomeLocSortedSet intervals ) { + final GenomeLocSortedSet intervals, + final boolean enableContigOrderCheck ) { - final SequenceDictionaryCompatibility type = compareDictionaries(dict1, dict2); + final SequenceDictionaryCompatibility type = compareDictionaries(dict1, dict2, enableContigOrderCheck); switch ( type ) { case IDENTICAL: @@ -175,7 +177,7 @@ public class SequenceDictionaryUtils { case OUT_OF_ORDER: { UserException ex = new UserException.IncompatibleSequenceDictionaries( - "The contig order in " + name1 + " and " + name2 + "is not " + "The contig order in " + name1 + " and " + name2 + " is not " + "the same; to fix this please see: " + "(https://www.broadinstitute.org/gatk/guide/article?id=1328), " + " which describes reordering contigs in BAM and VCF files.", @@ -227,10 +229,12 @@ public class SequenceDictionaryUtils { * * @param dict1 first sequence dictionary * @param dict2 second sequence dictionary + * @param enableContigOrderCheck enable checking the dictionary contig order * @return A SequenceDictionaryCompatibility enum value describing the compatibility of the two dictionaries */ - public static SequenceDictionaryCompatibility compareDictionaries( final SAMSequenceDictionary dict1, final SAMSequenceDictionary dict2) { - if ( nonCanonicalHumanContigOrder(dict1) || nonCanonicalHumanContigOrder(dict2) ) + public static SequenceDictionaryCompatibility compareDictionaries( final SAMSequenceDictionary dict1, final SAMSequenceDictionary dict2, final boolean enableContigOrderCheck) { + + if ( enableContigOrderCheck && (nonCanonicalHumanContigOrder(dict1) || nonCanonicalHumanContigOrder(dict2)) ) return SequenceDictionaryCompatibility.NON_CANONICAL_HUMAN_ORDER; final Set commonContigs = getCommonContigsByName(dict1, dict2); @@ -239,7 +243,7 @@ public class SequenceDictionaryUtils { return SequenceDictionaryCompatibility.NO_COMMON_CONTIGS; else if ( ! commonContigsHaveSameLengths(commonContigs, dict1, dict2) ) return SequenceDictionaryCompatibility.UNEQUAL_COMMON_CONTIGS; - else if ( ! commonContigsAreInSameRelativeOrder(commonContigs, dict1, dict2) ) + else if ( enableContigOrderCheck && ! commonContigsAreInSameRelativeOrder(commonContigs, dict1, dict2) ) return SequenceDictionaryCompatibility.OUT_OF_ORDER; else if ( commonContigs.size() == dict1.size() && commonContigs.size() == dict2.size() ) return SequenceDictionaryCompatibility.IDENTICAL; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java index 466f42b9b..a08b8fd34 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SequencerFlowClass.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java index 5101064fd..6e3a6af48 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/SimpleTimer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java index 1b7ac79da..a284d6d6f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/UnvalidatingGenomeLoc.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java index ce54e8f11..f4bbb48b2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/Utils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java index c09ebe4cc..00ae68e02 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/ValidationExclusion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java index 8a4deb51d..1fc67d482 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java index 57fd35908..289a427b2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionReadState.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java index cdc7cb806..bf53ecd1b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfile.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java index a1df0baf6..544a4b6b4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileState.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java index 8458b3a96..76d035eca 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfile.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java index af61415aa..8c16c9702 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcid.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java index e8bd5d1ec..05030979e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidTable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java index 175ea369a..9d7a84445 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/analysis/AminoAcidUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java index 91562b69e..b56305d86 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/baq/BAQ.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java index 329dfa19b..973002b3e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/JVMUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java index 7ef7a154c..b2b6c731b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PluginManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java index 7a2b53696..80b18094f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/ProtectedPackageSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java index dd2068bbd..d6d5a3640 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/classloader/PublicPackageSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java index ad0de1da1..26147e2e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingOp.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java index 8d556515b..e757e23d1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ClippingRepresentation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java index 3710698a2..d39ebedca 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/clipping/ReadClipper.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java index 8eaa316c2..057e09bef 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java index 39908366c..57830f882 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java index 8f49dd063..dd6641427 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java index 2dc23fc55..fb84d7ae6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/hapmap/RawHapMapFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java index 4a2d15c31..78c5f5dff 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java index 62d4b05ba..15cceeb17 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java index b5bca03d4..922027d4d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/refseq/Transcript.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java index 407cf8962..3571dde69 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -37,7 +37,7 @@ import java.util.regex.Pattern; import static org.broadinstitute.gatk.utils.codecs.sampileup.SAMPileupFeature.VariantType; /** - * Decoder for SAM pileup data. + * Decoder for SAM pileup data * *

      * From the SAMTools project documentation: diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java index 1768c1328..8452b229a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java index 447aa4761..d83dee271 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -34,7 +34,7 @@ import htsjdk.tribble.readers.LineIterator; import htsjdk.tribble.util.ParsingUtils; /** - * Decodes a simple SAM text string. + * Decodes a simple SAM text string * *

      * Reads in the SAM text version of a BAM file as a ROD. For testing only diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java index fda2e692b..c95195704 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java index 84c071f19..23d8b843d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/BedTableCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java index 9908ed632..b1d973b16 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java index 7960e1fdc..c6e8eef4c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/codecs/table/TableFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java index 0ae22648b..456a735c4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/DefaultHashMap.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java index 2f8adc392..add892555 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java index 671548e64..81df590a7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/IndexedSet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java index 746bb2c32..37e19fce1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/LoggingNestedIntegerArray.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java index 495f3dda7..764f38698 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/NestedIntegerArray.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java index 11229cbeb..955d58bee 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Pair.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java index 522847e9a..1c0e805b2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/Permutation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java index 563578f0d..78cb83b78 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/PrimitivePair.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java index 634fb36fb..d87705716 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/collections/RODMergingIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java index a7a98c7c9..58ecf9660 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Advanced.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java index 300d04c61..3d43446c5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Argument.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -81,6 +81,15 @@ public @interface Argument { */ String exclusiveOf() default ""; + /** + * Does this command-line argument require other arguments to go with it? + * Should be a string containing the name of the required argument. + * This option only supports a single required argument. + * @return A string with the other argument that this + * argument should require in order to work. + */ + String otherArgumentRequired() default ""; + /** * Provide a regexp-based validation string. * @return Non-empty regexp for validation, blank otherwise. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java index 30ba236ce..3a77144ae 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java index f5b542446..8fd0c998d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinition.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -96,6 +96,11 @@ public class ArgumentDefinition { */ public final String exclusiveOf; + /** + * Does this argument require another argument? + */ + public final String otherArgumentRequired; + /** * Can we validate this regular expression? */ @@ -119,6 +124,7 @@ public class ArgumentDefinition { * @param isHidden Whether or not this argument should be hidden from the command-line argument system. * @param componentType For multivalued arguments the type of the components. * @param exclusiveOf Whether this command line argument is mutually exclusive of other arguments. + * @param otherArgumentRequired Other argument the current argument requires in order to work. * @param validation A regular expression for command-line argument validation. * @param validOptions is there a particular list of options that's valid for this argument definition? List them if so, otherwise set this to null. */ @@ -133,6 +139,7 @@ public class ArgumentDefinition { boolean isHidden, Class componentType, String exclusiveOf, + String otherArgumentRequired, String validation, List validOptions) { this.ioType = ioType; @@ -146,6 +153,7 @@ public class ArgumentDefinition { this.isHidden = isHidden; this.componentType = componentType; this.exclusiveOf = exclusiveOf; + this.otherArgumentRequired = otherArgumentRequired; this.validation = validation; this.validOptions = validOptions; @@ -177,6 +185,7 @@ public class ArgumentDefinition { boolean isHidden, Class componentType, String exclusiveOf, + String otherArgumentRequired, String validation, List validOptions) { @@ -210,6 +219,7 @@ public class ArgumentDefinition { this.isHidden = isHidden; this.componentType = componentType; this.exclusiveOf = exclusiveOf; + this.otherArgumentRequired = otherArgumentRequired; this.validation = validation; this.validOptions = validOptions; } @@ -275,6 +285,16 @@ public class ArgumentDefinition { return exclusiveOf.trim().length() > 0 ? exclusiveOf.trim() : null; } + /** + * Specifies other argument that is required to be used in conjunction with this argument. + * @param annotation Original field annotation. + * @return A required argument, or null if none are present. + */ + public static String getOtherArgumentRequired( Annotation annotation ) { + String otherArgumentRequired = ((String) CommandLineUtils.getValue(annotation, "otherArgumentRequired")).trim(); + return otherArgumentRequired.length() > 0 ? otherArgumentRequired : null; + } + /** * A regular expression which can be used for validation. * @param annotation Original field annotation. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java index d6e2cb504..8744fb3e6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitionGroup.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java index 77c747f89..83151f0e4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentDefinitions.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java index e0985983c..ae3cfd8c8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java index b51023421..1db4dbf33 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentIOType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java index bbabd5eea..23cf31f41 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatch.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java index db54fb505..a8d3c21cf 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchFileValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java index 095ea9e99..7e79ede95 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSite.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java index 229af987a..ef7952eba 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java index d7990480c..b9acb6fc9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java index b663b5920..e6c2b611c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchStringValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java index b6ebdcb8f..f49b017d5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java index 6edd75f18..3ead063a5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatches.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java index a8c4e3feb..66199b2dc 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentSource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java index c583fb93f..66a10ef00 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ArgumentTypeDescriptor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -166,6 +166,7 @@ public abstract class ArgumentTypeDescriptor { source.isHidden(), makeRawTypeIfNecessary(getCollectionComponentType(source.field)), ArgumentDefinition.getExclusiveOf(argumentAnnotation), + ArgumentDefinition.getOtherArgumentRequired(argumentAnnotation), ArgumentDefinition.getValidationRegex(argumentAnnotation), getValidOptions(source) ); } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java index 2753c8f6f..9fa736fbb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ClassType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java index f29978ede..4f5afcc08 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineProgram.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -40,6 +40,8 @@ import java.util.*; public abstract class CommandLineProgram { + private static final int NUM_WARN_MESSAGES = 10; + /** The command-line program and the arguments it returned. */ public ParsingEngine parser = null; @@ -169,15 +171,21 @@ public abstract class CommandLineProgram { try { // setup our log layout - PatternLayout layout = new PatternLayout(); + PatternLayout layout = new PatternLayout(patternString); Logger logger = CommandLineUtils.getStingLogger(); + // Appender for saving logging messages to a list + final ListAppender listAppender = new ListAppender(layout, NUM_WARN_MESSAGES, Level.WARN); + + // add appender for saving logging messages to a list + logger.addAppender(listAppender); + // now set the layout of all the loggers to our layout CommandLineUtils.setLayout(logger, layout); // Initialize the logger using the defaults. - clp.setupLoggerLevel(layout); + clp.setupLoggerLevel(); // setup the parser ParsingEngine parser = clp.parser = new ParsingEngine(clp); @@ -200,7 +208,7 @@ public abstract class CommandLineProgram { parser.loadArgumentsIntoObject(clp); // Initialize the logger using the loaded command line. - clp.setupLoggerLevel(layout); + clp.setupLoggerLevel(); Class[] argumentSources = clp.getArgumentSources(); for (Class argumentSource : argumentSources) @@ -226,15 +234,14 @@ public abstract class CommandLineProgram { parser.loadArgumentsIntoObject(clp); // Initialize the logger using the loaded command line. - clp.setupLoggerLevel(layout); + clp.setupLoggerLevel(); } if ( ! dryRun ) { // if they specify a log location, output our data there if (clp.toFile != null) { - FileAppender appender; try { - appender = new FileAppender(layout, clp.toFile, false); + final FileAppender appender = new FileAppender(layout, clp.toFile, false); logger.addAppender(appender); } catch (IOException e) { throw new RuntimeException("Unable to re-route log output to " + clp.toFile + " make sure the destination exists"); @@ -246,6 +253,12 @@ public abstract class CommandLineProgram { // call the execute CommandLineProgram.result = clp.execute(); + + // write logging events + printDoneAndLogMessages(listAppender); + + // clear saved logging events + listAppender.close(); } } catch (ArgumentException e) { @@ -266,13 +279,10 @@ public abstract class CommandLineProgram { } /** - * this function checks the logger level passed in on the command line, taking the lowest - * level that was provided. - * @param layout Pattern layout to format based on the logger level. + * this function takes the logger level passed in on the command line and uses it to set the level of the logger + * @throws ArgumentException if the logging level is not valid (DEBUG, INFO, WARN, ERROR, FATAL, OFF) */ - private void setupLoggerLevel(PatternLayout layout) { - layout.setConversionPattern(patternString); - + private void setupLoggerLevel() { // set the default logger level Level par; if (logging_level.toUpperCase().equals("DEBUG")) { @@ -347,6 +357,18 @@ public abstract class CommandLineProgram { return parser.isArgumentPresent("version"); } + /** + * Print done and log messages saved in a list. + * + * @param listAppender Appender for saving logging messages to a list + */ + private static void printDoneAndLogMessages(final ListAppender listAppender) { + System.out.println("------------------------------------------------------------------------------------------"); + System.out.print("Done. "); + listAppender.write(); + System.out.println("------------------------------------------------------------------------------------------"); + } + /** * Print help and exit. */ @@ -376,7 +398,7 @@ public abstract class CommandLineProgram { * @param t the error */ public static void exitSystemWithError(String msg, final Throwable t) { - errorPrintf("------------------------------------------------------------------------------------------%n"); + errorPrintf("--%n"); errorPrintf("stack trace %n"); t.printStackTrace(); diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java index 62139fb48..1280990a0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/CommandLineUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java index be7a65b2a..ccbad6332 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/EnumerationArgumentDefault.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java index e8e8cde7c..a52af7bb9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gather.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java index 158095adf..45f3b425a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Gatherer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java index f5a02021d..9ae15e653 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Hidden.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java index 9fd49782b..fe72b481a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Input.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -75,6 +75,13 @@ public @interface Input { */ String exclusiveOf() default ""; + /** + * Does this command-line argument require another argument. + * This will be the other argument required (presently only supports one). + * @return A string with the other required argument. + */ + String otherArgumentRequired() default ""; + /** * Provide a regexp-based validation string. * @return Non-empty regexp for validation, blank otherwise. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java index 8d18177f3..555458f16 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalArgumentCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java index da7fa6ee0..7de0a3ed9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/IntervalBinding.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ListAppender.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ListAppender.java new file mode 100644 index 000000000..fe5a903d9 --- /dev/null +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ListAppender.java @@ -0,0 +1,146 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.utils.commandline; + +import org.apache.log4j.AppenderSkeleton; +import org.apache.log4j.Layout; +import org.apache.log4j.Level; +import org.apache.log4j.spi.LoggingEvent; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; + +import java.util.ArrayList; +import java.util.List; + +/** + * Appender for saving logging loggingEvents to a list + */ +public class ListAppender extends AppenderSkeleton { + /** + * List of logging events + * + */ + protected final List loggingEvents = new ArrayList<>(); + + /** + * number of logging events to keep + */ + protected int loggingEventsToKeep = 0; + + /** + * number of logging events to keep + */ + protected int numLoggingEvents = 0; + + /** + * Log warning level to keep + */ + protected Level logLevelToKeep = Level.WARN; + + /** + * Constructor + * + * @param layout output layout + * @param loggingEventsToKeep number of warnings to keep + * @param logLevelToKeep logging logLevelToKeep ( TRACE, DEBUG, INFO, WARN, ERROR, FATAL, OFF ) + */ + public ListAppender(final Layout layout, final int loggingEventsToKeep, final Level logLevelToKeep) { + this.layout = layout; + this.loggingEventsToKeep = loggingEventsToKeep; + this.logLevelToKeep = logLevelToKeep; + } + + /** + * Constructor + * + * Hide from use + */ + private ListAppender() {} + + /** + * Close the appender + * + * Clear out the logging events + */ + @Override + public synchronized void close() { + loggingEvents.clear(); + numLoggingEvents = 0; + } + + /** + * Is a message layout required? + * + * @return true + */ + @Override + public boolean requiresLayout() { + return true; + } + + /** + * Append log event to the list of logging events + * + * @param loggingEvent The logging events + */ + @Override + protected synchronized void append(final LoggingEvent loggingEvent) { + if ( loggingEvent.getLevel().equals(logLevelToKeep) ) { + numLoggingEvents++; + if ( numLoggingEvents <= loggingEventsToKeep ) + loggingEvents.add(loggingEvent); + } + } + + /** + * The string representation for the class data + * + * @return string containing the logging events + * @throws ReviewedGATKException if layout is null + */ + public synchronized String toString() { + final String msgType = logLevelToKeep.toString() + " messages"; + if ( loggingEvents.isEmpty() ) { + return "There were no " + new String(msgType).toLowerCase() + ".\n"; + } else { + String out = "There were " + Integer.toString(numLoggingEvents) + " " + msgType; + if ( layout == null ) + throw new ReviewedGATKException("layout cannot be null"); + out += ", the first " + loggingEvents.size() + " are repeated below.\n"; + for ( LoggingEvent event : loggingEvents ) { + out += layout.format(event); + } + return out; + } + } + + /** + * Write class data to standard out + */ + public void write() { + System.out.print(this); + } + +} diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java index f71aec78b..236590a2f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/MissingArgumentValueException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java index 199b71eb8..70a793765 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplex.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java index 643eae100..815087c78 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Multiplexer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java index d7512f65a..1bb164c95 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Output.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -82,6 +82,13 @@ public @interface Output { */ String exclusiveOf() default ""; + /** + * Does this command-line argument require another argument. + * This will be the other argument required (presently only supports one). + * @return A string with the other required argument. + */ + String otherArgumentRequired() default ""; + /** * Provide a regexp-based validation string. * @return Non-empty regexp for validation, blank otherwise. diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java index ba403a1c6..0fdfba208 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedArgs.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java index 0265c8feb..ad9a8d883 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsedListArgs.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java index e0fc36156..d85ab5467 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -270,7 +270,8 @@ public class ParsingEngine { InvalidArgumentValue, ValueMissingArgument, TooManyValuesForArgument, - MutuallyExclusive } + MutuallyExclusive, + OtherArgumentRequired} /** * Validates the list of command-line argument matches. @@ -372,6 +373,26 @@ public class ParsingEngine { if( !invalidPairs.isEmpty() ) throw new ArgumentsAreMutuallyExclusiveException( invalidPairs ); } + + // Find sets of options that have other required arguments + if( !skipValidationOf.contains(ValidationType.OtherArgumentRequired)) { + Collection missingRequiredPairs = new ArrayList(); + for( ArgumentMatch argumentMatch: argumentMatches.findSuccessfulMatches()) { + if(argumentMatch.definition.otherArgumentRequired != null) { + boolean otherRequiredArgumentSeen = false; + + for(ArgumentMatch otherRequiredMatch: argumentMatches.findSuccessfulMatches()) { + if(argumentMatch.definition.otherArgumentRequired.equals(otherRequiredMatch.label)) { + otherRequiredArgumentSeen = true; + } + } + if(!otherRequiredArgumentSeen) { + missingRequiredPairs.add(argumentMatch); + throw new OtherRequiredArgumentMissingException(missingRequiredPairs); + } + } + } + } } /** @@ -814,6 +835,19 @@ class ArgumentsAreMutuallyExclusiveException extends ArgumentException { } +class OtherRequiredArgumentMissingException extends ArgumentException { + public OtherRequiredArgumentMissingException( Collection arguments ) { + super( formatArguments(arguments) ); + } + + private static String formatArguments( Collection arguments ) { + StringBuilder sb = new StringBuilder(); + for( ArgumentMatch argument: arguments ) + sb.append( String.format("%nArguments '%s' and '%s' are required to go together.", argument.definition.fullName, argument.definition.otherArgumentRequired ) ); + return sb.toString(); + } +} + /** * An exception for when an argument doesn't match an of the enumerated options for that var type diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java index 7d8788210..121cfebef 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentFiles.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java index b5d5add7a..ed09f38f3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineArgumentProvider.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java index 5a4c99c3f..a93b60e4c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/ParsingMethod.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java index 3221d21f6..68bb4da49 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBinding.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java index 8f90f7d14..a6767acc9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java index 8ea28c881..6a697575e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/Tags.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java index 3dca4245f..da24c031a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/commandline/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java index 6add93bd2..a7b61add1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContext.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java index 92cfc74a1..93f3af659 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/AlignmentContextUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java index fca56dcc0..996b36231 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/contexts/ReferenceContext.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java index d06176e77..c423d78fe 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/BAMDiffableReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java index f9167ff00..c5d92d9e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffElement.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java index 569934585..cfdec3cc5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffEngine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java index f0e8476e6..036fcade1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffNode.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java index 24f2a40f2..c2a4c518a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java index aef5e8c53..619f2cf61 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/DiffableReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java index 9f67fd47f..b4757e1a2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/Difference.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java index 948fa2107..7318f0bd2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/GATKReportDiffableReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java index d5d305e20..eeded75a6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/diffengine/VCFDiffableReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java index 37810ba00..20bd1f7a7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java index 41b59ccc5..536a31785 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsampleType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java index 910409457..7aa92338c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/Downsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java index 569eb709c..8d50f445a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingMethod.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java index 0435e7cd6..36cc36573 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingReadsIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java index d1a895b63..b9a047e01 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/DownsamplingUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java index d480f23fc..d22163df7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java index 74037ea9f..ab4fa5945 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/FractionalDownsamplerFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java index 89fbea0f1..222d57407 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/LevelingDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java index e9161b739..5686ce0d8 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PassThroughDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java index fc7eb7719..d3ccf4890 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/PerSampleDownsamplingReadsIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java index 455269b6c..2eedac4d1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java index ea7e6b079..5c066f3ad 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReadsDownsamplerFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java index b7bf2be19..38d38c2cb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java index 50e89c2bc..bdf64aea9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/ReservoirDownsamplerFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java index 8a3da8a03..51722adaf 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsampler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java index bac785a91..1a65f6745 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/downsampling/SimplePositionalDownsamplerFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java index 9ce7fc4be..64a32389f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DupUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java index 7aef3730a..26134a9a9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/duplicates/DuplicateComp.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java index e39fd557d..7c9157569 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/DynamicClassResolutionException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java index 3584b79ab..acb4c26ad 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/GATKException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java index d7595d0e5..bf336468c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/ReviewedGATKException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java index ceb1d0f4f..b29fb2a41 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/exceptions/UserException.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -50,7 +50,7 @@ public class UserException extends ReviewedGATKException { /** * The URL where people can get help messages. Printed when an error occurs */ - public static final String PHONE_HOME_DOCS_URL = "http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest"; + public static final String PHONE_HOME_DOCS_URL = HelpConstants.articlePost(1250); public UserException(String msg) { super(msg); } public UserException(String msg, Throwable e) { super(msg, e); } @@ -136,7 +136,7 @@ public class UserException extends ReviewedGATKException { public static class BadTmpDir extends UserException { public BadTmpDir(String message) { - super(String.format("An error occurred while working with the tmp directory %s. You can specify -Djava.io.tmpdir=X on the command line (before the -jar argument) where X is a directory path, to use a more appropriate temporary directory. The exact error was %s", System.getProperties().get("java.io.tmpdir"), message)); + super(String.format("An error occurred while working with the tmp directory %s. You can specify -Djava.io.tmpdir=X on the command line (before the -jar argument) where X is a directory path, to use a more appropriate temporary directory. Note that this is a JVM argument, not a GATK argument. The exact error was %s", System.getProperties().get("java.io.tmpdir"), message)); } } @@ -160,7 +160,7 @@ public class UserException extends ReviewedGATKException { public static class ErrorWritingBamFile extends UserException { public ErrorWritingBamFile(String message) { - super(String.format("An error occurred when trying to write the BAM file. Usually this happens when there is not enough space in the directory to which the data is being written (generally the temp directory) or when your system's open file handle limit is too small. Your system administrator can help you resolve these issues. If you know what temporary directory to use, you can specify it by adding -Djava.io.tmpdir=X to the command line (before the -jar argument), where X is the directory path. The exact error was %s", message)); + super(String.format("An error occurred when trying to write the BAM file. Usually this happens when there is not enough space in the directory to which the data is being written (generally the temp directory) or when your system's open file handle limit is too small. Your system administrator can help you resolve these issues. If you know what temporary directory to use, you can specify it by adding -Djava.io.tmpdir=X to the command line (before the -jar argument), where X is the directory path. Note that this is a JVM argument, not a GATK argument. The exact error was %s", message)); } } @@ -225,20 +225,20 @@ public class UserException extends ReviewedGATKException { public static class MissortedBAM extends UserException { public MissortedBAM(SAMFileHeader.SortOrder order, File file, SAMFileHeader header) { - super(String.format("Missorted input SAM/BAM/CRAM files: %s must be sorted in %s order but order was: %s. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information.", file, order, header.getSortOrder())); + super(String.format("Missorted input SAM/BAM/CRAM files: %s must be sorted in %s order but order was: %s. Please see " + HelpConstants.articlePost(1317) + "for more information.", file, order, header.getSortOrder())); } public MissortedBAM(SAMFileHeader.SortOrder order, String message) { - super(String.format("Missorted input SAM/BAM/CRAM files: files are not sorted in %s order. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", order, message)); + super(String.format("Missorted input SAM/BAM/CRAM files: files are not sorted in %s order. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s", order, message)); } public MissortedBAM(SAMFileHeader.SortOrder order, SAMRecord read, String message) { - super(String.format("Missorted input SAM/BAM/CRAM file %s: file sorted in %s order but %s is required. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", + super(String.format("Missorted input SAM/BAM/CRAM file %s: file sorted in %s order but %s is required. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s", read.getFileSource().getReader(), read.getHeader().getSortOrder(), order, message)); } public MissortedBAM(String message) { - super(String.format("Missorted input SAM/BAM/CRAM files. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", message)); + super(String.format("Missorted input SAM/BAM/CRAM files. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s", message)); } } @@ -252,7 +252,7 @@ public class UserException extends ReviewedGATKException { } public MalformedBAM(String source, String message) { - super(String.format("SAM/BAM/CRAM file %s is malformed. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s", source, message)); + super(String.format("SAM/BAM/CRAM file %s is malformed. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s", source, message)); } } @@ -262,7 +262,7 @@ public class UserException extends ReviewedGATKException { } public MisencodedBAM(String source, String message) { - super(String.format("SAM/BAM/CRAM file %s appears to be using the wrong encoding for quality scores: %s. Please see https://www.broadinstitute.org/gatk/guide?id=6470 for more details and options related to this error.", source, message)); + super(String.format("SAM/BAM/CRAM file %s appears to be using the wrong encoding for quality scores: %s. Please see " + HelpConstants.articlePost(6470) + " for more details and options related to this error.", source, message)); } } @@ -294,13 +294,13 @@ public class UserException extends ReviewedGATKException { public static class ReadMissingReadGroup extends MalformedBAM { public ReadMissingReadGroup(final SAMRecord read) { - super(read, String.format("Read %s is missing the read group (RG) tag, which is required by the GATK. Please see " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName())); + super(read, String.format("Read %s is missing the read group (RG) tag, which is required by the GATK. Please see " + HelpConstants.articlePost(59), read.getReadName())); } } public static class ReadHasUndefinedReadGroup extends MalformedBAM { public ReadHasUndefinedReadGroup(final SAMRecord read, final String rgID) { - super(read, String.format("Read %s uses a read group (%s) that is not defined in the BAM header, which is not valid. Please see " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName(), rgID)); + super(read, String.format("Read %s uses a read group (%s) that is not defined in the BAM header, which is not valid. Please see " + HelpConstants.articlePost(59), read.getReadName(), rgID)); } } @@ -312,7 +312,7 @@ public class UserException extends ReviewedGATKException { public static class MissortedFile extends UserException { public MissortedFile(File file, String message, Exception e) { - super(String.format("Missorted input file: %s is must be sorted in coordinate order. Please see " + HelpConstants.forumPost("discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cram") + "for more information. Error details: %s and got error %s", file, message, getMessage(e))); + super(String.format("Missorted input file: %s is must be sorted in coordinate order. Please see " + HelpConstants.articlePost(1317) + "for more information. Error details: %s and got error %s", file, message, getMessage(e))); } } @@ -366,14 +366,14 @@ public class UserException extends ReviewedGATKException { public static class IncompatibleSequenceDictionaries extends UserException { public IncompatibleSequenceDictionaries(String message, String name1, SAMSequenceDictionary dict1, String name2, SAMSequenceDictionary dict2) { - super(String.format("Input files %s and %s have incompatible contigs. Please see " + HelpConstants.forumPost("discussion/63/input-files-have-incompatible-contigs") + "for more information. Error details: %s.\n %s contigs = %s\n %s contigs = %s", + super(String.format("Input files %s and %s have incompatible contigs. Please see " + HelpConstants.articlePost(63) + "for more information. Error details: %s.\n %s contigs = %s\n %s contigs = %s", name1, name2, message, name1, ReadUtils.prettyPrintSequenceRecords(dict1), name2, ReadUtils.prettyPrintSequenceRecords(dict2))); } } public static class LexicographicallySortedSequenceDictionary extends UserException { public LexicographicallySortedSequenceDictionary(String name, SAMSequenceDictionary dict) { - super(String.format("Lexicographically sorted human genome sequence detected in %s. Please see " + HelpConstants.forumPost("discussion/58/companion-utilities-reordersam") + "for more information. Error details: %s contigs = %s", + super(String.format("Lexicographically sorted human genome sequence detected in %s. Please see " + HelpConstants.articlePost(1328) + "for more information. Error details: %s contigs = %s", name, name, ReadUtils.prettyPrintSequenceRecords(dict))); } } @@ -409,7 +409,7 @@ public class UserException extends ReviewedGATKException { public MissingReferenceFaiFile( final File indexFile, final File fastaFile ) { super(String.format("Fasta index file %s for reference %s does not exist. Please see %s for help creating it.", indexFile.getAbsolutePath(), fastaFile.getAbsolutePath(), - HelpConstants.forumPost("discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference"))); + HelpConstants.articlePost(1601))); } } @@ -417,7 +417,7 @@ public class UserException extends ReviewedGATKException { public MissingReferenceDictFile( final File dictFile, final File fastaFile ) { super(String.format("Fasta dict file %s for reference %s does not exist. Please see %s for help creating it.", dictFile.getAbsolutePath(), fastaFile.getAbsolutePath(), - HelpConstants.forumPost("discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference"))); + HelpConstants.articlePost(1601))); } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java index cbf8c4259..d8b7b624b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/ArtificialFastaUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java index a456008a5..a193eebf4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFile.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java index d0d7a6a56..7d1a027c9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fasta/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java index 813d697aa..d922a90aa 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/file/FSLockWithShared.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java index f3811333e..c81df70cc 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentCollection.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java index cbcce0b3d..d1c99a375 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/fragments/FragmentUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java index 3d6c58113..49daae86d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java index a9423faa4..59e46871e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListPermutation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java index 249e270b3..bb6d28c0b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/AlleleListUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java index 0a57040cd..5eb2a0b31 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/DiploidGenotype.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java index 8c3f04885..ccc4a417b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedAlleleList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java index 95f2559aa..c1ba1b07a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/IndexedSampleList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java index f0a1d0be8..5b0a9d879 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/MostLikelyAllele.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java index c52278e9e..c19736b9f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/PerReadAlleleLikelihoodMap.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java index a4c8ca90b..3a588a1fa 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -25,6 +25,7 @@ package org.broadinstitute.gatk.utils.genotyper; +import com.google.common.annotations.VisibleForTesting; import htsjdk.variant.variantcontext.Allele; import it.unimi.dsi.fastutil.ints.IntArrayList; import it.unimi.dsi.fastutil.objects.Object2IntMap; @@ -34,6 +35,7 @@ import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; import org.broadinstitute.gatk.utils.variant.GATKVCFConstants; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import java.util.*; @@ -92,6 +94,11 @@ public class ReadLikelihoods implements SampleList, AlleleList */ private int referenceAlleleIndex = -1; + /** + * Index of the non-ref allele if any, otherwise - 1. + */ + private int nonRefAlleleIndex = -1; + /** * Caches the read-list per sample list returned by {@link #sampleReads} */ @@ -138,6 +145,7 @@ public class ReadLikelihoods implements SampleList, AlleleList readListBySampleIndex = new List[sampleCount]; valuesBySampleIndex = new double[sampleCount][][]; referenceAlleleIndex = findReferenceAllele(alleles); + nonRefAlleleIndex = findNonRefAllele(alleles); readIndexBySampleIndex = new Object2IntMap[sampleCount]; @@ -219,6 +227,15 @@ public class ReadLikelihoods implements SampleList, AlleleList return -1; } + private int findNonRefAllele(final AlleleList alleles) { + final int alleleCount = alleles.alleleCount(); + for (int i = alleleCount - 1; i >= 0; i--) { + if (alleles.alleleAt(i).equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE)) + return i; + } + return - 1; + } + /** * Returns the index of a sample within the likelihood collection. * @@ -419,16 +436,21 @@ public class ReadLikelihoods implements SampleList, AlleleList } - /** - * Search the best allele for a read. - * - * @param sampleIndex including sample index. - * @param readIndex target read index. - * - * @return never {@code null}, but with {@link BestAllele#allele allele} == {@code null} - * if non-could be found. - */ private BestAllele searchBestAllele(final int sampleIndex, final int readIndex, final boolean canBeReference) { + return searchBestAllele(sampleIndex, readIndex, canBeReference, alleles); + } + + /** + * Search the best allele for a read. + * + * @param sampleIndex including sample index. + * @param readIndex target read index. + * + * @return never {@code null}, but with {@link BestAllele#allele allele} == {@code null} + * if non-could be found. + */ + private BestAllele searchBestAllele(final int sampleIndex, final int readIndex, final boolean canBeReference, + final AlleleList allelesToConsider) { final int alleleCount = alleles.alleleCount(); if (alleleCount == 0 || (alleleCount == 1 && referenceAlleleIndex == 0 && !canBeReference)) return new BestAllele(sampleIndex,readIndex,-1,Double.NEGATIVE_INFINITY,Double.NEGATIVE_INFINITY); @@ -441,6 +463,10 @@ public class ReadLikelihoods implements SampleList, AlleleList for (int a = bestAlleleIndex + 1; a < alleleCount; a++) { if (!canBeReference && referenceAlleleIndex == a) continue; + if (nonRefAlleleIndex == a) + continue; + if (allelesToConsider.alleleIndex(alleles.alleleAt(a)) < 0) + continue; final double candidateLikelihood = sampleValues[a][readIndex]; if (candidateLikelihood > bestLikelihood) { bestAlleleIndex = a; @@ -501,6 +527,7 @@ public class ReadLikelihoods implements SampleList, AlleleList alleleList = null; int referenceIndex = this.referenceAlleleIndex; + int nonRefIndex = this.nonRefAlleleIndex; @SuppressWarnings("unchecked") final A[] newAlleles = (A[]) new Allele[newAlleleCount]; for (int a = 0; a < oldAlleleCount; a++) @@ -511,19 +538,20 @@ public class ReadLikelihoods implements SampleList, AlleleList if (referenceIndex != -1) throw new IllegalArgumentException("there cannot be more than one reference allele"); referenceIndex = newIndex; + } else if (allele.equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE)) { + if (nonRefAlleleIndex != -1) + throw new IllegalArgumentException(String.format("there cannot be more than one %s allele", GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE_NAME)); + nonRefIndex = newIndex; } newAlleles[newIndex++] = allele; } alleles = new IndexedAlleleList<>(newAlleles); - if (referenceIndex != -1) - referenceAlleleIndex = referenceIndex; - final int sampleCount = samples.sampleCount(); for (int s = 0; s < sampleCount; s++) { final int sampleReadCount = readsBySampleIndex[s].length; - final double[][] newValuesBySampleIndex = Arrays.copyOf(valuesBySampleIndex[s],newAlleleCount); + final double[][] newValuesBySampleIndex = Arrays.copyOf(valuesBySampleIndex[s], newAlleleCount); for (int a = oldAlleleCount; a < newAlleleCount; a++) { newValuesBySampleIndex[a] = new double[sampleReadCount]; if (defaultLikelihood != 0.0) @@ -531,8 +559,86 @@ public class ReadLikelihoods implements SampleList, AlleleList } valuesBySampleIndex[s] = newValuesBySampleIndex; } + + if (referenceIndex != -1) + referenceAlleleIndex = referenceIndex; + if (nonRefIndex != -1) { + nonRefAlleleIndex = nonRefIndex; + updateNonRefAlleleLikelihoods(); + } } + /** + * Modify this likelihood collection dropping some of its alleles. + * @param allelesToDrop set of alleles to be dropped. + * @throws IllegalArgumentException if {@code allelesToDrop} is {@code null} or contain elements that are + * not alleles in this collection. + */ + public void dropAlleles(final Set allelesToDrop) { + if (allelesToDrop == null) { + throw new IllegalArgumentException("the input allele to drop set cannot be null"); + } + if (allelesToDrop.isEmpty()) { + return; + } + final boolean[] indicesToDrop = new boolean[alleles.alleleCount()]; + for (final A allele : allelesToDrop) { + final int index = alleles.alleleIndex(allele); + if (index < 0) { + throw new IllegalArgumentException("unknown allele: " + allele); + } + indicesToDrop[index] = true; + } + + @SuppressWarnings("unchecked") + final A[] newAlleles = (A[]) new Allele[alleles.alleleCount() - allelesToDrop.size()]; + final int[] newAlleleIndices = new int[newAlleles.length]; + int nextIndex = 0; + for (int i = 0; i < alleles.alleleCount(); i++) { + if (indicesToDrop[i]) { + continue; + } + newAlleleIndices[nextIndex] = i; + newAlleles[nextIndex++] = alleles.alleleAt(i); + } + for (int i = 0; i < samples.sampleCount(); i++) { + final double[][] oldSampleValues = valuesBySampleIndex[i]; + final double[][] newSampleValues = new double[newAlleles.length][]; + for (int j = 0; j < newAlleles.length; j++) { + newSampleValues[j] = oldSampleValues[newAlleleIndices[j]]; + } + valuesBySampleIndex[i] = newSampleValues; + } + alleleList = Collections.unmodifiableList(Arrays.asList(newAlleles)); + alleles = new IndexedAlleleList<>(alleleList); + if (nonRefAlleleIndex >= 0) { + nonRefAlleleIndex = findNonRefAllele(alleles); + updateNonRefAlleleLikelihoods(); + } + if (referenceAlleleIndex >= 0) + referenceAlleleIndex = findReferenceAllele(alleles); + } + + /** + * Drop all the alleles not present in the subset passed as a parameter. + * @param subset the alleles to retain. + * @throws IllegalArgumentException if {@code alleles} is {@code null} or contain alleles unknown to this likelihood + * collection. + */ + public void retainAlleles(final Set subset) { + if (alleles == null) { + throw new IllegalArgumentException("the retain subset must not be null"); + } else if (!alleles().containsAll(subset) || subset.size() > alleleCount()) { + throw new IllegalArgumentException("some of the alleles to retain are not present in the read-likelihoods collection"); + } else if (subset.isEmpty() || (subset.size() == 1 && subset.contains(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE))) { + throw new IllegalArgumentException("there must be at least one allele to retain"); + } else { + final Set allelesToDrop = new HashSet<>(alleles()); + allelesToDrop.removeAll(subset); + dropAlleles(allelesToDrop); + } + } + /** * Likelihood matrix between a set of alleles and reads. * @param the allele-type. @@ -543,13 +649,13 @@ public class ReadLikelihoods implements SampleList, AlleleList * List of reads in the matrix sorted by their index therein. * @return never {@code null}. */ - public List reads(); + List reads(); /** * List of alleles in the matrix sorted by their index in the collection. * @return never {@code null}. */ - public List alleles(); + List alleles(); /** * Set the likelihood of a read given an allele through their indices. @@ -561,7 +667,7 @@ public class ReadLikelihoods implements SampleList, AlleleList * @throws IllegalArgumentException if {@code alleleIndex} or {@code readIndex} * are not valid allele and read indices respectively. */ - public void set(final int alleleIndex, final int readIndex, final double value); + void set(final int alleleIndex, final int readIndex, final double value); /** * Returns the likelihood of a read given a haplotype. @@ -575,7 +681,7 @@ public class ReadLikelihoods implements SampleList, AlleleList * @return the requested likelihood, whatever value was provided using {@link #set(int,int,double) set} * or 0.0 if none was set. */ - public double get(final int alleleIndex, final int readIndex); + double get(final int alleleIndex, final int readIndex); /** * Queries the index of an allele in the matrix. @@ -586,7 +692,7 @@ public class ReadLikelihoods implements SampleList, AlleleList * @return -1 if such allele does not exist, otherwise its index which 0 or greater. */ @SuppressWarnings("unused") - public int alleleIndex(final A allele); + int alleleIndex(final A allele); /** * Queries the index of a read in the matrix. @@ -599,19 +705,19 @@ public class ReadLikelihoods implements SampleList, AlleleList * which is 0 or greater. */ @SuppressWarnings("unused") - public int readIndex(final GATKSAMRecord read); + int readIndex(final GATKSAMRecord read); /** * Number of allele in the matrix. * @return never negative. */ - public int alleleCount(); + int alleleCount(); /** * Number of reads in the matrix. * @return never negative. */ - public int readCount(); + int readCount(); /** * Returns the allele given its index. @@ -621,7 +727,7 @@ public class ReadLikelihoods implements SampleList, AlleleList * @throws IllegalArgumentException if {@code alleleIndex} is not a valid allele index. * @return never {@code null}. */ - public A alleleAt(final int alleleIndex); + A alleleAt(final int alleleIndex); /** * Returns the allele given its index. @@ -631,7 +737,7 @@ public class ReadLikelihoods implements SampleList, AlleleList * @throws IllegalArgumentException if {@code readIndex} is not a valid read index. * @return never {@code null}. */ - public GATKSAMRecord readAt(final int readIndex); + GATKSAMRecord readAt(final int readIndex); /** @@ -640,7 +746,7 @@ public class ReadLikelihoods implements SampleList, AlleleList * @param dest the destination array. * @param offset the copy offset within the destination allele */ - public void copyAlleleLikelihoods(final int alleleIndex, final double[] dest, final int offset); + void copyAlleleLikelihoods(final int alleleIndex, final double[] dest, final int offset); } /** @@ -905,7 +1011,6 @@ public class ReadLikelihoods implements SampleList, AlleleList * * @throws IllegalArgumentException the location cannot be {@code null} nor unmapped. */ - @SuppressWarnings("unused") public void filterToOnlyOverlappingUnclippedReads(final GenomeLoc location) { if (location == null) throw new IllegalArgumentException("the location cannot be null"); @@ -921,7 +1026,6 @@ public class ReadLikelihoods implements SampleList, AlleleList final int alleleCount = alleles.alleleCount(); final IntArrayList removeIndices = new IntArrayList(10); for (int s = 0; s < sampleCount; s++) { - int readRemoveCount = 0; final GATKSAMRecord[] sampleReads = readsBySampleIndex[s]; final int sampleReadCount = sampleReads.length; for (int r = 0; r < sampleReadCount; r++) @@ -932,28 +1036,6 @@ public class ReadLikelihoods implements SampleList, AlleleList } } - // Compare the read coordinates to the location of interest. - private boolean readOverlapsLocation(final String contig, final int locStart, - final int locEnd, final GATKSAMRecord read) { - final boolean overlaps; - - if (read.getReadUnmappedFlag()) - overlaps = false; - else if (!read.getReferenceName().equals(contig)) - overlaps = false; - else { - int alnStart = read.getAlignmentStart(); - int alnStop = read.getAlignmentEnd(); - if (alnStart > alnStop) { // Paranoia? based on GLP.createGenomeLoc(Read) this can happen?. - final int end = alnStart; - alnStart = alnStop; - alnStop = end; - } - overlaps = !(alnStop < locStart || alnStart > locEnd); - } - return overlaps; - } - /** * Removes those read that the best possible likelihood given any allele is just too low. * @@ -991,7 +1073,7 @@ public class ReadLikelihoods implements SampleList, AlleleList } // Check whether the read is poorly modelled. - protected boolean readIsPoorlyModelled(final int sampleIndex, final int readIndex, final GATKSAMRecord read, final double maxErrorRatePerBase) { + private boolean readIsPoorlyModelled(final int sampleIndex, final int readIndex, final GATKSAMRecord read, final double maxErrorRatePerBase) { final double maxErrorsForRead = Math.min(2.0, Math.ceil(read.getReadLength() * maxErrorRatePerBase)); final double log10QualPerBase = -4.0; final double log10MaxLikelihoodForTrueAllele = maxErrorsForRead * log10QualPerBase; @@ -1089,37 +1171,25 @@ public class ReadLikelihoods implements SampleList, AlleleList throw new IllegalArgumentException("non-ref allele cannot be null"); if (!nonRefAllele.equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE)) throw new IllegalArgumentException("the non-ref allele is not valid"); - // Already present? - if (alleles.alleleIndex(nonRefAllele) != -1) - return; - - final int oldAlleleCount = alleles.alleleCount(); - final int newAlleleCount = oldAlleleCount + 1; - @SuppressWarnings("unchecked") - final A[] newAlleles = (A[]) new Allele[newAlleleCount]; - for (int a = 0; a < oldAlleleCount; a++) - newAlleles[a] = alleles.alleleAt(a); - newAlleles[oldAlleleCount] = nonRefAllele; - alleles = new IndexedAlleleList<>(newAlleles); - alleleList = null; // remove the cached alleleList. - - final int sampleCount = samples.sampleCount(); - for (int s = 0; s < sampleCount; s++) - addNonReferenceAlleleLikelihoodsPerSample(oldAlleleCount, newAlleleCount, s); + addMissingAlleles(Collections.singleton(nonRefAllele), Double.NEGATIVE_INFINITY); + updateNonRefAlleleLikelihoods(); } - // Updates per-sample structures according to the addition of the NON_REF allele. - private void addNonReferenceAlleleLikelihoodsPerSample(final int alleleCount, final int newAlleleCount, final int sampleIndex) { - final double[][] sampleValues = valuesBySampleIndex[sampleIndex] = Arrays.copyOf(valuesBySampleIndex[sampleIndex], newAlleleCount); - final int sampleReadCount = readsBySampleIndex[sampleIndex].length; + public void updateNonRefAlleleLikelihoods() { + updateNonRefAlleleLikelihoods(alleles); + } - final double[] nonRefAlleleLikelihoods = sampleValues[alleleCount] = new double [sampleReadCount]; - Arrays.fill(nonRefAlleleLikelihoods,Double.NEGATIVE_INFINITY); - for (int r = 0; r < sampleReadCount; r++) { - final BestAllele bestAllele = searchBestAllele(sampleIndex,r,true); - final double secondBestLikelihood = Double.isInfinite(bestAllele.confidence) ? bestAllele.likelihood - : bestAllele.likelihood - bestAllele.confidence; - nonRefAlleleLikelihoods[r] = secondBestLikelihood; + public void updateNonRefAlleleLikelihoods(final AlleleList allelesToConsider) { + if (nonRefAlleleIndex < 0) + return; + for (int s = 0; s < samples.sampleCount(); s++) { + final double[][] sampleValues = valuesBySampleIndex[s]; + for (int r = 0; r < sampleValues[0].length; r++) { + final BestAllele bestAllele = searchBestAllele(s, r, true, allelesToConsider); + final double secondBestLikelihood = Double.isInfinite(bestAllele.confidence) ? bestAllele.likelihood + : bestAllele.likelihood - bestAllele.confidence; + sampleValues[nonRefAlleleIndex][r] = secondBestLikelihood; + } } } @@ -1170,9 +1240,9 @@ public class ReadLikelihoods implements SampleList, AlleleList * * @return never {@code null}. */ - public static ReadLikelihoods fromPerAlleleReadLikelihoodsMap(final AlleleList alleleList, final Map map) { + @VisibleForTesting + static ReadLikelihoods fromPerAlleleReadLikelihoodsMap(final AlleleList alleleList, final Map map) { - //TODO add test code for this method. // First we need to create the read-likelihood collection with all required alleles, samples and reads. final SampleList sampleList = new IndexedSampleList(map.keySet()); final int alleleCount = alleleList.alleleCount(); @@ -1228,11 +1298,12 @@ public class ReadLikelihoods implements SampleList, AlleleList * @param sampleIndex the target sample. * @return never {@code null}, perhaps empty. */ - public Map> readsByBestAlleleMap(final int sampleIndex) { + @VisibleForTesting + Map> readsByBestAlleleMap(final int sampleIndex) { checkSampleIndex(sampleIndex); final int alleleCount = alleles.alleleCount(); final int sampleReadCount = readsBySampleIndex[sampleIndex].length; - final Map> result = new HashMap<>(alleleCount); + final Map> result = new LinkedHashMap<>(alleleCount); for (int a = 0; a < alleleCount; a++) result.put(alleles.alleleAt(a),new ArrayList(sampleReadCount)); readsByBestAlleleMap(sampleIndex,result); diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java index a171edd98..147762543 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java index 5a6364355..4955ec163 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/SampleListUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java index 5a2735d50..c0eb5ad32 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/EventMap.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java index 5b0ec5aae..28df151c9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/Haplotype.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java index d03f0b6bb..e23fa32ed 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java index f294076e4..19bd99291 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java index 241ac7294..1c5c97b34 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java index 56b39ebdf..563ee79f9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ApplicationDetails.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java index ef154246d..cfed7463e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocletUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java index f00fcebaa..6dd64fb3c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -45,6 +45,4 @@ public @interface DocumentedGATKFeature { public String summary() default ""; /** Are there links to other docs that we should include? CommandLineGATK.class for walkers, for example? */ public Class[] extraDocs() default {}; - /** Who is the go-to developer for operation/documentation issues? */ - public String gotoDev() default "NA"; } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java index ce4ea5f88..3f7d4c8bb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java index 1d0186c6e..8106caa9a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureObject.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -36,20 +36,19 @@ class DocumentedGATKFeatureObject { private final Class classToDoc; /** Are we enabled? */ private final boolean enable; - private final String groupName, summary, gotoDev; + private final String groupName, summary; private final Class[] extraDocs; - public DocumentedGATKFeatureObject(Class classToDoc, final boolean enable, final String groupName, final String summary, final Class[] extraDocs, final String gotoDev) { + public DocumentedGATKFeatureObject(Class classToDoc, final boolean enable, final String groupName, final String summary, final Class[] extraDocs) { this.classToDoc = classToDoc; this.enable = enable; this.groupName = groupName; this.summary = summary; this.extraDocs = extraDocs; - this.gotoDev = gotoDev; } - public DocumentedGATKFeatureObject(Class classToDoc, final String groupName, final String summary, final String gotoDev) { - this(classToDoc, true, groupName, summary, new Class[]{}, gotoDev); + public DocumentedGATKFeatureObject(Class classToDoc, final String groupName, final String summary) { + this(classToDoc, true, groupName, summary, new Class[]{}); } public Class getClassToDoc() { return classToDoc; } @@ -57,5 +56,4 @@ class DocumentedGATKFeatureObject { public String groupName() { return groupName; } public String summary() { return summary; } public Class[] extraDocs() { return extraDocs; } - public String gotoDev() { return gotoDev; } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java index 4a7853b6e..bbd9313a2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumAPIUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java index a1818dc0b..2d0c0762b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ForumDiscussion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java index 75701d660..7512a0f99 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -30,14 +30,6 @@ public class GATKDocUtils { * The URL root for RELEASED GATKDOC units */ public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = HelpConstants.GATK_DOCS_URL; - /** - * The URL root for STABLE GATKDOC units //TODO: do sthing with this or remove -- URL goes nowhere - */ - public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/"; - /** - * The URL root for UNSTABLE GATKDOC units //TODO: do sthing with this or remove -- URL goes nowhere - */ - public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/"; /** * Return the filename of the GATKDoc PHP that would be generated for Class. This @@ -59,7 +51,7 @@ public class GATKDocUtils { /** * Returns a full URL http://etc/ linking to the documentation for class (assuming it - * exists). Currently points to the RELEASE doc path only. //TODO: do sthing with other paths or remove ? + * exists). Currently points to the RELEASE doc path only. * * @param c * @return @@ -68,8 +60,6 @@ public class GATKDocUtils { String classPath = phpFilenameForClass(c); StringBuilder b = new StringBuilder(); b.append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath); - //b.append("stable version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n"); - //b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n"); return b.toString(); } } \ No newline at end of file diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java index 89cdabbe1..3cdddebbb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocWorkUnit.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java index 015f2d306..e0bd7365e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -79,9 +79,9 @@ public abstract class GATKDoclet { final private static String FORUM_KEY_PATH = "/local/gsa-engineering/gatkdocs_publisher/forum.key"; - final private static String OUTPUT_FILE_EXTENSION = "php"; + final private static String OUTPUT_FILE_EXTENSION = "html"; - /** Controls the extension of the non-json output files, and also the HREFs to these files. Default: php */ + /** Controls the extension of the non-json output files, and also the HREFs to these files. Default: html */ final private static String OUTPUT_FILE_EXTENSION_OPTION = "-output-file-extension"; // ---------------------------------------------------------------------- // @@ -120,8 +120,7 @@ public abstract class GATKDoclet { static { STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class, HelpConstants.DOCS_CAT_RODCODECS, - "Tribble codecs for reading reference ordered data (ROD) files such as VCF or BED", - "NA")); + "Codecs for reading resource files in reference ordered data (ROD) files such as BED")); } /** @@ -264,7 +263,7 @@ public abstract class GATKDoclet { List old = ForumAPIUtils.getPostedTools(forumKey); for (String s : old) - System.out.println(s); + //System.out.println(s); System.out.printf("Forum has %d items%n", old.size()); System.out.printf("Docs have %d items%n", docWorkUnits.size()); @@ -354,11 +353,11 @@ public abstract class GATKDoclet { if (docClass.isAnnotationPresent(DocumentedGATKFeature.class)) { DocumentedGATKFeature f = docClass.getAnnotation(DocumentedGATKFeature.class); - return new DocumentedGATKFeatureObject(docClass, f.enable(), f.groupName(), f.summary(), f.extraDocs(), f.gotoDev()); + return new DocumentedGATKFeatureObject(docClass, f.enable(), f.groupName(), f.summary(), f.extraDocs()); } else { for (DocumentedGATKFeatureObject staticDocs : STATIC_DOCS) { if (staticDocs.getClassToDoc().isAssignableFrom(docClass)) { - return new DocumentedGATKFeatureObject(docClass, staticDocs.enable(), staticDocs.groupName(), staticDocs.summary(), staticDocs.extraDocs(), staticDocs.gotoDev()); + return new DocumentedGATKFeatureObject(docClass, staticDocs.enable(), staticDocs.groupName(), staticDocs.summary(), staticDocs.extraDocs()); } } return null; @@ -469,11 +468,12 @@ public abstract class GATKDoclet { if (annotation.groupName().endsWith(" Tools")) supercatValue = "tools"; else if (annotation.groupName().endsWith(" Utilities")) supercatValue = "utilities"; else if (annotation.groupName().startsWith("Engine ")) supercatValue = "engine"; - else if (annotation.groupName().endsWith(" (DevZone)")) supercatValue = "dev"; + else if (annotation.groupName().endsWith(" (Exclude)")) supercatValue = "exclude"; else supercatValue = "other"; - root.put("supercat", supercatValue); - + //if (!supercatValue.contentEquals("exclude")) { + root.put("supercat", supercatValue); + //} return root; } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java index d08115601..0f1d8b93b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONArgument.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java index e9f2d4acd..a1290d8e3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GSONWorkUnit.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java index 6dad68092..cb959d0a2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GenericDocumentationHandler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -117,8 +117,6 @@ public abstract class GenericDocumentationHandler extends DocumentedGATKFeatureH for (Tag tag : toProcess.classDoc.tags()) { root.put(tag.name(), tag.text()); } - - root.put("gotoDev", toProcess.annotation.gotoDev()); } /** @@ -190,7 +188,6 @@ public abstract class GenericDocumentationHandler extends DocumentedGATKFeatureH argBindings.put("maxValue", "NA"); argBindings.put("minRecValue", "NA"); argBindings.put("maxRecValue", "NA"); - argBindings.put("defaultValue", "NA"); } // Finalize argument bindings args.get(kind).add(argBindings); @@ -276,9 +273,9 @@ public abstract class GenericDocumentationHandler extends DocumentedGATKFeatureH final Object instance = makeInstanceIfPossible(toProcess.clazz); if (instance != null) { final Object value = getFieldValue(instance, argumentSource.field.getName()); - if (value != null) + if (value != null) { return value; - + } if (argumentSource.createsTypeDefault()) { try { // handle the case where there's an implicit default return argumentSource.typeDefaultDocString(); @@ -391,7 +388,7 @@ public abstract class GenericDocumentationHandler extends DocumentedGATKFeatureH } /** - * Pretty prints value + * Pretty prints value TODO I think this is what I need to fix the value problem *

      * Assumes value != null * @@ -512,7 +509,7 @@ public abstract class GenericDocumentationHandler extends DocumentedGATKFeatureH if (field.isAnnotationPresent(ArgumentCollection.class)) { ClassDoc typeDoc = getRootDoc().classNamed(fieldDoc.type().qualifiedTypeName()); if (typeDoc == null) - throw new ReviewedGATKException("Tried to get javadocs for ArgumentCollection field " + fieldDoc + " but could't find the class in the RootDoc"); + throw new ReviewedGATKException("Tried to get javadocs for ArgumentCollection field " + fieldDoc + " but couldn't find the class in the RootDoc"); else { FieldDoc result = getFieldDoc(typeDoc, name, false); if (result != null) @@ -563,7 +560,7 @@ public abstract class GenericDocumentationHandler extends DocumentedGATKFeatureH /** * Returns a human readable string that describes the Type type of a GATK argument. *

      - * This will include parameterized types, so that Set{T} shows up as Set(T) and not + * This will include parametrized types, so that Set{T} shows up as Set(T) and not * just Set in the docs. * * @param type @@ -644,9 +641,7 @@ public abstract class GenericDocumentationHandler extends DocumentedGATKFeatureH FeatureManager manager = new FeatureManager(); List rodTypes = new ArrayList(); for (FeatureManager.FeatureDescriptor descriptor : manager.getByFeature(featureClass)) { - rodTypes.add(String.format("%s", - GATKDocUtils.phpFilenameForClass(descriptor.getCodecClass()), - descriptor.getName())); + rodTypes.add(descriptor.getName()); } root.put("rodTypes", Utils.join(", ", rodTypes)); @@ -658,6 +653,10 @@ public abstract class GenericDocumentationHandler extends DocumentedGATKFeatureH root.put("summary", def.doc != null ? def.doc : ""); root.put("fulltext", fieldDoc.commentText()); + // Does this argument interact with any others? + root.put("otherArgumentRequired", def.otherArgumentRequired != null ? def.otherArgumentRequired : "NA"); + root.put("exclusiveOf", def.otherArgumentRequired != null ? def.exclusiveOf : "NA"); + // What are our enum options? if (def.validOptions != null) { root.put("options", docForEnumArgument(source.field.getType())); diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java index 707cc8f5e..f9a23dd84 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpConstants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -27,8 +27,9 @@ package org.broadinstitute.gatk.utils.help; public class HelpConstants { - public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk"; + public final static String BASE_GATK_URL = "https://www.broadinstitute.org/gatk"; public final static String GATK_DOCS_URL = BASE_GATK_URL + "/guide/tooldocs/"; + public final static String GATK_ARTICLE_URL = BASE_GATK_URL + "/guide/article"; public final static String GATK_FORUM_URL = "http://gatkforums.broadinstitute.org/"; public final static String GATK_FORUM_API_URL = "https://gatkforums.broadinstitute.org/api/v1/"; @@ -43,40 +44,21 @@ public class HelpConstants { * The names get parsed to make supercategories in the doc index, * so be careful when making big changes -- see GATKDoclet.java toMap() */ - public final static String DOCS_CAT_DATA = "Sequence Data Processing Tools"; - public final static String DOCS_CAT_QC = "Diagnostics and Quality Control Tools"; public final static String DOCS_CAT_ENGINE = "Engine Parameters (available to all tools)"; - public final static String DOCS_CAT_RF = "Read Filters"; - public final static String DOCS_CAT_REFUTILS = "Reference Utilities"; - public final static String DOCS_CAT_RODCODECS = "ROD Codecs"; - public final static String DOCS_CAT_USRERR = "User Exceptions (DevZone)"; - public final static String DOCS_CAT_VALIDATION = "Validation Utilities"; - public final static String DOCS_CAT_ANNOT = "Variant Annotations"; + public final static String DOCS_CAT_QC = "Diagnostics and Quality Control Tools"; + public final static String DOCS_CAT_DATA = "Sequence Data Processing Tools"; public final static String DOCS_CAT_VARDISC = "Variant Discovery Tools"; - public final static String DOCS_CAT_VARMANIP = "Variant Evaluation and Manipulation Tools"; - public final static String DOCS_CAT_TOY = "Toy Walkers (DevZone)"; - public final static String DOCS_CAT_HELPUTILS = "Help Utilities"; + public final static String DOCS_CAT_VAREVAL = "Variant Evaluation Tools"; + public final static String DOCS_CAT_VARMANIP = "Variant Manipulation Tools"; + public final static String DOCS_CAT_ANNOT = "Annotation Modules"; + public final static String DOCS_CAT_RF = "Read Filters"; + public final static String DOCS_CAT_RODCODECS = "Resource File Codecs"; + public final static String DOCS_CAT_REFUTILS = "Reference Utilities"; + public final static String DOCS_CAT_USRERR = "User Exceptions (Exclude)"; + public final static String DOCS_CAT_TOY = "Toy Examples (Exclude)"; - public static String forumPost(String post) { - return GATK_FORUM_URL + post; + public static String articlePost(Integer id) { + return GATK_ARTICLE_URL + "?id=" + id.toString(); } - /** - * Go-to developer name codes for tracking and display purposes. Only current team members should be in this list. - * When someone leaves, their charges should be redistributed. The actual string should be closest to the dev's - * abbreviated name or two/three-letter nickname as possible. The code can be something else if necessary to - * disambiguate from other variable. - */ - public final static String MC = "MC"; // Mauricio Carneiro - public final static String EB = "EB"; // Eric Banks - public final static String RP = "RP"; // Ryan Poplin - public final static String GVDA = "GG"; // Geraldine Van der Auwera - public final static String VRR = "VRR"; // Valentin Ruano-Rubio - public final static String ALM = "ALM"; // Ami Levy-Moonshine - public final static String BH = "BH"; // Bertrand Haas - public final static String JoT = "JT"; // Joel Thibault - public final static String DR = "DR"; // David Roazen - public final static String KS = "KS"; // Khalid Shakir - - } \ No newline at end of file diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java index 5a55f2792..e553ba02d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/HelpFormatter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -204,6 +204,7 @@ public class HelpFormatter { builder.append(Utils.join("|",argumentDefinition.validOptions)); builder.append(")"); } + return builder.toString(); } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java index 83af1d9f1..c1610ed2c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/ResourceBundleExtractorDoclet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java index c61d895f5..681954e26 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/instrumentation/Sizeof.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java index ba196a1b0..f357a04e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalMergingRule.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java index 424485adf..77fbf3d53 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalSetRule.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java index e272eaca9..b2ff1708e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java index 22ec9fe8c..1782da6e2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/FileExtension.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java index 1a38ea089..bb65af037 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/HardThresholdingOutputStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java index 98e1e62dd..543a0ee84 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/IOUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java index bb5e80b7d..0cb5c163f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/ReferenceBacked.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java index 9b8682a7f..3dc42dc20 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/io/Resource.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java index 61d8b9140..8480bd3fa 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java index 82aa8660b..3a94be46e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/GATKSAMIteratorAdapter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java index 836a14929..7f748068d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/iterators/PushbackIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java index cebf5e4d6..8182e6cc6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/JNAUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java index 91baead01..4ec0957a6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/clibrary/LibC.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java index ea5fd19d8..23f188aa5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobInfo.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java index 1afd96cb0..93460d044 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaJobTemplate.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java index 0c0745c4f..58edb8c6e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSession.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java index d97be2b3a..1264170ea 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java index 73ff9cb6e..493def184 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaa.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java index 299b331a7..dbe5f2f17 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBat.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java index 9c8e563c6..262117f77 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibLsf.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java index 15b0e011e..3f2d2d1ea 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachine.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java index efbf33dcc..14f3ca629 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSDownsamplingInfo.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java index aaa518d36..55a4efe64 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LIBSPerformance.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java index 0d2893567..d9501b9ec 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java index c5bf32dd7..3ce8783b5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByState.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java index af9953eaf..b8fd1dfe6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java index 84912897b..586e0f1a7 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/ReadStateManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java index 9ff3998d3..07c80999a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/locusiterator/SamplePartitioner.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java index b0c9d8fd6..6e87ffb4e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/EOFMarkedValue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java index 5676c75bd..50314e0a3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java index ab737f25c..79b6db82e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResult.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java index 3d6682312..2beba61da 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultsQueue.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java index 31ad7e0aa..f29726c19 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSMapFunction.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java index 9b1c40626..30ddcf75a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSProgressFunction.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java index 7f1027fce..b1ffb165f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NSReduceFunction.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java index 50139ddab..13fd921a6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoScheduler.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java index cb3263c5b..b4cc8cea4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/nanoScheduler/Reducer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java index 25907ebd9..53f172fe4 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java index 52b51c0cd..8794a458e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/BatchPairHMM.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java index 4ee17c803..6b9a67eb1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/Log10PairHMM.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java index 387171151..e76550c2c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/N2MemoryPairHMM.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java index 9f57779ae..697777408 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -372,7 +372,7 @@ public abstract class PairHMM { { doProfiling = (numThreads == 1); if(numThreads > 1) - logger.info("Performance profiling for PairHMM is disabled because HaplotypeCaller is being run with multiple threads (-nct>1) option\nProfiling is enabled only when running in single thread mode\n"); + logger.info("Performance profiling for PairHMM is disabled because the program is being run with multiple threads (-nct>1) option\nProfiling is enabled only when running in single thread mode\n"); } /** diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java index 6644c2058..7fa82208a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMModel.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java index a6fcb2bed..aab43cd62 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMReadyHaplotypes.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java index f078d76b0..3d0292792 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/MergingPileupElementIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java index c90669877..a647de993 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElement.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java index 93f39ab1e..d1f62fe8f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementFilter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java index b2a7e84ce..75710c65e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/PileupElementTracker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java index ad2108933..ee2b59da0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileup.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java index 5dd3c6a35..7bee0f92b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupImpl.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java index 07d5075c8..b68a5b9e0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java index 850b9f19b..eb18cb16c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemon.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java index 0b8e984eb..82ee659cc 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterData.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java index 5a74f7245..6e24dbcbb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/recalibration/EventType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java index 7b82ae236..b4915caff 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RODRecordListImpl.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java index 680091662..5aa0fe4fe 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTracker.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java index 72f61b20b..37633c628 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceDependentFeatureCodec.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java index c54f9c55f..32d0c279b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/ReferenceOrderedDatum.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java index 0e0bfda98..0fdbc6413 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/SeekableRODIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java index 8b451780e..868106bc6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java index ea24c2b5a..5e9e8226a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java index a450fce8b..1b55d7d35 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManager.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java index 30bd8ec6f..46dd48b5c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/IndexDictionaryUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -108,7 +108,7 @@ public class IndexDictionaryUtils { Set trackSequences = new TreeSet(); for (SAMSequenceRecord dictionaryEntry : trackDict.getSequences()) trackSequences.add(dictionaryEntry.getSequenceName()); - SequenceDictionaryUtils.validateDictionaries(logger, validationExclusionType, trackName, trackDict, "reference", referenceDict, false, null); + SequenceDictionaryUtils.validateDictionaries(logger, validationExclusionType, trackName, trackDict, "reference", referenceDict, false, null, true); } } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java index 76f2046af..9de109e3b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrack.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java index 0b84c05a2..9e48fa75f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -182,7 +182,7 @@ public class RMDTrackBuilder { // extends PluginManager { final SAMSequenceDictionary vcfDictionary = new SAMSequenceDictionary(vcfContigRecords); final SAMSequenceDictionary sequenceDictionary = new SAMSequenceDictionary(dict.getSequences()); - SequenceDictionaryUtils.validateDictionaries(logger, validationExclusionType, name, vcfDictionary, "sequence", sequenceDictionary, false, null); + SequenceDictionaryUtils.validateDictionaries(logger, validationExclusionType, name, vcfDictionary, "sequence", sequenceDictionary, false, null, false); } } } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java index 743ee95ae..8ea73f775 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java index 4f50460a5..4e61e6932 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java index 4f947d119..34e63b152 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/GATKFeature.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java index 0bee072c2..7a89fab6e 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/LocationAwareSeekableRODIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java index dc35f7e01..de5df4148 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RMDTriplet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java index 4bba78dc9..8f4f2db68 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/utils/RODRecordList.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java index 70a7c6a33..5098bfdd2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReport.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java index 0dbeb3b8e..033c23dee 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumn.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java index 6249f4f21..10c8d0502 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportColumnFormat.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java index a6e640feb..f5342d476 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportDataType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java index f7f5196b3..c749a7999 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportGatherer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java index e40c3f37a..85d2386a0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportTable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java index cf985d5e5..a35c13108 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/report/GATKReportVersion.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java index ee6dfbd96..788ee23c3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/CapturedStreamOutput.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java index 2fdc5bee2..16ac91c71 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/InputStreamSettings.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java index 25375edf1..35a8e2777 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/OutputStreamSettings.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java index 682c25800..ccfeeacd2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessController.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java index 71d90eb31..29553f802 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessOutput.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java index 52d2f0688..5e8f6b2bb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/ProcessSettings.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java index 241ebd212..404464017 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java index bd4298967..461568729 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamLocation.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java index e4a8b571d..0b76e26ff 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/runtime/StreamOutput.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java index 8aac52dfa..ef43feee1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java index b64bbaccf..f8b2385d0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentStartWithNoTiesComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java index 04e3ccbe5..4cc189aea 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/AlignmentUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java index 371e0f326..b69794ed9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java index d430ab7c4..c4d586b21 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialGATKSAMFileWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java index 3d7c3c784..4dea034e5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialMultiSampleReadStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java index 99b317446..5921a0a59 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java index 74b953188..9491ed254 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java index aa035233c..2b218e3c2 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java index e4f8b799a..16ab9434a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java index 2d192d32d..1f565efb6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -26,10 +26,10 @@ package org.broadinstitute.gatk.utils.sam; import htsjdk.samtools.*; -import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.utils.GenomeLoc; import org.broadinstitute.gatk.utils.Utils; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.iterators.GATKSAMIterator; import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState; import org.broadinstitute.gatk.utils.pileup.PileupElement; import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup; @@ -108,13 +108,39 @@ public class ArtificialSAMUtils { // make up some sequence records for (int x = startingChromosome; x < startingChromosome + numberOfChromosomes; x++) { SAMSequenceRecord rec = new SAMSequenceRecord("chr" + (x), chromosomeSize /* size */); - rec.setSequenceLength(chromosomeSize); dict.addSequence(rec); } header.setSequenceDictionary(dict); return header; } + + /** + * Creates an artificial sam header, matching the parameters, + * + * @param contigNames List of names for contigs + * @param contigLengths List of lengths for contigs. the two lists must be of the same size. + * @return a SAMFileHeader with the references with the inputed names and lengths. + **/ + public static SAMFileHeader createArtificialSamHeader(List contigNames, List contigLengths) { + SAMFileHeader header = new SAMFileHeader(); + header.setSortOrder(htsjdk.samtools.SAMFileHeader.SortOrder.coordinate); + SAMSequenceDictionary dict = new SAMSequenceDictionary(); + + // make up some sequence records + if (contigLengths.size() != contigNames.size()) { + throw new ReviewedGATKException("Passed in contigLengths is different from contigNames"); + } + + for (int i = 0; i < contigLengths.size(); i++) { + SAMSequenceRecord rec = new SAMSequenceRecord(contigNames.get(i), contigLengths.get(i)); + dict.addSequence(rec); + } + header.setSequenceDictionary(dict); + return header; + } + + /** * Creates an artificial sam header based on the sequence dictionary dict * diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java index d3eb73dca..1fed6ec2c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStream.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java index 3c7b2aff8..6ad367d3a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java index 3017b56f2..ea2a58869 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/CigarUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java index e04787f22..25af04260 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMFileWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java index 6d85d7d0b..f283dee8b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMReadGroupRecord.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java index 8a9f0448c..d0337638d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecord.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -131,6 +131,10 @@ public class GATKSAMRecord extends SAMRecord implements Cloneable { return ArtificialSAMUtils.createArtificialRead(cigar); } + public Integer getMateMappingQuality(){ + return (Integer) this.getAttribute(SAMTagUtil.getSingleton().MQ); + } + /////////////////////////////////////////////////////////////////////////////// // *** support for reads without meaningful strand information ***// /////////////////////////////////////////////////////////////////////////////// diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java index 1560dce92..9eec7b69f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java index d57238ef6..134b779e3 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUnclippedStartWithNoTiesComparator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java index b3d945ec0..75617e87d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -32,8 +32,9 @@ import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.broadinstitute.gatk.utils.exceptions.UserException; +import org.broadinstitute.gatk.utils.help.HelpConstants; -import java.io.File; import java.util.*; /** @@ -63,11 +64,26 @@ public class ReadUtils { * @return list of strings representing the sample names */ public static Set getSAMFileSamples(final SAMFileHeader header) { + if ( header == null ) { + throw new IllegalArgumentException("Missing SAM file header. " + + "For more information on read groups, see " + HelpConstants.articlePost(6472)); + } + // get all of the unique sample names final Set samples = new TreeSet(); - List readGroups = header.getReadGroups(); - for ( SAMReadGroupRecord readGroup : readGroups ) + final List readGroups = header.getReadGroups(); + if ( readGroups == null ) { + throw new UserException("SAM file header is missing the Read Group (@RG). " + + "For more information on read groups, see " + HelpConstants.articlePost(6472)); + } + for ( final SAMReadGroupRecord readGroup : readGroups ) { + final String sample = readGroup.getSample(); + if ( sample == null ) { + throw new UserException("SAM file header is missing the sample field (SM) in the Read Group (@RG). " + + "For more information on read groups, see " + HelpConstants.articlePost(6472)); + } samples.add(readGroup.getSample()); + } return samples; } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java index 6b72d0c08..4e505eef0 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderBuilder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java index 1338f7cda..e0697516a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SAMReaderID.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java index c431528b1..97dd2ae83 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/SimplifyingSAMFileWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java index c41b5bfeb..20c3c136f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java index 66b897054..153432688 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java index f423a1ad1..f9c3b1be5 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/Parameters.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java index b750b35ca..3c79bdb75 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignment.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java index 40e45d93c..8d1f0fe6c 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWPairwiseAlignmentMain.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java index a5152735e..1a91b17be 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SWParameterSet.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java index a913c5abe..8f60f11e9 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWaterman.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java index 91db56bf3..75a56b110 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/ListFileUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java index 044a65783..06b313613 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/TextFormattingUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java index 267ab5f0c..591080a31 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/text/XReadLines.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java index 97d280a64..c6c446deb 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java index ceb238052..c6fac2d4f 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/NamedThreadFactory.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java index 8d9bddd17..2470c4bd1 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadEfficiencyMonitor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java index 61d4c0d4d..500509535 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadLocalArray.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java index 9af1b366b..f2a6b4e1b 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitor.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java index 6865d11ac..527a417de 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/threading/package-info.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java index 8b1aa1d44..62b4beb3a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/ChromosomeCountConstants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java index ff04c2971..5c7494d7d 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -35,9 +35,12 @@ import htsjdk.variant.variantcontext.Allele; public final class GATKVCFConstants { //INFO keys + public static final String ALLELE_SPECIFIC_PREFIX = "AS_"; public static final String RAW_RMS_MAPPING_QUALITY_KEY = "RAW_MQ"; public static final String AS_RMS_MAPPING_QUALITY_KEY = "AS_MQ"; public static final String AS_RAW_RMS_MAPPING_QUALITY_KEY = "AS_RAW_MQ"; + public static final String AS_MATE_MAP_QUAL_RANK_SUM_KEY = "AS_MateMQRankSum"; + public static final String AS_RAW_MATE_MAP_QUAL_RANK_SUM_KEY = "AS_RAW_MateMQRankSum"; public static final String ALLELE_BALANCE_HET_KEY = "ABHet"; public static final String ALLELE_BALANCE_HOM_KEY = "ABHom"; public static final String ORIGINAL_AC_KEY = "AC_Orig"; //SelectVariants @@ -53,6 +56,7 @@ public final class GATKVCFConstants { public static final String GENOTYPE_AND_VALIDATE_STATUS_KEY = "callStatus"; public static final String CLIPPING_RANK_SUM_KEY = "ClippingRankSum"; public static final String CULPRIT_KEY = "culprit"; + public static final String AS_CULPRIT_KEY = "AS_culprit"; public static final String SPANNING_DELETIONS_KEY = "Dels"; public static final String ORIGINAL_DP_KEY = "DP_Orig"; //SelectVariants public static final String DOWNSAMPLED_KEY = "DS"; @@ -62,6 +66,7 @@ public final class GATKVCFConstants { public static final String FISHER_STRAND_KEY = "FS"; public static final String AS_FISHER_STRAND_KEY = "AS_FS"; public static final String FRACTION_INFORMATIVE_READS_KEY = "FractionInformativeReads"; + public static final String AS_FILTER_STATUS_KEY = "AS_FilterStatus"; public static final String AS_SB_TABLE_KEY = "AS_SB_TABLE"; public static final String GC_CONTENT_KEY = "GC"; public static final String GQ_MEAN_KEY = "GQ_MEAN"; @@ -121,11 +126,14 @@ public final class GATKVCFConstants { public static final String TUMOR_LOD_KEY = "TLOD"; //M2 public static final String VARIANT_TYPE_KEY = "VariantType"; public static final String VQS_LOD_KEY = "VQSLOD"; + public static final String AS_VQS_LOD_KEY = "AS_VQSLOD"; public static final String OXOG_ALT_F1R2_KEY = "ALT_F1R2"; public static final String OXOG_ALT_F2R1_KEY = "ALT_F2R1"; public static final String OXOG_REF_F1R2_KEY = "REF_F1R2"; public static final String OXOG_REF_F2R1_KEY = "REF_F2R1"; public static final String OXOG_FRACTION_KEY = "FOXOG"; + public static final String AS_INSERT_SIZE_RANK_SUM_KEY = "AS_InsertSizeRankSum"; + public static final String AS_RAW_INSERT_SIZE_RANK_SUM_KEY = "AS_RAW_InsertSizeRankSum"; //FORMAT keys public static final String ALLELE_BALANCE_KEY = "AB"; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java index f0fa0724c..e8f960bff 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -119,7 +119,10 @@ public class GATKVCFHeaderLines { addInfoLine(new VCFInfoHeaderLine(BASE_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities")); addInfoLine(new VCFInfoHeaderLine(AS_BASE_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score from Wilcoxon rank sum test of each Alt Vs. Ref base qualities")); addInfoLine(new VCFInfoHeaderLine(AS_RAW_BASE_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "raw data for allele specific rank sum test of base qualities")); + addInfoLine(new VCFInfoHeaderLine(AS_MATE_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "allele specific Z-score from Wilcoxon rank sum test of mate mapping qualities")); + addInfoLine(new VCFInfoHeaderLine(AS_RAW_MATE_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "raw data for allele specific rank sum tes of mate mapping qualities")); addInfoLine(new VCFInfoHeaderLine(CLIPPING_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases")); + addInfoLine(new VCFInfoHeaderLine(AS_FILTER_STATUS_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.String, "Filter status for each allele, as assessed by ApplyRecalibration. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles.")); addInfoLine(new VCFInfoHeaderLine(FISHER_STRAND_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled p-value using Fisher's exact test to detect strand bias")); addInfoLine(new VCFInfoHeaderLine(AS_FISHER_STRAND_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific phred-scaled p-value using Fisher's exact test to detect strand bias of each alt allele")); addInfoLine(new VCFInfoHeaderLine(AS_SB_TABLE_KEY, 1, VCFHeaderLineType.String, "Allele-specific forward/reverse read counts for strand bias tests")); @@ -141,10 +144,11 @@ public class GATKVCFHeaderLines { addInfoLine(new VCFInfoHeaderLine(AS_RAW_RMS_MAPPING_QUALITY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specfic raw data for RMS Mapping Quality")); addInfoLine(new VCFInfoHeaderLine(AS_RMS_MAPPING_QUALITY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific RMS Mapping Quality")); addInfoLine(new VCFInfoHeaderLine(RAW_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Raw data for Mapping Quality Rank Sum")); - addInfoLine(new VCFInfoHeaderLine(AS_RAW_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "Allele-specfic raw data for Mapping Quality Rank Sum")); + addInfoLine(new VCFInfoHeaderLine(AS_RAW_MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "Allele-specific raw data for Mapping Quality Rank Sum")); addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific Mapping Quality Rank Sum")); addInfoLine(new VCFInfoHeaderLine(FRACTION_INFORMATIVE_READS_KEY, 1, VCFHeaderLineType.Float, "The fraction of informative reads out of the total reads")); - + addInfoLine(new VCFInfoHeaderLine(AS_RAW_INSERT_SIZE_RANK_SUM_KEY, 1, VCFHeaderLineType.String, "Allele-specific raw data for Insert Size Rank Sum")); + addInfoLine(new VCFInfoHeaderLine(AS_INSERT_SIZE_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific Insert Size Rank Sum")); addInfoLine(new VCFInfoHeaderLine(MENDEL_VIOLATION_LR_KEY, 1, VCFHeaderLineType.Float, "Mendelian violation likelihood ratio: L[MV] - L[No MV]")); addInfoLine(new VCFInfoHeaderLine(HI_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "High confidence possible de novo mutation (GQ >= 20 for all trio members)=[comma-delimited list of child samples]")); addInfoLine(new VCFInfoHeaderLine(LO_CONF_DENOVO_KEY, 1, VCFHeaderLineType.String, "Low confidence possible de novo mutation (GQ >= 10 for child, GQ > 0 for parents)=[comma-delimited list of child samples]")); @@ -172,7 +176,9 @@ public class GATKVCFHeaderLines { addInfoLine(new VCFInfoHeaderLine(ORIGINAL_CONTIG_KEY, 1, VCFHeaderLineType.String, "Original contig name for the record")); addInfoLine(new VCFInfoHeaderLine(ORIGINAL_START_KEY, 1, VCFHeaderLineType.Integer, "Original start position for the record")); addInfoLine(new VCFInfoHeaderLine(VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "Log odds of being a true variant versus being false under the trained gaussian mixture model")); + addInfoLine(new VCFInfoHeaderLine(AS_VQS_LOD_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.String, "For each alt allele, the log odds of being a true variant versus being false under the trained gaussian mixture model")); addInfoLine(new VCFInfoHeaderLine(CULPRIT_KEY, 1, VCFHeaderLineType.String, "The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out")); + addInfoLine(new VCFInfoHeaderLine(AS_CULPRIT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.String, "For each alt allele, the annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out")); addInfoLine(new VCFInfoHeaderLine(POSITIVE_LABEL_KEY, 1, VCFHeaderLineType.Flag, "This variant was used to build the positive training set of good variants")); addInfoLine(new VCFInfoHeaderLine(NEGATIVE_LABEL_KEY, 1, VCFHeaderLineType.Flag, "This variant was used to build the negative training set of bad variants")); addInfoLine(new VCFInfoHeaderLine(RBP_INCONSISTENT_KEY, 0, VCFHeaderLineType.Flag, "Are the reads significantly haplotype-inconsistent?")); diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java index 0ca4a341f..62f7d60ab 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFIndexType.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java index 520582a47..3bf41d947 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -558,6 +558,12 @@ public class GATKVariantContextUtils { */ SET_TO_NO_CALL, + /** + * set all of the genotype GT values to NO_CALL and remove annotations + */ + SET_TO_NO_CALL_NO_ANNOTATIONS, + + /** * Use the subsetted PLs to greedily assigned genotypes */ @@ -589,7 +595,7 @@ public class GATKVariantContextUtils { } /** - * subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately) + * Subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately) * * @param vc variant context with genotype likelihoods * @param allelesToUse which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC *** @@ -601,6 +607,7 @@ public class GATKVariantContextUtils { final GenotypeAssignmentMethod assignGenotypes) { if ( vc == null ) throw new IllegalArgumentException("the VariantContext cannot be null"); if ( allelesToUse == null ) throw new IllegalArgumentException("the alleles to use cannot be null"); + if ( allelesToUse.isEmpty() ) throw new IllegalArgumentException("must have alleles to use"); if ( allelesToUse.get(0).isNonReference() ) throw new IllegalArgumentException("First allele must be the reference allele"); if ( allelesToUse.size() == 1 ) throw new IllegalArgumentException("Cannot subset to only 1 alt allele"); @@ -859,7 +866,7 @@ public class GATKVariantContextUtils { newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true); } - if ( newLikelihoods == null || likelihoodsAreUninformative(newLikelihoods) ) + if ( newLikelihoods == null || (originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0) == 0 && likelihoodsAreUninformative(newLikelihoods) )) gb.noPL(); else gb.PL(newLikelihoods); @@ -896,6 +903,10 @@ public class GATKVariantContextUtils { final GenotypeAssignmentMethod assignmentMethod, final double[] newLikelihoods, final List allelesToUse) { + if ( originalGT == null ) throw new IllegalArgumentException("originalGT cannot be null"); + if ( gb == null ) throw new IllegalArgumentException("gb cannot be null"); + if ( allelesToUse.isEmpty() || allelesToUse == null ) throw new IllegalArgumentException("allelesToUse cannot be empty or null"); + switch ( assignmentMethod ) { case DO_NOT_ASSIGN_GENOTYPES: break; @@ -903,6 +914,13 @@ public class GATKVariantContextUtils { gb.alleles(NO_CALL_ALLELES); gb.noGQ(); break; + case SET_TO_NO_CALL_NO_ANNOTATIONS: + gb.alleles(NO_CALL_ALLELES); + gb.noGQ(); + gb.noAD(); + gb.noPL(); + gb.noAttributes(); + break; case USE_PLS_TO_ASSIGN: if ( newLikelihoods == null || likelihoodsAreUninformative(newLikelihoods) ) { // if there is no mass on the (new) likelihoods, then just no-call the sample @@ -918,12 +936,10 @@ public class GATKVariantContextUtils { break; case BEST_MATCH_TO_ORIGINAL: final List best = new LinkedList<>(); - final Allele ref = allelesToUse.get(0); // WARNING -- should be checked in input argument + final Allele ref = allelesToUse.get(0); for ( final Allele originalAllele : originalGT ) { best.add(allelesToUse.contains(originalAllele) ? originalAllele : ref); } - gb.noGQ(); - gb.noPL(); gb.alleles(best); break; } @@ -970,7 +986,7 @@ public class GATKVariantContextUtils { /** * Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs * - * @param vc variant context with genotype likelihoods + * @param vc variant context with genotype likelihoods * @return genotypes context */ public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) { @@ -999,7 +1015,6 @@ public class GATKVariantContextUtils { * Split variant context into its biallelic components if there are more than 2 alleles * * For VC has A/B/C alleles, returns A/B and A/C contexts. - * Genotypes are all no-calls now (it's not possible to fix them easily) * Alleles are right trimmed to satisfy VCF conventions * * If vc is biallelic or non-variant it is just returned @@ -1008,21 +1023,63 @@ public class GATKVariantContextUtils { * * @param vc a potentially multi-allelic variant context * @param trimLeft if true, we will also left trim alleles, potentially moving the resulting vcs forward on the genome + * @param genotypeAssignmentMethod assignment strategy for the (subsetted) PLs * @return a list of bi-allelic (or monomorphic) variant context */ - public static List splitVariantContextToBiallelics(final VariantContext vc, final boolean trimLeft, final GenotypeAssignmentMethod genotypeAssignmentMethod) { + public static List splitVariantContextToBiallelics(final VariantContext vc, final boolean trimLeft, final GenotypeAssignmentMethod genotypeAssignmentMethod){ + return splitVariantContextToBiallelics(vc, trimLeft,genotypeAssignmentMethod, false); + } + + /** + * Split variant context into its biallelic components if there are more than 2 alleles + * + * For VC has A/B/C alleles, returns A/B and A/C contexts. + * Alleles are right trimmed to satisfy VCF conventions + * + * If vc is biallelic or non-variant it is just returned + * + * Chromosome counts are updated (but they are by definition 0) + * + * @param vc a potentially multi-allelic variant context + * @param trimLeft if true, we will also left trim alleles, potentially moving the resulting vcs forward on the genome + * @param genotypeAssignmentMethod assignment strategy for the (subsetted) PLs + * @param keepOriginalChrCounts keep the orignal chromosome counts before subsetting + * @return a list of bi-allelic (or monomorphic) variant context + */ + public static List splitVariantContextToBiallelics(final VariantContext vc, final boolean trimLeft, final GenotypeAssignmentMethod genotypeAssignmentMethod, + final boolean keepOriginalChrCounts) { + if ( vc == null ) throw new IllegalArgumentException("vc cannot be null"); + if ( ! vc.isVariant() || vc.isBiallelic() ) // non variant or biallelics already satisfy the contract return Collections.singletonList(vc); else { final List biallelics = new LinkedList<>(); + // if any of the genotypes ar ehet-not-ref (i.e. 1/2), set all of them to no-call + final GenotypeAssignmentMethod genotypeAssignmentMethodUsed = hasHetNonRef(vc.getGenotypes()) ? GATKVariantContextUtils.GenotypeAssignmentMethod.SET_TO_NO_CALL_NO_ANNOTATIONS : genotypeAssignmentMethod; + for ( final Allele alt : vc.getAlternateAlleles() ) { - VariantContextBuilder builder = new VariantContextBuilder(vc); + final VariantContextBuilder builder = new VariantContextBuilder(vc); + + // make biallelic alleles final List alleles = Arrays.asList(vc.getReference(), alt); builder.alleles(alleles); - builder.genotypes(subsetDiploidAlleles(vc, alleles, genotypeAssignmentMethod)); - VariantContextUtils.calculateChromosomeCounts(builder, true); + + // since the VC has been subset, remove the invalid attributes + for ( final String key : vc.getAttributes().keySet() ) { + if ( !(key.equals(VCFConstants.ALLELE_COUNT_KEY) || key.equals(VCFConstants.ALLELE_FREQUENCY_KEY) || key.equals(VCFConstants.ALLELE_NUMBER_KEY)) || + genotypeAssignmentMethodUsed == GATKVariantContextUtils.GenotypeAssignmentMethod.SET_TO_NO_CALL_NO_ANNOTATIONS ) { + builder.rmAttribute(key); + } + } + + // subset INFO field annotations if available if genotype is called + if ( genotypeAssignmentMethodUsed != GATKVariantContextUtils.GenotypeAssignmentMethod.SET_TO_NO_CALL_NO_ANNOTATIONS && + genotypeAssignmentMethodUsed != GATKVariantContextUtils.GenotypeAssignmentMethod.SET_TO_NO_CALL ) + addInfoFiledAnnotations(vc, builder, alt, keepOriginalChrCounts); + + builder.genotypes(subsetDiploidAlleles(vc, alleles, genotypeAssignmentMethodUsed)); final VariantContext trimmed = trimAlleles(builder.make(), trimLeft, true); biallelics.add(trimmed); } @@ -1031,6 +1088,21 @@ public class GATKVariantContextUtils { } } + /** + * Check if any of the genotypes is heterozygous, non-reference (i.e. 1/2) + * + * @param genotypesContext genotype information + * @return true if any of the genotypes are heterozygous, non-reference, false otherwise + */ + private static boolean hasHetNonRef(final GenotypesContext genotypesContext ){ + for (final Genotype gt : genotypesContext ) { + if (gt.isHetNonRef()) + return true; + } + return false; + } + + public static Genotype removePLsAndAD(final Genotype g) { return ( g.hasLikelihoods() || g.hasAD() ) ? new GenotypeBuilder(g).noPL().noAD().make() : g; } @@ -1336,7 +1408,7 @@ public class GATKVariantContextUtils { * * @param originalGs the original GenotypesContext * @param originalVC the original VariantContext - * @param allelesToUse the new (sub)set of alleles to use + * @param allelesToUse the new subset of alleles to use * @return a new non-null GenotypesContext */ static private GenotypesContext fixDiploidGenotypesFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List allelesToUse) { @@ -2121,4 +2193,142 @@ public class GATKVariantContextUtils { return -1; } + + /** + * Add the VCF INFO field annotations for the used alleles + * + * @param vc original variant context + * @param builder variant context builder with subset of original variant context's alleles + * @param altAllele alternate allele + * @param keepOriginalChrCounts keep the orignal chromosome counts before subsetting + * @return variant context builder with updated INFO field attribute values + */ + private static void addInfoFiledAnnotations(final VariantContext vc, final VariantContextBuilder builder, final Allele altAllele, + final boolean keepOriginalChrCounts){ + + if (vc == null) throw new IllegalArgumentException("the variant context cannot be null"); + if (builder == null) throw new IllegalArgumentException("the variant context builder cannot be null"); + if (builder.getAlleles() == null) throw new IllegalArgumentException("the variant context builder alleles cannot be null"); + + final List alleles = builder.getAlleles(); + if (alleles.size() < 2) throw new IllegalArgumentException("the variant context builder must contain at least 2 alleles"); + + // don't have to subset, the original vc has the same number and hence, the same alleles + boolean keepOriginal = ( vc.getAlleles().size() == builder.getAlleles().size() ); + + if ( keepOriginalChrCounts ) { + if (vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) + builder.attribute(GATKVCFConstants.ORIGINAL_AC_KEY, keepOriginal ? + vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY) : getAltAlleleInfoFieldValue(VCFConstants.ALLELE_COUNT_KEY, vc, altAllele)); + if (vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)) + builder.attribute(GATKVCFConstants.ORIGINAL_AF_KEY, keepOriginal ? + vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) : getAltAlleleInfoFieldValue(VCFConstants.ALLELE_FREQUENCY_KEY, vc, altAllele)); + if (vc.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY)) { + builder.attribute(GATKVCFConstants.ORIGINAL_AN_KEY, vc.getAttribute(VCFConstants.ALLELE_NUMBER_KEY)); + } + } + + VariantContextUtils.calculateChromosomeCounts(builder, true); + } + + + /** + * Get the alternate allele INFO field value + * + * @param infoFieldName VCF INFO field name + * @param vc variant context + * @param altAllele the alternate allele + * @return alternate allele INFO field value + * @throws ReviewedGATKException if the alternate allele is part of the variant context + */ + private static Object getAltAlleleInfoFieldValue(final String infoFieldName, final VariantContext vc, final Allele altAllele) { + + //final String[] splitOriginalField = vc.getAttribute(infoFieldName).toString().split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR); + final Object[] splitOriginalField = getVAttributeValues(vc.getAttribute(infoFieldName)); + + // subset the field + final boolean[] alleleIndexesToUse = getAlleleIndexBitset(vc, Arrays.asList(altAllele)); + + // skip the first allele, which is the reference + for (int i = 1; i < alleleIndexesToUse.length; i++) { + if (alleleIndexesToUse[i] == true) + return splitOriginalField[i-1]; + } + + throw new ReviewedGATKException("Alternate allele " + altAllele.toString() + " not in Variant Context " + vc.toString()); + } + + /** + * Pulls out the appropriate values for the INFO field attribute + * + * @param attribute INFO field attribute + * @return tokenized attribute values + */ + private static Object[] getVAttributeValues(final Object attribute) { + + if (attribute == null) throw new IllegalArgumentException("the attribute cannot be null"); + + // break the original attributes into separate tokens + final Object[] tokens; + if ( attribute.getClass().isArray() ) + tokens = (Object[])attribute; + else if ( List.class.isAssignableFrom(attribute.getClass()) ) + tokens = ((List)attribute).toArray(); + else + tokens = attribute.toString().split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR); + + return tokens; + } + + /** + * Increment the number of called alternate and reference plus alternate alleles for a genotype + * + * @param calledAltAlleles number of called alternate alleles for all genotypes + * @param calledAlleles number of called alleles for all genotypes + * @param genotype genotype + * @return incremented called alleles + * @throws IllegalArgumentException if calledAltAlleles or genotype are null + */ + public static int incrementChromosomeCountsInfo(final Map calledAltAlleles, final int calledAlleles, final Genotype genotype) { + if ( calledAltAlleles == null ) throw new IllegalArgumentException("Called alternate alleles can not be null"); + if ( genotype == null ) throw new IllegalArgumentException("Genotype can not be null"); + + int incrementedCalledAlleles = calledAlleles; + if (genotype.isCalled()) { + for (final Allele allele : genotype.getAlleles()) { + incrementedCalledAlleles++; + if (allele.isNonReference()) { + calledAltAlleles.put(allele, calledAltAlleles.get(allele) + 1); + } + } + } + + return incrementedCalledAlleles; + } + + /** + * Update the variant context chromosome counts info fields (AC, AN, AF) + * + * @param calledAltAlleles number of called alternate alleles for all genotypes + * @param calledAlleles number of called alleles for all genotypes + * @param builder builder for variant context + * @throws IllegalArgumentException if calledAltAlleles or builder are null + */ + public static void updateChromosomeCountsInfo(final Map calledAltAlleles, final int calledAlleles, + final VariantContextBuilder builder) { + if ( calledAltAlleles == null ) throw new IllegalArgumentException("Called alternate alleles can not be null"); + if ( builder == null ) throw new IllegalArgumentException("Variant context builder can not be null"); + + builder.attribute(VCFConstants.ALLELE_COUNT_KEY, calledAltAlleles.values().toArray()). + attribute(VCFConstants.ALLELE_NUMBER_KEY, calledAlleles); + // Add AF is there are called alleles + if ( calledAlleles != 0 ) { + final Set alleleFrequency = new LinkedHashSet(calledAltAlleles.size()); + for ( final Integer value : calledAltAlleles.values() ) { + alleleFrequency.add(value.doubleValue()/calledAlleles); + } + builder.attribute(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFrequency.toArray()); + } + } } + diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java index a8695fe84..216fe9d5a 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/HomoSapiensConstants.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java index 85f2ba3ec..0289e3937 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/VCIterable.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java index 4368ffd70..852b85ffd 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleHeader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java index c7071f1dd..e1818ccd6 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/wiggle/WiggleWriter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java index f0a1c9c17..ec14bb5f7 100644 --- a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java +++ b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java index 234bbcf7e..1e0a7ae07 100644 --- a/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java +++ b/public/gatk-utils/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java index fb95d6777..41e8da95b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/AutoFormattingTimeUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java index e151541aa..4d11a43cd 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java index 92a412f93..6b4483e01 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BaseUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java index 0124a0862..c5f629175 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/BitSetUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java index 6f8a6789d..186f39f84 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/ExampleToCopyUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java index 69e66fbda..76f26411a 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GATKTextReporter.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java index 402e3edaf..43af1502c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java index 2f49bbd60..5432e236f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocParserUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -29,17 +29,17 @@ package org.broadinstitute.gatk.utils; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; +import htsjdk.samtools.util.CollectionUtil; import htsjdk.tribble.Feature; import htsjdk.tribble.SimpleFeature; -import org.broadinstitute.gatk.utils.BaseTest; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils; import org.broadinstitute.gatk.utils.sam.GATKSAMRecord; -import htsjdk.variant.variantcontext.Allele; -import htsjdk.variant.variantcontext.VariantContext; -import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; @@ -47,9 +47,7 @@ import org.testng.annotations.Test; import java.io.File; import java.io.FileNotFoundException; -import java.util.Arrays; -import java.util.LinkedList; -import java.util.List; +import java.util.*; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; @@ -65,12 +63,88 @@ public class GenomeLocParserUnitTest extends BaseTest { private GenomeLocParser genomeLocParser; private SAMFileHeader header; + private GenomeLocParser bizareGenomeLocParser; + private SAMFileHeader bizareHeader; + @BeforeClass - public void init() { + public void init() { header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10); genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); + + //Crazy contig names that are all allowed by the SAM-Spec + bizareHeader = ArtificialSAMUtils.createArtificialSamHeader( + CollectionUtil.makeList("LooksLikeHasPos:01",//1 + "LooksLikeARange:01-02",//2 + "LooksLikeWhole:1+",//3 + "\'Quoted\'",//4 + "***Stars***",//5 + "TwoColons:01:02",//6 + "ConfusingElements:1-2",//7 + "ConfusingElements:1",//8 + "ConfusingElements:1+"//9 + // , "ConfusingElements" //10 ... This element causes trouble + ), + CollectionUtil.makeList(20, 20, 20, 20, 20, 20, 20, 20, 20 + // ,20 // ... not sure how to deal with it. + )); + bizareGenomeLocParser = new GenomeLocParser(bizareHeader.getSequenceDictionary()); } + + @DataProvider() + public Object[][] TestConfusingContigNamesData(){ + List tests=new ArrayList<>(); + + tests.add(new Object[]{CollectionUtil.makeList("ConfusingElements:1-2","ConfusingElements")}); + tests.add(new Object[]{CollectionUtil.makeList("ConfusingElements:1-2","ConfusingElements:1-")}); + tests.add(new Object[]{CollectionUtil.makeList("ConfusingElements:1-2","ConfusingElements:1")}); + tests.add(new Object[]{CollectionUtil.makeList("ConfusingElements:1-2,00","ConfusingElements:1")}); + tests.add(new Object[]{CollectionUtil.makeList("ConfusingElements:1,0-200","ConfusingElements:1,0")}); + tests.add(new Object[]{CollectionUtil.makeList("ConfusingElements:1-2,00","ConfusingElements:1")}); + tests.add(new Object[]{CollectionUtil.makeList("ConfusingElements:1-3","ConfusingElements")}); + tests.add(new Object[]{CollectionUtil.makeList("ConfusingElements:1","ConfusingElements")}); + tests.add(new Object[]{CollectionUtil.makeList("ConfusingElements:1+","ConfusingElements")}); + + return tests.toArray(new Object[tests.size()][]); + } + + @Test(dataProvider = "TestConfusingContigNamesData" ) + void TestConfusingContigNames(final List contigNames){ + + ValidationAppender checkWarning = new ValidationAppender(GenomeLocParser.AMBIGUOUS_CONTIG_WARNINIG); + + final SAMFileHeader confusingHeader = ArtificialSAMUtils.createArtificialSamHeader( + contigNames, Collections.nCopies(contigNames.size(), 20)); + + logger.addAppender(checkWarning); + new GenomeLocParser(confusingHeader.getSequenceDictionary()); + + Assert.assertTrue(checkWarning.foundString(),"Expected warning about prefixes"); + } + + + @DataProvider + public Object[][] testBizzarreContigNamesData() { + List tests = new ArrayList<>(); + + for (final SAMSequenceRecord sequence : bizareGenomeLocParser.getContigs().getSequences()) { + String name = sequence.getSequenceName(); + tests.add(new Object[]{name, new GenomeLoc(name, bizareGenomeLocParser.getContigIndex(name), 1, sequence.getSequenceLength())}); + tests.add(new Object[]{name + ":1", new GenomeLoc(name, bizareGenomeLocParser.getContigIndex(name), 1, 1)}); + tests.add(new Object[]{name + ":1+", new GenomeLoc(name, bizareGenomeLocParser.getContigIndex(name), 1, sequence.getSequenceLength())}); + tests.add(new Object[]{name + ":1-10", new GenomeLoc(name, bizareGenomeLocParser.getContigIndex(name), 1, 10)}); + } + + return tests.toArray(new Object[tests.size()][]); + } + + @Test(dataProvider = "testBizzarreContigNamesData") + public void testBizzarreContigNames(String inputString, GenomeLoc expectedResult) { + + Assert.assertEquals(bizareGenomeLocParser.parseGenomeLoc(inputString), expectedResult); + } + + @Test(expectedExceptions=UserException.MalformedGenomeLoc.class) public void testGetContigIndex() { assertEquals(genomeLocParser.getContigIndex("blah"), -1); // should not be in the reference diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java index cc6315df5..47c1f4d0f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocSortedSetUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java index c60356942..9f4b34c27 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/GenomeLocUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java index 2f88c4e04..27ff55f61 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java index a85debde1..ff19686a6 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MD5Mismatch.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java index ef6ef7738..e5bebacdc 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MRUCachingSAMSequencingDictionaryUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java index fb0057898..a3e781343 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MWUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -25,13 +25,13 @@ package org.broadinstitute.gatk.utils; -import org.broadinstitute.gatk.utils.BaseTest; -import org.broadinstitute.gatk.utils.collections.Pair; - import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import org.testng.Assert; +import java.util.Arrays; + /** * Created by IntelliJ IDEA. * User: Ghost @@ -40,92 +40,103 @@ import org.testng.Assert; * To change this template use File | Settings | File Templates. */ public class MWUnitTest extends BaseTest { + private static double DELTA_PRECISION = 0.00001; + @BeforeClass public void init() { } - @Test - private void testMWU() { - logger.warn("Testing MWU"); - MannWhitneyU mwu = new MannWhitneyU(); - mwu.add(0, MannWhitneyU.USet.SET1); - mwu.add(1,MannWhitneyU.USet.SET2); - mwu.add(2,MannWhitneyU.USet.SET2); - mwu.add(3,MannWhitneyU.USet.SET2); - mwu.add(4,MannWhitneyU.USet.SET2); - mwu.add(5,MannWhitneyU.USet.SET2); - mwu.add(6,MannWhitneyU.USet.SET1); - mwu.add(7,MannWhitneyU.USet.SET1); - mwu.add(8,MannWhitneyU.USet.SET1); - mwu.add(9,MannWhitneyU.USet.SET1); - mwu.add(10,MannWhitneyU.USet.SET1); - mwu.add(11,MannWhitneyU.USet.SET2); - Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwu.getObservations(), MannWhitneyU.USet.SET1),25L); - Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwu.getObservations(),MannWhitneyU.USet.SET2),11L); + private static final MannWhitneyU rst = new MannWhitneyU(); - MannWhitneyU mwu2 = new MannWhitneyU(); - MannWhitneyU mwuNoDither = new MannWhitneyU(false); - for ( int dp : new int[]{2,4,5,6,8} ) { - mwu2.add(dp,MannWhitneyU.USet.SET1); - mwuNoDither.add(dp,MannWhitneyU.USet.SET1); - } + @DataProvider(name="rankSumTestData") + public Object[][] dataProvider() { + return new Object[][] { + new Object[] {"test1", new double[] {20,20,20,20,20}, new double[] {20,20,20,20,21}, 10d}, + new Object[] {"test2", new double[] {20,20,20,20,21}, new double[] {20,20,20,20,21}, 12.5d}, + new Object[] {"test3", new double[] {13,14,15,15,16}, new double[] {16,20,20,21,21}, 0.5d}, + new Object[] {"test4", new double[] {13,14,15,15,16}, new double[] {16,20,20,21,21,21,21,22,23,27}, 0.5d}, + new Object[] {"test5", new double[] {13,14,15,15,16,18,20,22,25,24,25,26,27,28,22,23,19,30,28,22,17}, + new double[] {16,20,20,21,21,21,21,22,23,27,26,28,29,32,31,22,21,19,16,24,29}, + 180.5d}, + new Object[] {"test6", new double[] {13,14,15,15,16,18,13,14,15,15,16,18,13,14,15,15,16,18,13,14,15,15,16,18}, + new double[] {21,22,23,27,26,28,29,21,22,23,27,26,28,29,21,22,23,27,26,28,29,21,22,23,27,26,28,29}, + 0d}, + new Object[] {"test7", new double[] {11,11,12,12,13,13,14,14,15,15,16,16,17,17,18,18,19,19,20}, + new double[] {12,12,13,13,14,14,15,15,16,16,17,17,18,18,19,19,20,20,21}, + 145d}, + new Object[] {"test7", new double[] {11,11,12,12,13,13,14,14,15,15,16,16,17,17,18,18,19,19,20,20}, + new double[] {12,12,13,13,14,14,15,15,16,16,17,17,18,18,19,19,20,20,21,21}, + 162d}, + new Object[] {"test8", new double[] {20,20,20,20,20}, new double[] {20,20,20,20,20,20,20,20,20,20}, 25d}, + }; + } - for ( int dp : new int[]{1,3,7,9,10,11,12,13} ) { - mwu2.add(dp,MannWhitneyU.USet.SET2); - mwuNoDither.add(dp,MannWhitneyU.USet.SET2); - } + @Test(dataProvider = "rankSumTestData") + public void testSimpleU(String name, double[] series1, double[] series2, double U) { + MannWhitneyU.Result test = rst.test(series1, series2, MannWhitneyU.TestType.TWO_SIDED); + System.out.println("=========================================================="); + System.out.println("Series 1: " + Arrays.toString(series1)); + System.out.println("Series 2: " + Arrays.toString(series2)); + System.out.println(" U: " + test.getU()); + System.out.println(" Z: " + test.getZ()); + System.out.println("2-side p: " + test.getP()); + Assert.assertEquals(test.getU(), U, name); + } - MannWhitneyU.ExactMode pm = MannWhitneyU.ExactMode.POINT; - MannWhitneyU.ExactMode cm = MannWhitneyU.ExactMode.CUMULATIVE; + @DataProvider(name="oneSidedPTestData") + public Object[][] oneSidedDataProvider() { + return new Object[][] { + new Object[] {"test0", new double[] {0,0}, new double[] {1,1}, 0.083333333}, + new Object[] {"test1", new double[] {20,20,20,20,20}, new double[] {20,20,20,20,21}, .25}, + new Object[] {"test2", new double[] {20,20,20,20,21}, new double[] {20,20,20,20,21}, .5}, + new Object[] {"test3", new double[] {13,14,15,15,16}, new double[] {16,20,20,21,21}, 0.00396825}, + new Object[] {"test4", new double[] {13,14,15,15,16}, new double[] {16,20,20,21,21,21,21,22,23,27}, 0.001469192}, + new Object[] {"test5", new double[] {20,20,20,20,20}, new double[] {20,20,20,20,20,20,20,20,20,20}, .5}, + new Object[] {"test6", new double[] {1,2,3,4,5}, new double[] {6,7,8,9,10}, 0.001984}, + new Object[] {"test7", new double[] {6,7,8,9,10}, new double[] {1,2,3,4,5}, 0.99801587}, + new Object[] {"test8", new double[] {16,20,20,21,21,21,21,22,23,27,16,20,20,21,21,21,21,22,23,27}, + new double[] {22,23,27,16,20,20,21,21,21,21,22,23,27,60,60}, .08303102}, + new Object[] {"test9", new double[] {16,20,20,21,21,21,21,21,20}, + new double[] {22,23,27,16,20,20,20,20,21}, 0.388204}, + }; + } - // tests using the hypothesis that set 2 dominates set 1 (U value = 10) - Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwu2.getObservations(),MannWhitneyU.USet.SET1),10L); - Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwu2.getObservations(),MannWhitneyU.USet.SET2),30L); - Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwuNoDither.getObservations(),MannWhitneyU.USet.SET1),10L); - Assert.assertEquals(MannWhitneyU.calculateOneSidedU(mwuNoDither.getObservations(),MannWhitneyU.USet.SET2),30L); + @Test(dataProvider = "oneSidedPTestData") + public void testOnesidedP(String name, double[] series1, double[] series2, double P) { + MannWhitneyU.Result test = rst.test(series1, series2, MannWhitneyU.TestType.FIRST_DOMINATES); + System.out.println("=========================================================="); + System.out.println("Series 1: " + Arrays.toString(series1)); + System.out.println("Series 2: " + Arrays.toString(series2)); + System.out.println(" U: " + test.getU()); + System.out.println(" Z: " + test.getZ()); + System.out.println("1-side p: " + test.getP()); + Assert.assertEquals(test.getP(), P, DELTA_PRECISION, name); + } - Pair sizes = mwu2.getSetSizes(); - - Assert.assertEquals(MannWhitneyU.calculatePUniformApproximation(sizes.first,sizes.second,10L),0.4180519701814064,1e-14); - Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.first,sizes.second,10L,false,pm).second,0.021756021756021756,1e-14); - Assert.assertEquals(MannWhitneyU.calculatePNormalApproximation(sizes.first,sizes.second,10L,false).second,0.06214143703127617,1e-14); - logger.warn("Testing two-sided"); - Assert.assertEquals((double)mwu2.runTwoSidedTest().second,2*0.021756021756021756,1e-8); - - // tests using the hypothesis that set 1 dominates set 2 (U value = 30) -- empirical should be identical, normall approx close, uniform way off - Assert.assertEquals(MannWhitneyU.calculatePNormalApproximation(sizes.second,sizes.first,30L,true).second,2.0*0.08216463976903321,1e-14); - Assert.assertEquals(MannWhitneyU.calculatePUniformApproximation(sizes.second,sizes.first,30L),0.0023473625009559074,1e-14); - Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,30L,false,pm).second,0.021756021756021756,1e-14); // note -- exactly same value as above - Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,29L,false,cm).second,1.0-0.08547008547008,1e-14); // r does a correction, subtracting 1 from U - Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,11L,false,cm).second,0.08547008547008,1e-14); // r does a correction, subtracting 1 from U - Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,11L,false,cm).first,-1.36918910442,1e-2); // apache inversion set to be good only to 1e-2 - Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,29L,false,cm).first,1.36918910442,1e-2); // apache inversion set to be good only to 1e-2 - Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,29L,false,pm).first,1.2558754796642067,1e-8); // PDF should be similar - Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,11L,false,pm).first,-1.2558754796642067,1e-8); // PDF should be similar - Assert.assertEquals(MannWhitneyU.calculatePRecursively(4,5,10L,false,pm).second,0.0952381,1e-5); - Assert.assertEquals(MannWhitneyU.calculatePRecursively(4,5,10L,false,pm).first,0.0,1e-14); - - logger.warn("Set 1"); - Assert.assertEquals((double)mwu2.runOneSidedTest(MannWhitneyU.USet.SET1).second,0.021756021756021756,1e-8); - logger.warn("Set 2"); - Assert.assertEquals((double)mwu2.runOneSidedTest(MannWhitneyU.USet.SET2).second,0.021756021756021756,1e-8); - - MannWhitneyU mwu3 = new MannWhitneyU(); - for ( int dp : new int[]{0,2,4} ) { - mwu3.add(dp,MannWhitneyU.USet.SET1); - } - for ( int dp : new int[]{1,5,6,7,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34} ) { - mwu3.add(dp,MannWhitneyU.USet.SET2); - } - long u = MannWhitneyU.calculateOneSidedU(mwu3.getObservations(),MannWhitneyU.USet.SET1); - //logger.warn(String.format("U is: %d",u)); - Pair nums = mwu3.getSetSizes(); - //logger.warn(String.format("Corrected p is: %.4e",MannWhitneyU.calculatePRecursivelyDoNotCheckValuesEvenThoughItIsSlow(nums.first,nums.second,u))); - //logger.warn(String.format("Counted sequences: %d",MannWhitneyU.countSequences(nums.first, nums.second, u))); - //logger.warn(String.format("Possible sequences: %d", (long) Arithmetic.binomial(nums.first+nums.second,nums.first))); - //logger.warn(String.format("Ratio: %.4e",MannWhitneyU.countSequences(nums.first,nums.second,u)/Arithmetic.binomial(nums.first+nums.second,nums.first))); - Assert.assertEquals(MannWhitneyU.calculatePRecursivelyDoNotCheckValuesEvenThoughItIsSlow(nums.first, nums.second, u), 3.665689149560116E-4, 1e-14); - Assert.assertEquals(MannWhitneyU.calculatePNormalApproximation(nums.first,nums.second,u,false).second,0.0032240865760884696,1e-14); - Assert.assertEquals(MannWhitneyU.calculatePUniformApproximation(nums.first,nums.second,u),0.0026195003025784036,1e-14); + @DataProvider(name="oneSidedZTestData") + public Object[][] oneSidedZDataProvider() { + return new Object[][] { + new Object[] {"test1", new double[] {20}, new double[] {20,20,20}, 0}, + new Object[] {"test2", new double[] {1}, new double[] {1,2,3}, -0.67448975}, + new Object[] {"test3", new double[] {1,2,3}, new double[] {3}, -0.67448975}, + new Object[] {"test4", new double[] {1,2,3}, new double[] {1}, 0.67448975}, + new Object[] {"test5", new double[] {3,3}, new double[] {1,2,3}, 1.036433}, + new Object[] {"test6", new double[] {20,20,20}, new double[] {20,20,20}, 0}, + new Object[] {"test7", new double[] {20,20,20,20,20}, new double[] {20,20,20,20,20,20,20,20,20,20,20,20,20}, 0}, + new Object[] {"test8", new double[] {1}, new double[] {2}, -0.67448975}, + new Object[] {"test9", new double[] {1}, new double[] {1}, 0}, + new Object[] {"test10", new double[] {60,70,70,60,60,60,60,60}, new double[] {60,60,60,60,60}, .91732119} + }; + } + @Test(dataProvider = "oneSidedZTestData") + public void testOnesidedZ(String name, double[] series1, double[] series2, double Z) { + MannWhitneyU.Result test = rst.test(series1, series2, MannWhitneyU.TestType.FIRST_DOMINATES); + System.out.println("=========================================================="); + System.out.println("Series 1: " + Arrays.toString(series1)); + System.out.println("Series 2: " + Arrays.toString(series2)); + System.out.println(" U: " + test.getU()); + System.out.println(" Z: " + test.getZ()); + System.out.println("1-side p: " + test.getP()); + Assert.assertEquals(test.getZ(), Z, DELTA_PRECISION, name); } } diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java index 283558256..022340177 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MathUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java index 74dfdb909..bf04176fa 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/MedianUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java index 998ef1d6f..1f8b1f49c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/NGSPlatformUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java index 45bef5866..3f98c71f9 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/PathUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java index 993878bf1..f42dadc90 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/QualityUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java index 98f973690..373a9c499 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptExecutorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java index ac3118ecb..282a1bc43 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RScriptLibraryUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java index 8e96d62f9..aab34be37 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/R/RUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java index bbbcb94e7..817dcc769 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SequenceDictionaryUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -181,7 +181,8 @@ public class SequenceDictionaryUtilsUnitTest extends BaseTest { "secondDictionary", secondDictionary, isReadsToReferenceComparison, - intervals); + intervals, + true); } catch ( Exception e ) { exceptionThrown = e; @@ -218,7 +219,7 @@ public class SequenceDictionaryUtilsUnitTest extends BaseTest { SequenceDictionaryUtils.getDictionaryAsString(secondDictionary)); final SequenceDictionaryUtils.SequenceDictionaryCompatibility reportedCompatibility = - SequenceDictionaryUtils.compareDictionaries(firstDictionary, secondDictionary); + SequenceDictionaryUtils.compareDictionaries(firstDictionary, secondDictionary, true); Assert.assertTrue(reportedCompatibility == dictionaryCompatibility, String.format("Dictionary comparison should have returned %s but instead returned %s. %s", diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java index 05203ad11..e2c455216 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/SimpleTimerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java index e4772b3af..b05a4d8e0 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/TestNGTestTransformer.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java index 22e534844..cc5172894 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/UtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java index 8fc6420a4..4a0b38215 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActiveRegionUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java index dfc30ae03..f83ddce49 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileStateUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java index 7ee1040e7..cd0a44d73 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/ActivityProfileUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java index fa75e7163..1796940cf 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/activeregion/BandPassActivityProfileUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java index 1e9fd88b1..0f065eef6 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/baq/BAQUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java index 96ec5f6b2..b67e7b17c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/classloader/JVMUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java index 06b70b744..2ac2c6a81 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperTestUtils.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java index 69abeb2b5..43f7341bd 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/clipping/ReadClipperUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java index 05632d6db..2b3f1be1a 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/beagle/BeagleCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java index cf6bc20a7..f41f728ec 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java index 1f1f6b99e..86637d54a 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/refseq/RefSeqCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java index 301d671c9..a0e610a15 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/sampileup/SAMPileupCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java index f5c0f5ff5..42eaeba06 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/samread/SAMReadCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java index 33ec130b4..71f01211d 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/table/TableCodecUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java index 78865bee0..ad2233c94 100755 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/DefaultHashMapUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java index 78b19d6ff..41e9a5e7f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/collections/ExpandingArrayListUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java index 32cec45b9..e2334a2e8 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSiteUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java index 418bfe151..8628c8187 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ArgumentMatchSourceUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ListAppenderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ListAppenderUnitTest.java new file mode 100644 index 000000000..124bea323 --- /dev/null +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ListAppenderUnitTest.java @@ -0,0 +1,95 @@ +/* +* Copyright 2012-2016 Broad Institute, Inc. +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +package org.broadinstitute.gatk.utils.commandline; + +import org.apache.log4j.Level; +import org.apache.log4j.Logger; +import org.apache.log4j.PatternLayout; +import org.apache.commons.lang.StringUtils; +import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException; +import org.testng.Assert; +import org.testng.annotations.Test; + +public class ListAppenderUnitTest { + + private final static int EVENTS_TO_KEEP = 10; + private final static int EVENTS = 200; + private final static String MSG_TO_LOG = ": All work and no play makes Jack a dull boy."; + private final static String MSG_TOO_LONG = ": Don't write this one."; + private final static Logger LOGGER = Logger.getLogger(ListAppenderUnitTest.class); + + @Test + public void testListAppender() { + + LOGGER.removeAllAppenders(); + final ListAppender listAppender = new ListAppender(new PatternLayout(PatternLayout.DEFAULT_CONVERSION_PATTERN), EVENTS_TO_KEEP, Level.WARN); + LOGGER.addAppender(listAppender); + + for ( int i = 0; i < EVENTS; i++ ) { + LOGGER.warn(i + MSG_TO_LOG); + LOGGER.info(i + MSG_TOO_LONG); + } + + final String listAppenderString = listAppender.toString(); + listAppender.write(); + + Assert.assertEquals(StringUtils.countMatches(listAppenderString, MSG_TO_LOG), EVENTS_TO_KEEP); + Assert.assertFalse(listAppenderString.contains(MSG_TOO_LONG)); + Assert.assertTrue(listAppenderString.contains(Integer.toString(EVENTS_TO_KEEP))); + Assert.assertTrue(listAppenderString.contains(listAppender.logLevelToKeep.toString())); + Assert.assertEquals(listAppender.numLoggingEvents, EVENTS); + } + + @Test + public void testListAppenderNoWarnMsgs() { + + LOGGER.removeAllAppenders(); + final ListAppender listAppender = new ListAppender(new PatternLayout(PatternLayout.DEFAULT_CONVERSION_PATTERN), EVENTS_TO_KEEP, Level.WARN); + LOGGER.addAppender(listAppender); + + for ( int i = 0; i < EVENTS; i++ ) { + LOGGER.info(i + MSG_TOO_LONG); + } + + final String listAppenderString = listAppender.toString(); + Assert.assertEquals(StringUtils.countMatches(listAppenderString, MSG_TO_LOG), 0); + Assert.assertFalse(listAppenderString.contains(MSG_TOO_LONG)); + Assert.assertFalse(listAppenderString.contains(Integer.toString(EVENTS_TO_KEEP))); + Assert.assertTrue(listAppenderString.contains(listAppender.logLevelToKeep.toString().toLowerCase())); + Assert.assertEquals(listAppender.numLoggingEvents, 0); + } + + @Test(expectedExceptions = ReviewedGATKException.class) + public void testListAppenderMissingLayout() { + + LOGGER.removeAllAppenders(); + final ListAppender listAppender = new ListAppender(null, 1, Level.WARN); + LOGGER.addAppender(listAppender); + LOGGER.warn("Warning"); + + final String listAppenderString = listAppender.toString(); + } +} diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java index 6b80ebd4b..4e0db008c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/ParsingEngineUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -86,7 +86,7 @@ public class ParsingEngineUnitTest extends BaseTest { MultiCharShortNameArgProvider argProvider = new MultiCharShortNameArgProvider(); parsingEngine.loadArgumentsIntoObject( argProvider ); - Assert.assertEquals(argProvider.outputFile,"out.txt","Argument is not correctly initialized"); + Assert.assertEquals(argProvider.outputFile, "out.txt", "Argument is not correctly initialized"); } @@ -114,11 +114,11 @@ public class ParsingEngineUnitTest extends BaseTest { final String[] commandLine = new String[] {" --input_file ", "na12878.bam"}; parsingEngine.addArgumentSource( InputFileArgProvider.class ); - parsingEngine.parse( commandLine ); + parsingEngine.parse(commandLine); parsingEngine.validate(); InputFileArgProvider argProvider = new InputFileArgProvider(); - parsingEngine.loadArgumentsIntoObject( argProvider ); + parsingEngine.loadArgumentsIntoObject(argProvider); Assert.assertEquals(argProvider.inputFile,"na12878.bam","Argument is not correctly initialized"); } @@ -167,7 +167,7 @@ public class ParsingEngineUnitTest extends BaseTest { AllLociArgProvider argProvider = new AllLociArgProvider(); parsingEngine.loadArgumentsIntoObject( argProvider ); - Assert.assertTrue(argProvider.allLoci,"Argument is not correctly initialized"); + Assert.assertTrue(argProvider.allLoci, "Argument is not correctly initialized"); } private class AllLociArgProvider { @@ -214,12 +214,12 @@ public class ParsingEngineUnitTest extends BaseTest { public void enumMixedCaseTest() { final String[] commandLine = new String[] { "--test_enum", "oNe" }; - parsingEngine.addArgumentSource( EnumArgProvider.class ); - parsingEngine.parse( commandLine ); + parsingEngine.addArgumentSource(EnumArgProvider.class); + parsingEngine.parse(commandLine); parsingEngine.validate(); EnumArgProvider argProvider = new EnumArgProvider(); - parsingEngine.loadArgumentsIntoObject( argProvider ); + parsingEngine.loadArgumentsIntoObject(argProvider); Assert.assertEquals(argProvider.testEnum, TestEnum.ONE, "Enum value is not correct"); } @@ -228,12 +228,12 @@ public class ParsingEngineUnitTest extends BaseTest { public void enumDefaultTest() { final String[] commandLine = new String[] {}; - parsingEngine.addArgumentSource( EnumArgProvider.class ); - parsingEngine.parse( commandLine ); + parsingEngine.addArgumentSource(EnumArgProvider.class); + parsingEngine.parse(commandLine); parsingEngine.validate(); EnumArgProvider argProvider = new EnumArgProvider(); - parsingEngine.loadArgumentsIntoObject( argProvider ); + parsingEngine.loadArgumentsIntoObject(argProvider); Assert.assertEquals(argProvider.testEnum, TestEnum.THREE, "Enum value is not correct"); } @@ -300,7 +300,7 @@ public class ParsingEngineUnitTest extends BaseTest { final String[] commandLine = new String[0]; parsingEngine.addArgumentSource( RequiredArgProvider.class ); - parsingEngine.parse( commandLine ); + parsingEngine.parse(commandLine); parsingEngine.validate(); } @@ -345,10 +345,10 @@ public class ParsingEngineUnitTest extends BaseTest { parsingEngine.addArgumentSource( RequiredArgProvider.class ); parsingEngine.parse( commandLine ); - parsingEngine.validate( EnumSet.of(ParsingEngine.ValidationType.MissingRequiredArgument) ); + parsingEngine.validate(EnumSet.of(ParsingEngine.ValidationType.MissingRequiredArgument)); RequiredArgProvider argProvider = new RequiredArgProvider(); - parsingEngine.loadArgumentsIntoObject(argProvider ); + parsingEngine.loadArgumentsIntoObject(argProvider); Assert.assertNull(argProvider.value, "Value should have remain unset"); } @@ -396,7 +396,7 @@ public class ParsingEngineUnitTest extends BaseTest { @Test(expectedExceptions= ReviewedGATKException.class) public void duplicateShortNameTest() { - parsingEngine.addArgumentSource( DuplicateShortNameProvider.class ); + parsingEngine.addArgumentSource(DuplicateShortNameProvider.class); } @@ -444,7 +444,7 @@ public class ParsingEngineUnitTest extends BaseTest { final String[] commandLine = new String[] {"--value","1","--value","2","--value","3"}; parsingEngine.addArgumentSource( RequiredArgProvider.class ); - parsingEngine.parse( commandLine ); + parsingEngine.parse(commandLine); parsingEngine.validate(); } @@ -491,7 +491,7 @@ public class ParsingEngineUnitTest extends BaseTest { @Test public void correctDefaultArgNameTest() { - parsingEngine.addArgumentSource( CamelCaseArgProvider.class ); + parsingEngine.addArgumentSource(CamelCaseArgProvider.class); DefinitionMatcher matcher = ArgumentDefinitions.FullNameDefinitionMatcher; ArgumentDefinition definition = parsingEngine.argumentDefinitions.findArgumentDefinition("myarg", matcher); @@ -510,7 +510,7 @@ public class ParsingEngineUnitTest extends BaseTest { final String[] commandLine = new String[] {"--mybool", "true"}; parsingEngine.addArgumentSource( BooleanArgProvider.class ); - parsingEngine.parse( commandLine ); + parsingEngine.parse(commandLine); parsingEngine.validate(); } @@ -524,14 +524,14 @@ public class ParsingEngineUnitTest extends BaseTest { public void validParseForAnalysisTypeTest() { final String[] commandLine = new String[] {"--analysis_type", "Pileup" }; - parsingEngine.addArgumentSource( AnalysisTypeArgProvider.class ); - parsingEngine.parse( commandLine ); - parsingEngine.validate( EnumSet.of(ParsingEngine.ValidationType.MissingRequiredArgument) ); + parsingEngine.addArgumentSource(AnalysisTypeArgProvider.class); + parsingEngine.parse(commandLine); + parsingEngine.validate(EnumSet.of(ParsingEngine.ValidationType.MissingRequiredArgument)); AnalysisTypeArgProvider argProvider = new AnalysisTypeArgProvider(); - parsingEngine.loadArgumentsIntoObject( argProvider ); + parsingEngine.loadArgumentsIntoObject(argProvider); - Assert.assertEquals(argProvider.Analysis_Name,"Pileup","Argument is not correctly initialized"); + Assert.assertEquals(argProvider.Analysis_Name, "Pileup", "Argument is not correctly initialized"); } private class AnalysisTypeArgProvider { @@ -578,6 +578,36 @@ public class ParsingEngineUnitTest extends BaseTest { Integer bar; } + @Test(expectedExceptions=OtherRequiredArgumentMissingException.class) + public void otherArgumentRequiredTestWithoutRequiredArguments() { + String[] commandLine = new String[] {"--foo","5"}; + + parsingEngine.addArgumentSource( OtherArgumentRequiredArgProvider.class ); + parsingEngine.parse( commandLine ); + parsingEngine.validate(); + } + + @Test + public void otherArgumentRequiredTestWithRequiredArguments() { + String[] commandLine = new String[] {"--foo","5", "--bar", "6"}; + + parsingEngine.addArgumentSource( OtherArgumentRequiredArgProvider.class ); + parsingEngine.parse( commandLine ); + parsingEngine.validate(); + } + + @SuppressWarnings("unused") + private class OtherArgumentRequiredArgProvider { + @Argument(doc="foo", otherArgumentRequired="bar") + Integer foo; + + @Argument(doc="bar",required=false) + Integer bar; + + @Argument(doc="OtherIrrelevantArgument", required = false) + Integer OtherIrrelevantArgument; + } + @Test(expectedExceptions=InvalidArgumentValueException.class) public void argumentValidationTest() { // Passing only foo should work fine... diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java index 7fdd7b835..31587b185 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingCollectionUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java index efed9c195..6a466f727 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/commandline/RodBindingUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java index b5bea3247..93c4502c4 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java index ef8565dba..d55c3ad59 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java index 7dbf3472c..08d369e36 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/file/FSLockWithSharedUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java index decb8284a..ef87e35d6 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java index 1700baf12..1791f2274 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java index 2188dbce8..918f58d5e 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/EventMapUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java index 42801a39c..988b93f76 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java index 0fbb0b2a8..07b49d480 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/interval/IntervalUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java index 66f619007..556616ae7 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/io/IOUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java index 7d622868f..d1945356f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/clibrary/LibCUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java index e2dc57b9c..15a65a6bb 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/JnaSessionQueueTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java index ecc0f9a8e..1faf1611f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/drmaa/v1_0/LibDrmaaQueueTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java index 29b7ad015..00b6af45e 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java index df20a7e27..d10d151d8 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/AlignmentStateMachineUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java index 60bbe6a87..f7e1dc67b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LIBS_position.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java index ea7165b2f..224c43ba2 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java index e39045782..434086ec4 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java index 78185d817..3fecd369c 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java index 2522b8c35..33794f7e2 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/PerSampleReadStateManagerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java index ff4280e36..c1b50c3b5 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/InputProducerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java index 2b6243745..3d399a5b7 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/MapResultUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java index f45daa270..cd9126644 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java index 03c92a02d..c70c1dceb 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/ReducerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java index 5c4987401..c7f5fbf0d 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/PileupElementUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java index 70377e1c7..0e82ffc54 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/pileup/ReadBackedPileupUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java index 57ce9d956..720658715 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDaemonUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java index 2f11f2543..cf26b406e 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeterDataUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java index e514b670f..bee23d609 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/recalibration/EventTypeUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java index 3dbfbfcd6..2345ce6ee 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/RefMetaDataTrackerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java index 0194d4941..de14e0f43 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/FeatureManagerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java index 7b25724ce..3131f92d6 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/tracks/RMDTrackBuilderUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java index 191c68993..e928b9755 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/CheckableCloseableTribbleIterator.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java index 789ef1886..da12cf506 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java index 5ca887edf..42312c427 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/FlashBackIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java index 7b9a0feeb..21a83b044 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestFeatureReader.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java index 436c4f422..bdfa4d487 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/refdata/utils/TestRMDTrackBuilder.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java index d67851771..97e498083 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/GATKReportUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java index 5d9478ab8..43285f5ab 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/report/ReportMarshallerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java index eeaac020a..b23935b4b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/ProcessControllerUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java index 8f60ff0a8..0f2cf1955 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/runtime/RuntimeUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java index 6dca140ba..24351842f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/AlignmentUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java index d3a7c5c0b..c4dfdbe65 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialBAMBuilderUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java index b556c0eaf..d6daf677b 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java index 0df8bbf6d..88f63f2b9 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMFileWriterUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java index 19ef63f6e..db84ac631 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMQueryIteratorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java index 70d25a585..431162985 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSAMUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java index 5f6b36c1c..8f3e4664d 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java index 470671d09..d0698add5 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/GATKSAMRecordUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java index c6233f17d..372a711b0 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -25,11 +25,13 @@ package org.broadinstitute.gatk.utils.sam; +import htsjdk.samtools.SAMReadGroupRecord; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.BaseUtils; import org.broadinstitute.gatk.utils.Utils; +import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; import org.testng.Assert; import org.testng.annotations.DataProvider; @@ -336,4 +338,18 @@ public class ReadUtilsUnitTest extends BaseTest { private void testHasWellDefinedFragmentSize(final String name, final GATKSAMRecord read, final boolean expected) { Assert.assertEquals(ReadUtils.hasWellDefinedFragmentSize(read), expected); } + + @Test(expectedExceptions = IllegalArgumentException.class) + public void testGetSAMFileMissingHeader() { + ReadUtils.getSAMFileSamples(null); + } + + @Test(expectedExceptions = UserException.class) + public void testGetSAMFileMissingReadGroupsSamples() { + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(); + final SAMReadGroupRecord samGroup = new SAMReadGroupRecord("id"); + final List list = new ArrayList<>(Arrays.asList(samGroup)); + header.setReadGroups(list); + ReadUtils.getSAMFileSamples(header); + } } diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java index f6aff7ba4..b283c80fc 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/smithwaterman/SmithWatermanBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java index aeb1101cf..1131fe9a3 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/ListFileUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java index b8bf04b56..a7571a49f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/text/TextFormattingUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java index bbd594d27..78480c9b7 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/EfficiencyMonitoringThreadFactoryUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java index ecc611f7e..48eaff0c4 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/threading/ThreadPoolMonitorUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java index c64c04dc1..33684cda1 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation @@ -26,6 +26,7 @@ package org.broadinstitute.gatk.utils.variant; import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.gatk.utils.*; import org.broadinstitute.gatk.utils.collections.Pair; import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile; @@ -178,7 +179,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest { new MergeAllelesTest(Arrays.asList(ATref, ATC, Anoref, G), Arrays.asList(Aref, ATCATC, G), - Arrays.asList(ATref, ATC, Anoref, G, ATCATCT, GT)); + Arrays.asList(ATref, ATC, Anoref, G, GT, ATCATCT)); return MergeAllelesTest.getTests(MergeAllelesTest.class); } @@ -1661,5 +1662,75 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest { attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{5, 10, 15, 20}).make(); Assert.assertEquals(GATKVariantContextUtils.makeNewSACs(g, Arrays.asList(1, 3)), expected); } + + @Test + public void testIncrementChromosomeCountsInfo() { + final Map calledAltAlleles = new LinkedHashMap<>(); + final Map expectedCalledAltAlleles = new LinkedHashMap<>(); + final List alleles = new ArrayList<>(Arrays.asList(Aref, C)); + for ( final Allele allele : alleles ) { + if ( allele.isNonReference() ) { + calledAltAlleles.put(allele, 0); + expectedCalledAltAlleles.put(allele, 1); + } + } + int calledAlleles = 0; + final Genotype genotype = new GenotypeBuilder().alleles(alleles).make(); + calledAlleles = GATKVariantContextUtils.incrementChromosomeCountsInfo(calledAltAlleles, calledAlleles, genotype); + Assert.assertEquals(calledAlleles, alleles.size()); + Assert.assertEquals(calledAltAlleles, expectedCalledAltAlleles); + } + + @Test(expectedExceptions = IllegalArgumentException.class) + public void testIncrementChromosomeCountsInfoCalledAltAllelesException() { + int calledAlleles = 0; + final Genotype genotype = new GenotypeBuilder().make(); + calledAlleles = GATKVariantContextUtils.incrementChromosomeCountsInfo(null, calledAlleles, genotype); + } + + @Test(expectedExceptions = IllegalArgumentException.class) + public void testIncrementChromosomeCountsInfoGenotypeException() { + final Map calledAltAlleles = new LinkedHashMap<>(); + int calledAlleles = 0; + calledAlleles = GATKVariantContextUtils.incrementChromosomeCountsInfo(calledAltAlleles, calledAlleles, null); + } + + @Test + public void testUpdateChromosomeCountsInfo() { + final Map calledAltAlleles = new LinkedHashMap<>(); + final Set alleleFrequency = new LinkedHashSet(calledAltAlleles.size()); + final List alleles = new ArrayList<>(Arrays.asList(Aref, C)); + final int calledAlleles = alleles.size(); + final List numAltAlleles = new ArrayList<>(); + + final int alleleOccurence = 1; + for ( final Allele allele : alleles ) { + if ( allele.isNonReference() ) { + calledAltAlleles.put(allele, alleleOccurence); + alleleFrequency.add( ((double) alleleOccurence)/calledAlleles ); + numAltAlleles.add(1); + } + } + final VariantContextBuilder builder = new VariantContextBuilder("test", "chr1", 1, Aref.length(), alleles); + GATKVariantContextUtils.updateChromosomeCountsInfo(calledAltAlleles, calledAlleles, builder); + final VariantContext vc = builder.make(); + Assert.assertEquals(vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY), numAltAlleles.toArray()); + Assert.assertEquals(vc.getAttribute(VCFConstants.ALLELE_NUMBER_KEY), alleles.size()); + Assert.assertEquals(vc.getAttribute(VCFConstants.ALLELE_FREQUENCY_KEY), alleleFrequency.toArray()); + } + + @Test(expectedExceptions = IllegalArgumentException.class) + public void testUpdateChromosomeCountsInfoCalledAltAllelesException() { + final int calledAlleles = 0; + final VariantContextBuilder builder = new VariantContextBuilder("test", "chr1", 1, Aref.length(), Arrays.asList(Aref, C)); + GATKVariantContextUtils.updateChromosomeCountsInfo(null, calledAlleles, builder); + } + + @Test(expectedExceptions = IllegalArgumentException.class) + public void testUpdateChromosomeCountsInfoBuilderException() { + final int calledAlleles = 0; + final Map calledAltAlleles = new LinkedHashMap<>(); + GATKVariantContextUtils.updateChromosomeCountsInfo(calledAltAlleles, calledAlleles, null); + } } diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java index 79ee95611..3a7a88e72 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextBenchmark.java @@ -1,5 +1,5 @@ /* -* Copyright 2012-2015 Broad Institute, Inc. +* Copyright 2012-2016 Broad Institute, Inc. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation diff --git a/public/gsalib/pom.xml b/public/gsalib/pom.xml index df9e7fce9..4925afd36 100644 --- a/public/gsalib/pom.xml +++ b/public/gsalib/pom.xml @@ -5,7 +5,7 @@ org.broadinstitute.gatk gatk-aggregator - 3.5 + 3.6-SNAPSHOT ../.. diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml index 809f23e54..39ec25c8b 100644 --- a/public/package-tests/pom.xml +++ b/public/package-tests/pom.xml @@ -9,7 +9,7 @@ org.broadinstitute.gatk gatk-root - 3.5 + 3.6-SNAPSHOT ../gatk-root diff --git a/public/pom.xml b/public/pom.xml index 18a35a366..e5b08e554 100644 --- a/public/pom.xml +++ b/public/pom.xml @@ -5,7 +5,7 @@ org.broadinstitute.gatk gatk-root - 3.5 + 3.6-SNAPSHOT gatk-root diff --git a/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom index 92fbea553..fb3102be3 100644 --- a/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom +++ b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom @@ -80,9 +80,9 @@ com.sun tools - 1.5.0 + 1.8.0 system - ${toolsjar} + ${java.home}/lib/tools.jar diff --git a/settings/helpTemplates/common.html b/settings/helpTemplates/common.html index 54001626d..20e144400 100644 --- a/settings/helpTemplates/common.html +++ b/settings/helpTemplates/common.html @@ -1,30 +1,7 @@ - - <#-- - This file contains all the theming neccesary to present GATKDocs on the GATK website - Included are the paths to our bootstrap assets as well as helper functions to generate relevant links + This file contains part of the theming neccesary to present GATKDocs on the GATK website. Included are the + paths to our bootstrap assets as well as helper functions to generate relevant links. Styling is separated + out, so pages will be minimalistic html unless replacement styling is provided. --> @@ -37,8 +14,8 @@

      Return to top

      See also - Guide Index | - Tool Documentation Index | + GATK Documentation Index | + Tool Docs Index | Support Forum

      @@ -62,7 +39,7 @@ }