diff --git a/.gitignore b/.gitignore index 927caf98d..9a20b68ca 100644 --- a/.gitignore +++ b/.gitignore @@ -12,6 +12,7 @@ *.ipr *.iws *.iml +*.pyc .DS_Store queueScatterGather /foo* @@ -23,3 +24,4 @@ dist/ dump/ lib/ out/ +/atlassian-ide-plugin.xml diff --git a/build.xml b/build.xml index 2dfff0cc2..e92e41c10 100644 --- a/build.xml +++ b/build.xml @@ -873,10 +873,6 @@ - - - - @@ -885,10 +881,6 @@ - - - - @@ -939,15 +931,10 @@ - - - - - @@ -956,13 +943,8 @@ - - - - - @@ -1006,14 +988,10 @@ - - - - @@ -1363,13 +1341,8 @@ - - - - - diff --git a/licensing/private_license.txt b/licensing/private_license.txt deleted file mode 120000 index d83474e7a..000000000 --- a/licensing/private_license.txt +++ /dev/null @@ -1 +0,0 @@ -protected_license.txt \ No newline at end of file diff --git a/licensing/private_license.txt b/licensing/private_license.txt new file mode 100644 index 000000000..2f40c5089 --- /dev/null +++ b/licensing/private_license.txt @@ -0,0 +1,43 @@ + 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). + + WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. + 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. OWNERSHIP OF INTELLECTUAL PROPERTY + LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. + Copyright 2012 Broad Institute, Inc. + Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. + LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. + + 4. 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. + + 5. 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. + + 6. 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. + + 7. MISCELLANEOUS + 7.1 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. + 7.2 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. + 7.3 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. + 7.4 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. + 7.5 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. + 7.6 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. + 7.7 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. diff --git a/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java index bb31b410e..3a1532bb1 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java @@ -109,13 +109,6 @@ public class StandardCallerArgumentCollection { @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) public int MAX_ALTERNATE_ALLELES = 6; - /** - * Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus. - */ - @Advanced - @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false) - public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel(); - /** * If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads. * Basically, it will ignore the contamination fraction of reads for each alternate allele. So if the pileup contains N total bases, then we @@ -125,6 +118,13 @@ public class StandardCallerArgumentCollection { public double CONTAMINATION_FRACTION = DEFAULT_CONTAMINATION_FRACTION; public static final double DEFAULT_CONTAMINATION_FRACTION = 0.05; + /** + * Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus. + */ + @Hidden + @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false) + public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel(); + @Hidden @Argument(fullName = "logRemovedReadsFromContaminationFiltering", shortName="contaminationLog", required=false) public PrintStream contaminationLog = null; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java deleted file mode 100644 index a7bb58d0c..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java +++ /dev/null @@ -1,318 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.downsampling; - -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.pileup.*; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.utils.BaseUtils; -import org.broadinstitute.variant.variantcontext.Allele; - -import java.io.PrintStream; -import java.util.*; - -public class AlleleBiasedDownsamplingUtils { - - /** - * Computes an allele biased version of the given pileup - * - * @param pileup the original pileup - * @param downsamplingFraction the fraction of total reads to remove per allele - * @param log logging output - * @return allele biased pileup - */ - public static ReadBackedPileup createAlleleBiasedBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { - // special case removal of all or no reads - if ( downsamplingFraction <= 0.0 ) - return pileup; - if ( downsamplingFraction >= 1.0 ) - return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList()); - - final ArrayList[] alleleStratifiedElements = new ArrayList[4]; - for ( int i = 0; i < 4; i++ ) - alleleStratifiedElements[i] = new ArrayList(); - - // keep all of the reduced reads - final ArrayList reducedReadPileups = new ArrayList(); - - // start by stratifying the reads by the alleles they represent at this position - for( final PileupElement pe : pileup ) { - // we do not want to remove a reduced read - if ( pe.getRead().isReducedRead() ) - reducedReadPileups.add(pe); - - final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase()); - if ( baseIndex != -1 ) - alleleStratifiedElements[baseIndex].add(pe); - } - - // Unfortunately, we need to maintain the original pileup ordering of reads or FragmentUtils will complain later. - int numReadsToRemove = (int)(pileup.getNumberOfElements() * downsamplingFraction); // floor - final TreeSet elementsToKeep = new TreeSet(new Comparator() { - @Override - public int compare(PileupElement element1, PileupElement element2) { - final int difference = element1.getRead().getAlignmentStart() - element2.getRead().getAlignmentStart(); - return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName()); - } - }); - elementsToKeep.addAll(reducedReadPileups); - - // make a listing of allele counts - final int[] alleleCounts = new int[4]; - for ( int i = 0; i < 4; i++ ) - alleleCounts[i] = alleleStratifiedElements[i].size(); - - // do smart down-sampling - final int[] targetAlleleCounts = runSmartDownsampling(alleleCounts, numReadsToRemove); - - for ( int i = 0; i < 4; i++ ) { - final ArrayList alleleList = alleleStratifiedElements[i]; - // if we don't need to remove any reads, keep them all - if ( alleleList.size() <= targetAlleleCounts[i] ) - elementsToKeep.addAll(alleleList); - else - elementsToKeep.addAll(downsampleElements(alleleList, alleleList.size() - targetAlleleCounts[i], log)); - } - - // clean up pointers so memory can be garbage collected if needed - for ( int i = 0; i < 4; i++ ) - alleleStratifiedElements[i].clear(); - - return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList(elementsToKeep)); - } - - private static int scoreAlleleCounts(final int[] alleleCounts) { - if ( alleleCounts.length < 2 ) - return 0; - - // sort the counts (in ascending order) - final int[] alleleCountsCopy = alleleCounts.clone(); - Arrays.sort(alleleCountsCopy); - - final int maxCount = alleleCountsCopy[alleleCounts.length - 1]; - final int nextBestCount = alleleCountsCopy[alleleCounts.length - 2]; - - int remainderCount = 0; - for ( int i = 0; i < alleleCounts.length - 2; i++ ) - remainderCount += alleleCountsCopy[i]; - - // try to get the best score: - // - in the het case the counts should be equal with nothing else - // - in the hom case the non-max should be zero - return Math.min(maxCount - nextBestCount + remainderCount, Math.abs(nextBestCount + remainderCount)); - } - - /** - * Computes an allele biased version of the given pileup - * - * @param alleleCounts the original pileup - * @param numReadsToRemove fraction of total reads to remove per allele - * @return allele biased pileup - */ - protected static int[] runSmartDownsampling(final int[] alleleCounts, final int numReadsToRemove) { - final int numAlleles = alleleCounts.length; - - int maxScore = scoreAlleleCounts(alleleCounts); - int[] alleleCountsOfMax = alleleCounts; - - final int numReadsToRemovePerAllele = numReadsToRemove / 2; - - for ( int i = 0; i < numAlleles; i++ ) { - for ( int j = i; j < numAlleles; j++ ) { - final int[] newCounts = alleleCounts.clone(); - - // split these cases so we don't lose on the floor (since we divided by 2) - if ( i == j ) { - newCounts[i] = Math.max(0, newCounts[i] - numReadsToRemove); - } else { - newCounts[i] = Math.max(0, newCounts[i] - numReadsToRemovePerAllele); - newCounts[j] = Math.max(0, newCounts[j] - numReadsToRemovePerAllele); - } - - final int score = scoreAlleleCounts(newCounts); - - if ( score < maxScore ) { - maxScore = score; - alleleCountsOfMax = newCounts; - } - } - } - - return alleleCountsOfMax; - } - - /** - * Performs allele biased down-sampling on a pileup and computes the list of elements to keep - * - * @param elements original list of records - * @param numElementsToRemove the number of records to remove - * @param log logging output - * @return the list of pileup elements TO KEEP - */ - private static List downsampleElements(final ArrayList elements, final int numElementsToRemove, final PrintStream log) { - if ( numElementsToRemove == 0 ) - return elements; - - final int pileupSize = elements.size(); - if ( numElementsToRemove == pileupSize ) { - logAllElements(elements, log); - return new ArrayList(0); - } - - final BitSet itemsToRemove = new BitSet(pileupSize); - for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) { - itemsToRemove.set(selectedIndex); - } - - ArrayList elementsToKeep = new ArrayList(pileupSize - numElementsToRemove); - for ( int i = 0; i < pileupSize; i++ ) { - if ( itemsToRemove.get(i) ) - logRead(elements.get(i).getRead(), log); - else - elementsToKeep.add(elements.get(i)); - } - - return elementsToKeep; - } - - /** - * Computes reads to remove based on an allele biased down-sampling - * - * @param alleleReadMap original list of records per allele - * @param downsamplingFraction the fraction of total reads to remove per allele - * @param log logging output - * @return list of reads TO REMOVE from allele biased down-sampling - */ - public static List selectAlleleBiasedReads(final Map> alleleReadMap, final double downsamplingFraction, final PrintStream log) { - int totalReads = 0; - for ( final List reads : alleleReadMap.values() ) - totalReads += reads.size(); - - int numReadsToRemove = (int)(totalReads * downsamplingFraction); - - // make a listing of allele counts - final List alleles = new ArrayList(alleleReadMap.keySet()); - alleles.remove(Allele.NO_CALL); // ignore the no-call bin - final int numAlleles = alleles.size(); - final int[] alleleCounts = new int[numAlleles]; - for ( int i = 0; i < numAlleles; i++ ) - alleleCounts[i] = alleleReadMap.get(alleles.get(i)).size(); - - // do smart down-sampling - final int[] targetAlleleCounts = runSmartDownsampling(alleleCounts, numReadsToRemove); - - final List readsToRemove = new ArrayList(numReadsToRemove); - for ( int i = 0; i < numAlleles; i++ ) { - final List alleleBin = alleleReadMap.get(alleles.get(i)); - - if ( alleleBin.size() > targetAlleleCounts[i] ) { - readsToRemove.addAll(downsampleReads(alleleBin, alleleBin.size() - targetAlleleCounts[i], log)); - } - } - - return readsToRemove; - } - - /** - * Performs allele biased down-sampling on a pileup and computes the list of elements to remove - * - * @param reads original list of records - * @param numElementsToRemove the number of records to remove - * @param log logging output - * @return the list of pileup elements TO REMOVE - */ - private static List downsampleReads(final List reads, final int numElementsToRemove, final PrintStream log) { - final ArrayList readsToRemove = new ArrayList(numElementsToRemove); - - if ( numElementsToRemove == 0 ) - return readsToRemove; - - final int pileupSize = reads.size(); - if ( numElementsToRemove == pileupSize ) { - logAllReads(reads, log); - return reads; - } - - final BitSet itemsToRemove = new BitSet(pileupSize); - for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) { - itemsToRemove.set(selectedIndex); - } - - for ( int i = 0; i < pileupSize; i++ ) { - if ( itemsToRemove.get(i) ) { - final GATKSAMRecord read = reads.get(i); - readsToRemove.add(read); - logRead(read, log); - } - } - - return readsToRemove; - } - - private static void logAllElements(final List elements, final PrintStream log) { - if ( log != null ) { - for ( final PileupElement p : elements ) - logRead(p.getRead(), log); - } - } - - private static void logAllReads(final List reads, final PrintStream log) { - if ( log != null ) { - for ( final GATKSAMRecord read : reads ) - logRead(read, log); - } - } - - private static void logRead(final SAMRecord read, final PrintStream log) { - if ( log != null ) { - final SAMReadGroupRecord readGroup = read.getReadGroup(); - log.println(String.format("%s\t%s\t%s\t%s", read.getReadName(), readGroup.getSample(), readGroup.getLibrary(), readGroup.getPlatformUnit())); - } - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java deleted file mode 100644 index 146f71e16..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypesContext; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - - -/** - * The allele balance (fraction of ref bases over ref + alt bases) across all bialleleic het-called samples - */ -public class AlleleBalance extends InfoFieldAnnotation { - - - char[] BASES = {'A','C','G','T'}; - public Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc, - final Map stratifiedPerReadAlleleLikelihoodMap) { - if ( stratifiedContexts.size() == 0 ) - return null; - - if ( !vc.isBiallelic() ) - return null; - final GenotypesContext genotypes = vc.getGenotypes(); - if ( !vc.hasGenotypes() ) - return null; - - double ratioHom = 0.0; - double ratioHet = 0.0; - double weightHom = 0.0; - double weightHet = 0.0; - double overallNonDiploid = 0.0; - for ( Genotype genotype : genotypes ) { - // we care only about het calls - - AlignmentContext context = stratifiedContexts.get(genotype.getSampleName()); - if ( context == null ) - continue; - - final ReadBackedPileup pileup = context.getBasePileup(); - if ( vc.isSNP() ) { - final String bases = new String(pileup.getBases()); - if ( bases.length() == 0 ) - return null; - - double pTrue = 1.0 - Math.pow(10.0,genotype.getLog10PError()); - if ( genotype.isHet() ) { - final char refChr = vc.getReference().toString().charAt(0); - final char altChr = vc.getAlternateAllele(0).toString().charAt(0); - - final int refCount = MathUtils.countOccurrences(refChr, bases); - final int altCount = MathUtils.countOccurrences(altChr, bases); - final int otherCount = bases.length()-refCount-altCount; - - // sanity check - if ( refCount + altCount == 0 ) - continue; - - // weight the allele balance by genotype quality so that e.g. mis-called homs don't affect the ratio too much - ratioHet += pTrue * ((double)refCount / (double)(refCount + altCount)); - weightHet += pTrue; - overallNonDiploid += ( (double) otherCount )/(bases.length()*genotypes.size()); - } else if ( genotype.isHom() ) { - char alleleChr; - if ( genotype.isHomRef() ) { - alleleChr = vc.getReference().toString().charAt(0); - } else { - alleleChr = vc.getAlternateAllele(0).toString().charAt(0); - } - final int alleleCount = MathUtils.countOccurrences(alleleChr,bases); - int bestOtherCount = 0; - for ( char b : BASES ) { - if ( b == alleleChr ) - continue; - int count = MathUtils.countOccurrences(b,bases); - if ( count > bestOtherCount ) - bestOtherCount = count; - } - final int otherCount = bases.length() - alleleCount; - ratioHom += pTrue*( (double) alleleCount)/(alleleCount+bestOtherCount); - weightHom += pTrue; - overallNonDiploid += ((double ) otherCount)/(bases.length()*genotypes.size()); - } - // Allele Balance for indels was not being computed correctly (since there was no allele matching). Instead of - // prolonging the life of imperfect code, I've decided to delete it. If someone else wants to try again from - // scratch, be my guest - but make sure it's done correctly! [EB] - } - } - - // make sure we had a het genotype - - Map map = new HashMap(); - if ( weightHet > 0.0 ) { - map.put("ABHet",ratioHet/weightHet); - } - - if ( weightHom > 0.0 ) { - map.put("ABHom",ratioHom/weightHom); - } - - if ( overallNonDiploid > 0.0 ) { - map.put("OND",overallNonDiploid); - } - return map; - } - - - public List getKeyNames() { return Arrays.asList("ABHet","ABHom","OND"); } - - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ABHet", 1, VCFHeaderLineType.Float, "Allele Balance for hets (ref/(ref+alt))"), - new VCFInfoHeaderLine("ABHom", 1, VCFHeaderLineType.Float, "Allele Balance for homs (A/(A+O))"), - new VCFInfoHeaderLine("OND", 1, VCFHeaderLineType.Float, "Overall non-diploid ratio (alleles/(alleles+non-alleles))")); } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java deleted file mode 100644 index c501c2f5f..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +++ /dev/null @@ -1,131 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.Collection; -import java.util.List; - - -/** - * The allele balance (fraction of ref bases over ref + alt bases) separately for each bialleleic het-called sample - */ -public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation { - - public void annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final AlignmentContext stratifiedContext, - final VariantContext vc, - final Genotype g, - final GenotypeBuilder gb, - final PerReadAlleleLikelihoodMap alleleLikelihoodMap){ - if ( stratifiedContext == null ) - return; - - Double ratio = annotateSNP(stratifiedContext, vc, g); - if (ratio == null) - return; - - gb.attribute(getKeyNames().get(0), Double.valueOf(String.format("%.2f", ratio.doubleValue()))); - } - - private Double annotateSNP(AlignmentContext stratifiedContext, VariantContext vc, Genotype g) { - double ratio = -1; - - if ( !vc.isSNP() ) - return null; - - if ( !vc.isBiallelic() ) - return null; - - if ( g == null || !g.isCalled() ) - return null; - - if (!g.isHet()) - return null; - - Collection altAlleles = vc.getAlternateAlleles(); - if ( altAlleles.size() == 0 ) - return null; - - final String bases = new String(stratifiedContext.getBasePileup().getBases()); - if ( bases.length() == 0 ) - return null; - char refChr = vc.getReference().toString().charAt(0); - char altChr = vc.getAlternateAllele(0).toString().charAt(0); - - int refCount = MathUtils.countOccurrences(refChr, bases); - int altCount = MathUtils.countOccurrences(altChr, bases); - - // sanity check - if ( refCount + altCount == 0 ) - return null; - - ratio = ((double)refCount / (double)(refCount + altCount)); - return ratio; - } - - public List getKeyNames() { return Arrays.asList("AB"); } - - public List getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java deleted file mode 100644 index d5c9bcef2..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java +++ /dev/null @@ -1,138 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypesContext; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -/** - * Created by IntelliJ IDEA. - * User: chartl - * Date: 1/3/13 - * Time: 11:36 AM - * To change this template use File | Settings | File Templates. - */ -public class AverageAltAlleleLength extends InfoFieldAnnotation implements ActiveRegionBasedAnnotation, ExperimentalAnnotation { - - public List getDescriptions() { - return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Average Allele Length")); - } - - public List getKeyNames() { return Arrays.asList("AAL"); } - - public Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc, - final Map perReadAlleleLikelihoodMap ) { - if ( !vc.hasLog10PError() ) - return null; - - final GenotypesContext genotypes = vc.getGenotypes(); - if ( genotypes == null || genotypes.size() == 0 ) - return null; - - Map map = new HashMap(); - - double length = getMeanAltAlleleLength(vc); - map.put(getKeyNames().get(0),String.format("%.2f",length)); - return map; - } - - public static double getMeanAltAlleleLength(VariantContext vc) { - double averageLength = 1.0; - if ( ! vc.isSNP() && ! vc.isSymbolic() ) { - // adjust for the event length - int averageLengthNum = 0; - int averageLengthDenom = 0; - int refLength = vc.getReference().length(); - for ( Allele a : vc.getAlternateAlleles() ) { - int numAllele = vc.getCalledChrCount(a); - int alleleSize; - if ( a.length() == refLength ) { - // SNP or MNP - byte[] a_bases = a.getBases(); - byte[] ref_bases = vc.getReference().getBases(); - int n_mismatch = 0; - for ( int idx = 0; idx < a_bases.length; idx++ ) { - if ( a_bases[idx] != ref_bases[idx] ) - n_mismatch++; - } - alleleSize = n_mismatch; - } - else if ( a.isSymbolic() ) { - alleleSize = 1; - } else { - alleleSize = Math.abs(refLength-a.length()); - } - averageLengthNum += alleleSize*numAllele; - averageLengthDenom += numAllele; - } - averageLength = ( (double) averageLengthNum )/averageLengthDenom; - } - - return averageLength; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java deleted file mode 100644 index c3500fbc0..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +++ /dev/null @@ -1,97 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.utils.BaseUtils; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - - -/** - * Count of A, C, G, T bases across all samples - */ -public class BaseCounts extends InfoFieldAnnotation { - - public Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc, - final Map stratifiedPerReadAlleleLikelihoodMap) { - if ( stratifiedContexts.size() == 0 ) - return null; - - int[] counts = new int[4]; - - for ( Map.Entry sample : stratifiedContexts.entrySet() ) { - for (byte base : sample.getValue().getBasePileup().getBases() ) { - int index = BaseUtils.simpleBaseToBaseIndex(base); - if ( index != -1 ) - counts[index]++; - } - } - Map map = new HashMap(); - map.put(getKeyNames().get(0), counts); - return map; - } - - public List getKeyNames() { return Arrays.asList("BaseCounts"); } - - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseCounts", 4, VCFHeaderLineType.Integer, "Counts of each base")); } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index aeec36c18..4adb2ca71 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -99,7 +99,7 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno for (PerReadAlleleLikelihoodMap maps : perReadAlleleLikelihoodMap.values() ) { for (Map.Entry> el : maps.getLikelihoodReadMap().entrySet()) { final GATKSAMRecord read = el.getKey(); - depth += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1); + depth += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1); } } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index a194fe323..5acea12f6 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -144,7 +144,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa continue; // read is non-informative if (!vc.getAlleles().contains(a)) continue; // sanity check - shouldn't be needed - alleleCounts.put(a, alleleCounts.get(a) + (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1)); + alleleCounts.put(a, alleleCounts.get(a) + (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1)); } final int[] counts = new int[alleleCounts.size()]; counts[0] = alleleCounts.get(vc.getReference()); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 167e5df63..ff3d7940f 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -116,8 +116,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat else if (table1 == null) return annotationForOneTable(pValueForContingencyTable(table2)); else { // take the one with the best (i.e., least significant pvalue) - double pvalue1 = Math.max(pValueForContingencyTable(table1), MIN_PVALUE); - double pvalue2 = Math.max(pValueForContingencyTable(table2), MIN_PVALUE); + double pvalue1 = pValueForContingencyTable(table1); + double pvalue2 = pValueForContingencyTable(table2); return annotationForOneTable(Math.max(pvalue1, pvalue2)); } } @@ -129,7 +129,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat * @return a hash map from FS -> phred-scaled pValue */ private Map annotationForOneTable(final double pValue) { - final Object value = String.format("%.3f", QualityUtils.phredScaleErrorRate(pValue)); + final Object value = String.format("%.3f", QualityUtils.phredScaleErrorRate(Math.max(pValue, MIN_PVALUE))); // prevent INFINITYs return Collections.singletonMap(FS, value); // Map map = new HashMap(); // map.put(FS, String.format("%.3f", QualityUtils.phredScaleErrorRate(pValue))); @@ -265,24 +265,16 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat for (PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) { for (Map.Entry> el : maps.getLikelihoodReadMap().entrySet()) { - final boolean matchesRef = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()).equals(ref,true); - final boolean matchesAlt = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()).equals(alt,true); - - if ( !matchesRef && !matchesAlt ) - continue; - - boolean isFW = el.getKey().getReadNegativeStrandFlag(); - - int row = matchesRef ? 0 : 1; - int column = isFW ? 0 : 1; - + final Allele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()); final GATKSAMRecord read = el.getKey(); - table[row][column] += (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinate(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1); + final int representativeCount = read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1; + updateTable(table, mostLikelyAllele, read, ref, alt, representativeCount); } } return table; } + /** Allocate and fill a 2x2 strand contingency table. In the end, it'll look something like this: * fw rc @@ -299,31 +291,36 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat for ( Map.Entry sample : stratifiedContexts.entrySet() ) { for (PileupElement p : sample.getValue().getBasePileup()) { - // ignore reduced reads because they are always on the forward strand! - // TODO -- when het compression is enabled in RR, we somehow need to allow those reads through into the Fisher test - if ( p.getRead().isReducedRead() ) - continue; - if ( ! RankSumTest.isUsableBase(p, false) ) // ignore deletions continue; if ( p.getQual() < minQScoreToConsider || p.getMappingQual() < minQScoreToConsider ) continue; - final Allele base = Allele.create(p.getBase(), false); - final boolean isFW = !p.getRead().getReadNegativeStrandFlag(); - - final boolean matchesRef = ref.equals(base, true); - final boolean matchesAlt = alt.equals(base, true); - if ( matchesRef || matchesAlt ) { - int row = matchesRef ? 0 : 1; - int column = isFW ? 0 : 1; - - table[row][column] += p.getRepresentativeCount(); - } + updateTable(table, Allele.create(p.getBase(), false), p.getRead(), ref, alt, p.getRepresentativeCount()); } } return table; } + + private static void updateTable(final int[][] table, final Allele allele, final GATKSAMRecord read, final Allele ref, final Allele alt, final int representativeCount) { + // ignore reduced reads because they are always on the forward strand! + // TODO -- when het compression is enabled in RR, we somehow need to allow those reads through into the Fisher test + if ( read.isReducedRead() ) + return; + + final boolean matchesRef = allele.equals(ref, true); + final boolean matchesAlt = allele.equals(alt, true); + + if ( matchesRef || matchesAlt ) { + + final boolean isFW = !read.getReadNegativeStrandFlag(); + + int row = matchesRef ? 0 : 1; + int column = isFW ? 0 : 1; + + table[row][column] += representativeCount; + } + } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 3bb3d7d5a..93bdf8c9d 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -54,7 +54,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; @@ -95,9 +95,9 @@ public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnota for ( byte base : ref.getBases() ) { int baseIndex = BaseUtils.simpleBaseToBaseIndex(base); - if ( baseIndex == BaseUtils.gIndex || baseIndex == BaseUtils.cIndex ) + if ( baseIndex == BaseUtils.Base.G.ordinal() || baseIndex == BaseUtils.Base.C.ordinal() ) gc++; - else if ( baseIndex == BaseUtils.aIndex || baseIndex == BaseUtils.tIndex ) + else if ( baseIndex == BaseUtils.Base.A.ordinal() || baseIndex == BaseUtils.Base.T.ordinal() ) at++; else ; // ignore diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index fe4075117..13969eb54 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -55,8 +55,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.utils.BaseUtils; -import org.broadinstitute.sting.utils.Haplotype; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.variant.vcf.VCFHeaderLineType; @@ -236,8 +235,8 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot final byte[] haplotypeBases = new byte[contextSize]; Arrays.fill(haplotypeBases, (byte) REGEXP_WILDCARD); - final double[] baseQualities = new double[contextSize]; - Arrays.fill(baseQualities, 0.0); + final byte[] baseQualities = new byte[contextSize]; + Arrays.fill(baseQualities, (byte)0); byte[] readBases = read.getReadBases(); readBases = AlignmentUtils.readToAlignmentByteArray(read.getCigar(), readBases); // Adjust the read bases based on the Cigar string @@ -267,7 +266,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot readQuals[baseOffset] = (byte) 0; } // quals less than 5 are used as codes and don't have actual probabilistic meaning behind them haplotypeBases[i] = readBases[baseOffset]; - baseQualities[i] = (double) readQuals[baseOffset]; + baseQualities[i] = readQuals[baseOffset]; } return new Haplotype(haplotypeBases, baseQualities); @@ -286,10 +285,10 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot final int length = a.length; final byte[] consensusChars = new byte[length]; - final double[] consensusQuals = new double[length]; + final int[] consensusQuals = new int[length]; - final double[] qualsA = haplotypeA.getQuals(); - final double[] qualsB = haplotypeB.getQuals(); + final int[] qualsA = haplotypeA.getQuals(); + final int[] qualsB = haplotypeB.getQuals(); for (int i = 0; i < length; i++) { chA = a[i]; @@ -300,7 +299,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot if ((chA == wc) && (chB == wc)) { consensusChars[i] = wc; - consensusQuals[i] = 0.0; + consensusQuals[i] = 0; } else if ((chA == wc)) { consensusChars[i] = chB; consensusQuals[i] = qualsB[i]; @@ -433,7 +432,6 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot } - public List getKeyNames() { return Arrays.asList("HaplotypeScore"); } @@ -441,4 +439,46 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("HaplotypeScore", 1, VCFHeaderLineType.Float, "Consistency of the site with at most two segregating haplotypes")); } + + private static class Haplotype { + private final byte[] bases; + private final int[] quals; + private int qualitySum = -1; + + public Haplotype( final byte[] bases, final int[] quals ) { + this.bases = bases; + this.quals = quals; + } + + public Haplotype( final byte[] bases, final int qual ) { + this.bases = bases; + quals = new int[bases.length]; + Arrays.fill(quals, qual); + } + + public Haplotype( final byte[] bases, final byte[] quals ) { + this.bases = bases; + this.quals = new int[quals.length]; + for ( int i = 0 ; i < quals.length; i++ ) + this.quals[i] = (int)quals[i]; + } + + public double getQualitySum() { + if ( qualitySum == -1 ) { + qualitySum = 0; + for ( final int qual : quals ) { + qualitySum += qual; + } + } + return qualitySum; + } + + public int[] getQuals() { + return quals.clone(); + } + + public byte[] getBases() { + return bases.clone(); + } + } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java deleted file mode 100644 index 94f5aac56..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +++ /dev/null @@ -1,100 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - - -/** - * Triplet annotation: fraction of MAQP == 0, MAPQ < 10, and count of all mapped reads - */ -public class LowMQ extends InfoFieldAnnotation { - - public Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc, - final Map stratifiedPerReadAlleleLikelihoodMap) { - if ( stratifiedContexts.size() == 0 ) - return null; - - double mq0 = 0; - double mq10 = 0; - double total = 0; - for ( Map.Entry sample : stratifiedContexts.entrySet() ) - { - for ( PileupElement p : sample.getValue().getBasePileup() ) - { - if ( p.getMappingQual() == 0 ) { mq0 += 1; } - if ( p.getMappingQual() <= 10 ) { mq10 += 1; } - total += 1; - } - } - Map map = new HashMap(); - map.put(getKeyNames().get(0), String.format("%.04f,%.04f,%.00f", mq0/total, mq10/total, total)); - return map; - } - - public List getKeyNames() { return Arrays.asList("LowMQ"); } - - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 3, VCFHeaderLineType.Float, "3-tuple: ,,")); } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java deleted file mode 100644 index 9e334847d..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +++ /dev/null @@ -1,99 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.List; - -/** - * Count for each sample of mapping quality zero reads - */ -public class MappingQualityZeroBySample extends GenotypeAnnotation { - public void annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final AlignmentContext stratifiedContext, - final VariantContext vc, - final Genotype g, - final GenotypeBuilder gb, - final PerReadAlleleLikelihoodMap alleleLikelihoodMap){ - if ( g == null || !g.isCalled() || stratifiedContext == null ) - return; - - int mq0 = 0; - final ReadBackedPileup pileup = stratifiedContext.getBasePileup(); - for (PileupElement p : pileup ) { - if ( p.getMappingQual() == 0 ) - mq0++; - } - - gb.attribute(getKeyNames().get(0), mq0); - } - - public List getKeyNames() { return Arrays.asList(VCFConstants.MAPPING_QUALITY_ZERO_KEY); } - - public List getDescriptions() { return Arrays.asList( - new VCFFormatHeaderLine(getKeyNames().get(0), 1, - VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample")); } - - -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java deleted file mode 100644 index 659a94d9e..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java +++ /dev/null @@ -1,106 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -/** - * Fraction of all reads across samples that have mapping quality zero - */ -public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation { - - public Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc, - final Map stratifiedPerReadAlleleLikelihoodMap) { - if ( stratifiedContexts.size() == 0 ) - return null; - - int mq0 = 0; - int depth = 0; - for ( Map.Entry sample : stratifiedContexts.entrySet() ) { - AlignmentContext context = sample.getValue(); - depth += context.size(); - final ReadBackedPileup pileup = context.getBasePileup(); - for (PileupElement p : pileup ) { - if ( p.getMappingQual() == 0 ) - mq0++; - } - } - if (depth > 0) { - double mq0f = (double)mq0 / (double )depth; - - Map map = new HashMap(); - map.put(getKeyNames().get(0), String.format("%1.4f", mq0f)); - return map; - } - else - return null; - } - - public List getKeyNames() { return Arrays.asList("MQ0Fraction"); } - - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Fraction of Mapping Quality Zero Reads")); } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java deleted file mode 100644 index c5142b285..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +++ /dev/null @@ -1,102 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.utils.BaseUtils; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -/** - * The number of N bases, counting only SOLiD data - */ -public class NBaseCount extends InfoFieldAnnotation { - public Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc, - final Map stratifiedPerReadAlleleLikelihoodMap) { - if( stratifiedContexts.size() == 0 ) - return null; - - int countNBaseSolid = 0; - int countRegularBaseSolid = 0; - - for( final AlignmentContext context : stratifiedContexts.values() ) { - for( final PileupElement p : context.getBasePileup()) { - final String platform = p.getRead().getReadGroup().getPlatform(); - if( platform != null && platform.toUpperCase().contains("SOLID") ) { - if( BaseUtils.isNBase( p.getBase() ) ) { - countNBaseSolid++; - } else if( BaseUtils.isRegularBase( p.getBase() ) ) { - countRegularBaseSolid++; - } - } - } - } - final Map map = new HashMap(); - map.put(getKeyNames().get(0), String.format("%.4f", (double)countNBaseSolid / (double)(countNBaseSolid + countRegularBaseSolid + 1))); - return map; - } - - public List getKeyNames() { return Arrays.asList("PercentNBaseSolid"); } - - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBaseSolid", 1, VCFHeaderLineType.Float, "Percentage of N bases in the pileup (counting only SOLiD reads)")); } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index 95b31b732..ddca5e0b8 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -107,7 +107,7 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true ); if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) continue; - int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, false, 0, 0 ); + int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, 0, 0 ); final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read ); if (readPos > numAlignedBases / 2) readPos = numAlignedBases - (readPos + 1); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java index 2ec53133d..2e0e759c2 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java @@ -54,10 +54,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.variant.vcf.VCFHeaderLineCount; import org.broadinstitute.variant.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java deleted file mode 100644 index 6d8f015f0..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java +++ /dev/null @@ -1,122 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator; - -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -/** - * Counts of bases from Illumina, 454, and SOLiD at this site - */ -@Hidden -public class TechnologyComposition extends InfoFieldAnnotation implements ExperimentalAnnotation { - private String nIllumina = "NumIllumina"; - private String n454 ="Num454"; - private String nSolid = "NumSOLiD"; - private String nOther = "NumOther"; - public Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc, - final Map stratifiedPerReadAlleleLikelihoodMap) { - if ( stratifiedContexts.size() == 0 ) - return null; - - int readsIllumina = 0; - int readsSolid = 0; - int reads454 = 0; - int readsOther = 0; - - for ( Map.Entry sample : stratifiedContexts.entrySet() ) { - AlignmentContext context = sample.getValue(); - final ReadBackedPileup pileup = context.getBasePileup(); - for ( PileupElement p : pileup ) { - if(ReadUtils.is454Read(p.getRead())) - reads454++; - else if (ReadUtils.isSOLiDRead(p.getRead())) - readsSolid++; - else if (ReadUtils.isIlluminaRead(p.getRead())) - readsIllumina++; - else - readsOther++; - } - } - - Map map = new HashMap(); - map.put(nIllumina, String.format("%d", readsIllumina)); - map.put(n454, String.format("%d", reads454)); - map.put(nSolid, String.format("%d", readsSolid)); - map.put(nOther, String.format("%d", readsOther)); - return map; - } - - public List getKeyNames() { return Arrays.asList(nIllumina,n454,nSolid,nOther); } - - public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(nIllumina, 1, VCFHeaderLineType.Integer, "Number of Illumina reads"), - new VCFInfoHeaderLine(n454, 1, VCFHeaderLineType.Integer, "Number of 454 reads"), - new VCFInfoHeaderLine(nSolid, 1, VCFHeaderLineType.Integer, "Number of SOLiD reads"), - new VCFInfoHeaderLine(nOther, 1, VCFHeaderLineType.Integer, "Number of Other technology reads")); } - -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java deleted file mode 100644 index 32ca332ca..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java +++ /dev/null @@ -1,63 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.List; -import java.util.Map; - -// TODO -- make this an abstract class when we move away from InfoFieldAnnotation -public interface ActiveRegionBasedAnnotation extends AnnotationType { - // return annotations for the given contexts split by sample and then read likelihood - public abstract Map annotate(final Map stratifiedContexts, final VariantContext vc); - - // return the descriptions used for the VCF INFO meta field - public abstract List getDescriptions(); -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java deleted file mode 100644 index 1e7a2fa80..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.exceptions.UserException; - -import java.util.*; - -public class AnnotationInterfaceManager { - private static PluginManager infoFieldAnnotationPluginManager = new PluginManager(InfoFieldAnnotation.class); - private static PluginManager genotypeAnnotationPluginManager = new PluginManager(GenotypeAnnotation.class); - private static PluginManager annotationTypePluginManager = new PluginManager(AnnotationType.class); - - public static List createAllInfoFieldAnnotations() { - return infoFieldAnnotationPluginManager.createAllTypes(); - } - - public static List createAllGenotypeAnnotations() { - return genotypeAnnotationPluginManager.createAllTypes(); - } - - public static void validateAnnotations(List annotationGroupsToUse, List annotationsToUse) { - HashMap classMap = new HashMap(); - for ( Class c : infoFieldAnnotationPluginManager.getPlugins() ) - classMap.put(c.getSimpleName(), c); - for ( Class c : genotypeAnnotationPluginManager.getPlugins() ) - classMap.put(c.getSimpleName(), c); - for ( Class c : annotationTypePluginManager.getInterfaces() ) - classMap.put(c.getSimpleName(), c); - - if ( annotationGroupsToUse.size() != 1 || !"none".equals(annotationGroupsToUse.get(0)) ) { - for ( String group : annotationGroupsToUse ) { - Class interfaceClass = classMap.get(group); - if ( interfaceClass == null ) - interfaceClass = classMap.get(group + "Annotation"); - if ( interfaceClass == null ) - throw new UserException.BadArgumentValue("group", "Class " + group + " is not found; please check that you have specified the class name correctly"); - } - } - - // validate the specific classes provided - for ( String annotation : annotationsToUse ) { - Class annotationClass = classMap.get(annotation); - if ( annotationClass == null ) - annotationClass = classMap.get(annotation + "Annotation"); - if ( annotationClass == null ) - throw new UserException.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly"); - } - } - - public static List createInfoFieldAnnotations(List annotationGroupsToUse, List annotationsToUse) { - return createAnnotations(infoFieldAnnotationPluginManager, annotationGroupsToUse, annotationsToUse); - } - - public static List createGenotypeAnnotations(List annotationGroupsToUse, List annotationsToUse) { - return createAnnotations(genotypeAnnotationPluginManager, annotationGroupsToUse, annotationsToUse); - } - - private static List createAnnotations(PluginManager pluginManager, List annotationGroupsToUse, List annotationsToUse) { - // get the instances - List annotations = new ArrayList(); - - // get the classes from the provided groups (interfaces) - // create a map for all annotation classes which implement our top-level interfaces - HashMap classMap = new HashMap(); - for ( Class c : pluginManager.getPlugins() ) - classMap.put(c.getSimpleName(), c); - for ( Class c : annotationTypePluginManager.getInterfaces() ) - classMap.put(c.getSimpleName(), c); - - // use a TreeSet so that classes are returned deterministically (the plugin manager apparently isn't deterministic) - TreeSet classes = new TreeSet(new Comparator() { - public int compare(Class o1, Class o2) { - return o1.getSimpleName().compareTo(o2.getSimpleName()); - } - }); - - if ( annotationGroupsToUse.size() != 1 || !"none".equals(annotationGroupsToUse.get(0)) ) { - for ( String group : annotationGroupsToUse ) { - Class interfaceClass = classMap.get(group); - if ( interfaceClass == null ) - interfaceClass = classMap.get(group + "Annotation"); - if ( interfaceClass != null ) - classes.addAll(pluginManager.getPluginsImplementing(interfaceClass)); - } - } - - // get the specific classes provided - for ( String annotation : annotationsToUse ) { - Class annotationClass = classMap.get(annotation); - if ( annotationClass == null ) - annotationClass = classMap.get(annotation + "Annotation"); - if ( annotationClass != null ) - classes.add(annotationClass); - } - - // note that technically an annotation can work on both the INFO and FORMAT fields - for ( Class c : classes ) - annotations.add(pluginManager.createByType(c)); - - return annotations; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java deleted file mode 100644 index 70cb5bef1..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java +++ /dev/null @@ -1,49 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -public interface AnnotationType {} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java deleted file mode 100644 index 44102899b..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java +++ /dev/null @@ -1,62 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.List; - -public interface AnnotatorCompatible { - - // getter methods for various used bindings - public abstract RodBinding getSnpEffRodBinding(); - public abstract RodBinding getDbsnpRodBinding(); - public abstract List> getCompRodBindings(); - public abstract List> getResourceRodBindings(); - public abstract boolean alwaysAppendDbsnpId(); -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java deleted file mode 100644 index ce6974101..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java +++ /dev/null @@ -1,49 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -public interface ExperimentalAnnotation extends AnnotationType {} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java deleted file mode 100644 index cb10de73d..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java +++ /dev/null @@ -1,75 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.List; - -public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation { - - // return annotations for the given contexts/genotype split by sample - public abstract void annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final AlignmentContext stratifiedContext, - final VariantContext vc, - final Genotype g, - final GenotypeBuilder gb, - final PerReadAlleleLikelihoodMap alleleLikelihoodMap); - - // return the descriptions used for the VCF FORMAT meta field - public abstract List getDescriptions(); - -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java deleted file mode 100644 index 092dc6e36..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ /dev/null @@ -1,83 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.List; -import java.util.Map; - -public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation { - // return annotations for the given contexts split by sample - public Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc) { - return annotate(tracker, walker, ref, stratifiedContexts, vc, null); - } - - public Map annotate(Map perReadAlleleLikelihoodMap, VariantContext vc) { - return annotate(null, null, null, null, vc, perReadAlleleLikelihoodMap); - } - - - public abstract Map annotate(final RefMetaDataTracker tracker, - final AnnotatorCompatible walker, - final ReferenceContext ref, - final Map stratifiedContexts, - final VariantContext vc, - final Map stratifiedPerReadAlleleLikelihoodMap); - - // return the descriptions used for the VCF INFO meta field - public abstract List getDescriptions(); -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java deleted file mode 100644 index 4b893cb01..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java +++ /dev/null @@ -1,49 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -public interface RodRequiringAnnotation extends AnnotationType {} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java deleted file mode 100644 index c63875ed6..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java +++ /dev/null @@ -1,49 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -public interface StandardAnnotation extends AnnotationType {} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java deleted file mode 100644 index f8442f4dc..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java +++ /dev/null @@ -1,63 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.variant.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; - -import java.util.List; -import java.util.Set; - -@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations") -public abstract class VariantAnnotatorAnnotation { - // return the INFO keys - public abstract List getKeyNames(); - - // initialization method (optional for subclasses, and therefore non-abstract) - public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set headerLines ) { } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java deleted file mode 100644 index eb6b617bf..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java +++ /dev/null @@ -1,49 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.annotator.interfaces; - -public interface WorkInProgressAnnotation extends AnnotationType {} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java deleted file mode 100644 index e5b5286b6..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java +++ /dev/null @@ -1,204 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.beagle; - -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; - -import java.io.PrintStream; -import java.util.Arrays; -import java.util.Set; - -/** - * Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample - * in input variant file. Will additionally hold back a fraction of the sites for evaluation, marking the - * genotypes at that sites as missing, and writing the truth of these sites to a second VCF file - */ -@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) -public class VariantsToBeagleUnphased extends RodWalker { - @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) - public RodBinding variants; - - @Output(doc="File to which BEAGLE unphased genotypes should be written",required=true) - protected PrintStream beagleWriter = null; - - @Argument(fullName = "bootstrap_fraction", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false) - public double bootstrap = 0.0; - - @Argument(fullName = "bootstrap_vcf",shortName = "bsvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false) - VariantContextWriter bootstrapVCFOutput = null; - - @Argument(fullName = "missing", shortName = "missing", doc = "String to identify missing data in beagle output", required = false) - public String MISSING = "?"; - - private Set samples = null; - private int bootstrapSetSize = 0; - private int testSetSize = 0; - - public void initialize() { - samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName())); - - beagleWriter.print("I marker alleleA alleleB"); - for ( String sample : samples ) - beagleWriter.print(String.format(" %s %s", sample, sample)); - - beagleWriter.println(); - - if ( bootstrap < 0.0 | bootstrap > 1.0 ) - throw new UserException.BadArgumentValue("bootstrap", "Bootstrap value must be fraction between 0 and 1"); - - if ( bootstrapVCFOutput != null ) { - Set hInfo = GATKVCFUtils.getHeaderFields(getToolkit()); - bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit()))); - } - } - - /** - * Iterate over each site, emitting the BEAGLE unphased genotypes file format - * @param tracker - * @param ref - * @param context - * @return - */ - public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) { - if( tracker != null ) { - GenomeLoc loc = context.getLocation(); - VariantContext vc = tracker.getFirstValue(variants, loc); - - if ( ProduceBeagleInput.canBeOutputToBeagle(vc) ) { - // do we want to hold back this site? - boolean makeMissing = dropSite(vc); - - // if we are holding it back and we are writing a bootstrap VCF, write it out - if ( makeMissing && bootstrapVCFOutput != null ) { - bootstrapVCFOutput.add(vc); - } - - // regardless, all sites are written to the unphased genotypes file, marked as missing if appropriate - writeUnphasedBeagleOutput(vc, makeMissing); - } - } - - return 0; - } - - /** - * Do we want to hold back this site for bootstrap? Considers the bootstrap fraction member variable - * - * @param vc - * @return - */ - public boolean dropSite(VariantContext vc) { - if ( (bootstrapSetSize+1.0)/(1.0+bootstrapSetSize+testSetSize) <= bootstrap ) { - bootstrapSetSize++; - return true; - } else { - testSetSize++; - return false; - } - } - - public void writeUnphasedBeagleOutput(VariantContext vc, boolean makeMissing) { - GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc); - StringBuffer beagleOut = new StringBuffer(); - - String marker = String.format("%s:%d ",currentLoc.getContig(), currentLoc.getStart()); - beagleOut.append("M ").append(marker); - - // write out the alleles at this site - for ( Allele allele : vc.getAlleles() ) { - beagleOut.append(allele.isNoCall() ? "-" : allele.getBaseString()).append(" "); - } - - // write out sample level genotypes - for ( String sample : samples ) { - Genotype genotype = vc.getGenotype(sample); - if ( ! makeMissing && genotype.isCalled() ) { - addAlleles(beagleOut, genotype); - } else { - addAlleles(beagleOut, MISSING, MISSING); - } - } - - beagleWriter.println(beagleOut.toString()); - } - - private void addAlleles(StringBuffer buf, Genotype g) { - addAlleles(buf, g.getAllele(0).getBaseString(), g.getAllele(1).getBaseString()); - - } - - private void addAlleles(StringBuffer buf, String a, String b) { - buf.append(a).append(" ").append(b); - } - - public Integer reduceInit() { return 0; } - public Integer reduce( Integer value, Integer sum ) { return value + sum; } - - public void onTraversalDone( Integer includedSites ) { - logger.info("Sites included in beagle genotypes file : " + includedSites); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 76e4374d1..354e508c2 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -60,7 +60,7 @@ import org.broadinstitute.sting.gatk.iterators.ReadTransformer; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.collections.Pair; @@ -280,7 +280,7 @@ public class BaseRecalibrator extends ReadWalker implements NanoSche * @param hasEvents a vector a vectors of 0 (no event) and 1 (has event) * @return the total number of events across all hasEvent arrays */ - private int nEvents(final int[]... hasEvents) { + protected static int nEvents(final int[]... hasEvents) { int n = 0; for ( final int[] hasEvent : hasEvents ) { n += MathUtils.sum(hasEvent); @@ -302,7 +302,7 @@ public class BaseRecalibrator extends ReadWalker implements NanoSche return ReadUtils.isSOLiDRead(read) && RAC.SOLID_RECAL_MODE != RecalUtils.SOLID_RECAL_MODE.DO_NOTHING && !RecalUtils.isColorSpaceConsistent(read, offset); } - protected boolean[] calculateKnownSites( final GATKSAMRecord read, final List features ) { + protected static boolean[] calculateKnownSites( final GATKSAMRecord read, final List features ) { final int readLength = read.getReadBases().length; final boolean[] knownSites = new boolean[readLength]; Arrays.fill(knownSites, false); @@ -464,7 +464,7 @@ public class BaseRecalibrator extends ReadWalker implements NanoSche * @return a BAQ-style non-null byte[] counting NO_BAQ_UNCERTAINTY values * // TODO -- could be optimized avoiding this function entirely by using this inline if the calculation code above */ - private byte[] flatBAQArray(final GATKSAMRecord read) { + protected static byte[] flatBAQArray(final GATKSAMRecord read) { final byte[] baq = new byte[read.getReadLength()]; Arrays.fill(baq, NO_BAQ_UNCERTAINTY); return baq; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java index 4c98a70a0..95b54102f 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java @@ -223,6 +223,18 @@ public class RecalibrationArgumentCollection { @Output(fullName = "recal_table_update_log", shortName = "recal_table_update_log", required = false, doc = "If provided, log all updates to the recalibration tables to the given file. For debugging/testing purposes only") public PrintStream RECAL_TABLE_UPDATE_LOG = null; + /** + * The repeat covariate will use a context of this size to calculate it's covariate value for base insertions and deletions + */ + @Hidden + @Argument(fullName = "max_str_unit_length", shortName = "maxstr", doc = "Max size of the k-mer context to be used for repeat covariates", required = false) + public int MAX_STR_UNIT_LENGTH = 8; + + @Hidden + @Argument(fullName = "max_repeat_length", shortName = "maxrep", doc = "Max number of repetitions to be used for repeat covariates", required = false) + public int MAX_REPEAT_LENGTH = 20; + + public File existingRecalibrationReport = null; public GATKReportTable generateReportTable(final String covariateNames) { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java index 9f2a7f270..bd7bdfe89 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.compression.reducereads; -import org.broadinstitute.sting.utils.GenomeLocComparator; +import org.broadinstitute.sting.utils.*; import java.util.Collection; import java.util.TreeSet; @@ -61,22 +61,22 @@ import java.util.TreeSet; * Date: 10/15/12 * Time: 4:08 PM */ -public class CompressionStash extends TreeSet { +public class CompressionStash extends TreeSet { public CompressionStash() { - super(new GenomeLocComparator()); + super(); } /** - * Adds a SimpleGenomeLoc to the stash and merges it with any overlapping (and contiguous) existing loc + * Adds a UnvalidatingGenomeLoc to the stash and merges it with any overlapping (and contiguous) existing loc * in the stash. * * @param insertLoc the new loc to be inserted * @return true if the loc, or it's merged version, wasn't present in the list before. */ @Override - public boolean add(SimpleGenomeLoc insertLoc) { - TreeSet removedLocs = new TreeSet(); - for (SimpleGenomeLoc existingLoc : this) { + public boolean add(final FinishedGenomeLoc insertLoc) { + TreeSet removedLocs = new TreeSet(); + for (FinishedGenomeLoc existingLoc : this) { if (existingLoc.isPast(insertLoc)) { break; // if we're past the loc we're done looking for overlaps. } @@ -87,17 +87,17 @@ public class CompressionStash extends TreeSet { removedLocs.add(existingLoc); // list the original loc for merging } } - for (SimpleGenomeLoc loc : removedLocs) { - this.remove(loc); // remove all locs that will be merged - } + + this.removeAll(removedLocs); // remove all locs that will be merged removedLocs.add(insertLoc); // add the new loc to the list of locs that will be merged - return super.add(SimpleGenomeLoc.merge(removedLocs)); // merge them all into one loc and add to the stash + + return super.add(new FinishedGenomeLoc(GenomeLoc.merge(removedLocs), insertLoc.isFinished())); } @Override - public boolean addAll(Collection locs) { + public boolean addAll(Collection locs) { boolean result = false; - for (SimpleGenomeLoc loc : locs) { + for (final FinishedGenomeLoc loc : locs) { result |= this.add(loc); } return result; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java similarity index 86% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java index 9c85a84c1..13010f905 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java @@ -44,34 +44,39 @@ * 7.7 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.sting.gatk.walkers.varianteval.stratifications; +package org.broadinstitute.sting.gatk.walkers.compression.reducereads; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.ArrayList; -import java.util.List; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc; /** - * Stratifies by the FILTER status (PASS, FAIL) of the eval records + * GenomeLocs are very useful objects to keep track of genomic locations and perform set operations + * with them. + * + * However, GenomeLocs are bound to strict validation through the GenomeLocParser and cannot + * be created easily for small tasks that do not require the rigors of the GenomeLocParser validation + * + * UnvalidatingGenomeLoc is a simple utility to create GenomeLocs without going through the parser. Should + * only be used outside of the engine. + * + * User: carneiro + * Date: 10/16/12 + * Time: 2:07 PM */ -public class Filter extends VariantStratifier { - @Override - public void initialize() { - states.add("called"); - states.add("filtered"); - states.add("raw"); +public class FinishedGenomeLoc extends UnvalidatingGenomeLoc { + private boolean finished; + + public FinishedGenomeLoc(final String contigName, final int contigIndex, final int start, final int stop, final boolean finished) { + super(contigName, contigIndex, start, stop); + this.finished = finished; } - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - ArrayList relevantStates = new ArrayList(); + public FinishedGenomeLoc(final GenomeLoc loc, final boolean finished) { + super(loc.getContig(), loc.getContigIndex(), loc.getStart(), loc.getStop()); + this.finished = finished; + } - relevantStates.add("raw"); - if (eval != null) { - relevantStates.add(eval.isFiltered() ? "filtered" : "called"); - } - - return relevantStates; + public boolean isFinished() { + return finished; } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java index 1e7805fce..13d3d1b4c 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java @@ -244,7 +244,7 @@ public class HeaderElement { * * @return whether or not the HeaderElement is variant due to excess insertions */ - private boolean isVariantFromMismatches(double minVariantProportion) { + protected boolean isVariantFromMismatches(double minVariantProportion) { BaseIndex mostCommon = consensusBaseCounts.baseIndexWithMostProbabilityWithoutIndels(); double mostCommonProportion = consensusBaseCounts.baseCountProportionWithoutIndels(mostCommon); return mostCommonProportion != 0.0 && mostCommonProportion < (1 - minVariantProportion); @@ -256,11 +256,11 @@ public class HeaderElement { * * @return true if we had more soft clipped bases contributing to this site than matches/mismatches. */ - private boolean isVariantFromSoftClips() { - return nSoftClippedBases >= (consensusBaseCounts.totalCount() - nSoftClippedBases); + protected boolean isVariantFromSoftClips() { + return nSoftClippedBases > 0 && nSoftClippedBases >= (consensusBaseCounts.totalCount() - nSoftClippedBases); } - private boolean basePassesFilters(byte baseQual, int minBaseQual, int baseMappingQuality, int minMappingQual) { + protected boolean basePassesFilters(byte baseQual, int minBaseQual, int baseMappingQuality, int minMappingQual) { return baseQual >= minBaseQual && baseMappingQuality >= minMappingQual; } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index 25006bb49..7e82629b8 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -64,7 +64,6 @@ import org.broadinstitute.sting.gatk.walkers.PartitionType; import org.broadinstitute.sting.gatk.walkers.ReadFilters; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocComparator; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -267,8 +266,8 @@ public class ReduceReads extends ReadWalker, ReduceRea public void initialize() { super.initialize(); GenomeAnalysisEngine toolkit = getToolkit(); - readNameHash = new HashMap(); // prepare the read name hash to keep track of what reads have had their read names compressed - intervalList = new TreeSet(new GenomeLocComparator()); // get the interval list from the engine. If no interval list was provided, the walker will work in WGS mode + readNameHash = new HashMap(); // prepare the read name hash to keep track of what reads have had their read names compressed + intervalList = new TreeSet(); // get the interval list from the engine. If no interval list was provided, the walker will work in WGS mode if (toolkit.getIntervals() != null) intervalList.addAll(toolkit.getIntervals()); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java index 58282e216..985fbba57 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java @@ -46,12 +46,14 @@ package org.broadinstitute.sting.gatk.walkers.compression.reducereads; +import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMFileHeader; import org.broadinstitute.sting.gatk.downsampling.ReservoirDownsampler; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.recalibration.EventType; @@ -135,6 +137,18 @@ public class SlidingWindow { return header.isEmpty() ? -1 : header.peek().getLocation(); } + // for testing only + protected SlidingWindow(final String contig, final int contigIndex, final int startLocation) { + this.contig = contig; + this.contigIndex = contigIndex; + + contextSize = 10; + nContigs = 1; + + this.windowHeader = new LinkedList(); + windowHeader.addFirst(new HeaderElement(startLocation)); + this.readsInWindow = new TreeSet(); + } public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader samHeader, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReads.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities, int nContigs, boolean allowPolyploidReduction) { this.contextSize = contextSize; @@ -193,14 +207,17 @@ public class SlidingWindow { } /** - * returns the next complete or incomplete variant region between 'from' (inclusive) and 'to' (exclusive) + * Returns the next complete (or incomplete if closeLastRegion is true) variant region between 'from' (inclusive) and 'to' (exclusive) + * but converted to global coordinates. * - * @param from beginning window header index of the search window (inclusive) - * @param to end window header index of the search window (exclusive) + * @param from beginning window header index of the search window (inclusive); note that this uses local coordinates + * @param to end window header index of the search window (exclusive); note that this uses local coordinates * @param variantSite boolean array with true marking variant regions - * @return null if nothing is variant, start/stop if there is a complete variant region, start/-1 if there is an incomplete variant region. + * @param closeLastRegion if the last index is variant (so it's an incomplete region), should we close (and return as an interval) the location or ignore it? + * @return null if nothing is variant, start/stop if there is a complete variant region, start/-1 if there is an incomplete variant region. All coordinates returned are global. */ - private SimpleGenomeLoc findNextVariantRegion(int from, int to, boolean[] variantSite, boolean forceClose) { + @Requires({"from >= 0", "from <= to", "to <= variantSite.length"}) + private FinishedGenomeLoc findNextVariantRegion(int from, int to, boolean[] variantSite, boolean closeLastRegion) { boolean foundStart = false; final int windowHeaderStart = getStartLocation(windowHeader); int variantRegionStartIndex = 0; @@ -210,27 +227,32 @@ public class SlidingWindow { foundStart = true; } else if(!variantSite[i] && foundStart) { - return(new SimpleGenomeLoc(contig, contigIndex, windowHeaderStart + variantRegionStartIndex, windowHeaderStart + i - 1, true)); + return(new FinishedGenomeLoc(contig, contigIndex, windowHeaderStart + variantRegionStartIndex, windowHeaderStart + i - 1, true)); } } final int refStart = windowHeaderStart + variantRegionStartIndex; final int refStop = windowHeaderStart + to - 1; - return (foundStart && forceClose) ? new SimpleGenomeLoc(contig, contigIndex, refStart, refStop, true) : null; + return (foundStart && closeLastRegion) ? new FinishedGenomeLoc(contig, contigIndex, refStart, refStop, true) : null; } /** * Creates a list with all the complete and incomplete variant regions within 'from' (inclusive) and 'to' (exclusive) * - * @param from beginning window header index of the search window (inclusive) - * @param to end window header index of the search window (exclusive) + * @param from beginning window header index of the search window (inclusive); note that this uses local coordinates + * @param to end window header index of the search window (exclusive); note that this uses local coordinates * @param variantSite boolean array with true marking variant regions - * @return a list with start/stops of variant regions following findNextVariantRegion description + * @return a list with start/stops of variant regions following findNextVariantRegion description in global coordinates */ - private CompressionStash findVariantRegions(int from, int to, boolean[] variantSite, boolean forceClose) { + @Requires({"from >= 0", "from <= to", "to <= variantSite.length"}) + @Ensures("result != null") + protected CompressionStash findVariantRegions(int from, int to, boolean[] variantSite, boolean closeLastRegion) { + final int windowHeaderStart = getStartLocation(windowHeader); + CompressionStash regions = new CompressionStash(); int index = from; while(index < to) { - SimpleGenomeLoc result = findNextVariantRegion(index, to, variantSite, forceClose); + // returns results in global coordinates + FinishedGenomeLoc result = findNextVariantRegion(index, to, variantSite, closeLastRegion); if (result == null) break; @@ -238,7 +260,7 @@ public class SlidingWindow { if (!result.isFinished()) break; - index = result.getStop() + 1; + index = result.getStop() - windowHeaderStart + 1; // go back to local coordinates } return regions; } @@ -274,7 +296,7 @@ public class SlidingWindow { } - private final class MarkedSites { + protected final class MarkedSites { private boolean[] siteIsVariant = new boolean[0]; private int startLocation = 0; @@ -283,6 +305,8 @@ public class SlidingWindow { public boolean[] getVariantSiteBitSet() { return siteIsVariant; } + protected int getStartLocation() { return startLocation; } + /** * Updates the variant site bitset given the new startlocation and size of the region to mark. * @@ -681,8 +705,8 @@ public class SlidingWindow { int lastStop = -1; int windowHeaderStart = getStartLocation(windowHeader); - for (SimpleGenomeLoc region : regions) { - if (region.isFinished() && region.getContig() == contig && region.getStart() >= windowHeaderStart && region.getStop() < windowHeaderStart + windowHeader.size()) { + for (GenomeLoc region : regions) { + if (((FinishedGenomeLoc)region).isFinished() && region.getContig() == contig && region.getStart() >= windowHeaderStart && region.getStop() < windowHeaderStart + windowHeader.size()) { int start = region.getStart() - windowHeaderStart; int stop = region.getStop() - windowHeaderStart; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java similarity index 83% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java index bf370a9ad..281c1c55d 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/BaseCoverageDistribution.java @@ -44,35 +44,61 @@ * 7.7 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.sting.gatk.walkers.varianteval.evaluators; +package org.broadinstitute.sting.gatk.walkers.diagnostics.targets; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.sting.gatk.report.GATKReport; +import org.broadinstitute.sting.gatk.walkers.By; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.LocusWalker; -@Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites") -public class PrintMissingComp extends VariantEvaluator { - @DataPoint(description = "number of eval sites outside of comp sites", format = "%d") - public long nMissing = 0; +import java.io.PrintStream; +import java.util.HashMap; +import java.util.Map; - public String getName() { - return "PrintMissingComp"; +/** + * User: carneiro + * Date: 1/27/13 + * Time: 11:16 AM + */ +@By(DataSource.REFERENCE) +public class BaseCoverageDistribution extends LocusWalker> { + @Output(required = true) + private PrintStream out; + + @Override + public boolean includeReadsWithDeletionAtLoci() { + return true; } - public int getComparisonOrder() { - return 2; // we need to see each eval track and each comp track + @Override + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + return context.getBasePileup().getReads().size(); // I want the reads instead of the base pileup because I want to count deletions. } - public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - final boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP(); - final boolean evalIsGood = eval != null && eval.isSNP(); + @Override + public Map reduceInit() { + return new HashMap(10000); + } - if ( compIsGood & ! evalIsGood ) { - nMissing++; - super.getWalker().getLogger().info("MissingFrom" + eval.toString() + " is missing from " + comp.getSource()); + @Override + public Map reduce(Integer value, Map sum) { + Long curr = sum.get(value); + if (curr == null) + curr = 0L; + sum.put(value, curr + 1); + return sum; + } + + @Override + public void onTraversalDone(Map result) { + GATKReport report = GATKReport.newSimpleReport("BaseCoverageDistribution", "Coverage", "Count"); + for (Map.Entry entry : result.entrySet()) { + report.addRow(entry.getKey(), entry.getValue()); } + report.print(out); } -} \ No newline at end of file +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index 08de5a6aa..ac028d860 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -52,19 +52,19 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension; +import org.broadinstitute.sting.gatk.walkers.ActiveRegionTraversalParameters; import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; import org.broadinstitute.sting.gatk.walkers.PartitionBy; import org.broadinstitute.sting.gatk.walkers.PartitionType; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; +import org.broadinstitute.sting.utils.activeregion.ActivityProfileState; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; @DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} ) @PartitionBy(PartitionType.CONTIG) -@ActiveRegionExtension(extension = 0, maxRegion = 50000) +@ActiveRegionTraversalParameters(extension = 0, maxRegion = 50000) public class FindCoveredIntervals extends ActiveRegionWalker { @Output(required = true) private PrintStream out; @@ -74,18 +74,18 @@ public class FindCoveredIntervals extends ActiveRegionWalker { @Override // Look to see if the region has sufficient coverage - public ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { + public ActivityProfileState isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { int depth = ThresHolder.DEFAULTS.getFilteredCoverage(context.getBasePileup()); // note the linear probability scale - return new ActivityProfileResult(ref.getLocus(), Math.min(depth / coverageThreshold, 1)); + return new ActivityProfileState(ref.getLocus(), Math.min(depth / coverageThreshold, 1)); } @Override public GenomeLoc map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) { - if (activeRegion.isActive) + if (activeRegion.isActive()) return activeRegion.getLocation(); else return null; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java deleted file mode 100644 index 6badc0d78..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java +++ /dev/null @@ -1,139 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.diffengine; - -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMRecordIterator; -import net.sf.samtools.util.BlockCompressedInputStream; - -import java.io.*; -import java.util.Arrays; - - -/** - * Created by IntelliJ IDEA. - * User: depristo - * Date: 7/4/11 - * Time: 1:09 PM - * - * Class implementing diffnode reader for VCF - */ -public class BAMDiffableReader implements DiffableReader { - @Override - public String getName() { return "BAM"; } - - @Override - public DiffElement readFromFile(File file, int maxElementsToRead) { - final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index - reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT); - - DiffNode root = DiffNode.rooted(file.getName()); - SAMRecordIterator iterator = reader.iterator(); - - int count = 0; - while ( iterator.hasNext() ) { - final SAMRecord record = iterator.next(); - - // name is the read name + first of pair - String name = record.getReadName().replace('.', '_'); - if ( record.getReadPairedFlag() ) { - name += record.getFirstOfPairFlag() ? "_1" : "_2"; - } - - DiffNode readRoot = DiffNode.empty(name, root); - - // add fields - readRoot.add("NAME", record.getReadName()); - readRoot.add("FLAGS", record.getFlags()); - readRoot.add("RNAME", record.getReferenceName()); - readRoot.add("POS", record.getAlignmentStart()); - readRoot.add("MAPQ", record.getMappingQuality()); - readRoot.add("CIGAR", record.getCigarString()); - readRoot.add("RNEXT", record.getMateReferenceName()); - readRoot.add("PNEXT", record.getMateAlignmentStart()); - readRoot.add("TLEN", record.getInferredInsertSize()); - readRoot.add("SEQ", record.getReadString()); - readRoot.add("QUAL", record.getBaseQualityString()); - - for ( SAMRecord.SAMTagAndValue xt : record.getAttributes() ) { - readRoot.add(xt.tag, xt.value); - } - - // add record to root - if ( ! root.hasElement(name) ) - // protect ourselves from malformed files - root.add(readRoot); - count += readRoot.size(); - if ( count > maxElementsToRead && maxElementsToRead != -1) - break; - } - - reader.close(); - - return root.getBinding(); - } - - @Override - public boolean canRead(File file) { - final byte[] BAM_MAGIC = "BAM\1".getBytes(); - final byte[] buffer = new byte[BAM_MAGIC.length]; - try { - InputStream fstream = new BufferedInputStream(new FileInputStream(file)); - if ( !BlockCompressedInputStream.isValidFile(fstream) ) - return false; - final BlockCompressedInputStream BCIS = new BlockCompressedInputStream(fstream); - BCIS.read(buffer, 0, BAM_MAGIC.length); - BCIS.close(); - return Arrays.equals(buffer, BAM_MAGIC); - } catch ( IOException e ) { - return false; - } catch ( net.sf.samtools.FileTruncatedException e ) { - return false; - } - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java deleted file mode 100644 index a69ac4181..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.diffengine; - -import org.broadinstitute.sting.gatk.report.GATKReport; -import org.broadinstitute.sting.gatk.report.GATKReportColumn; -import org.broadinstitute.sting.gatk.report.GATKReportTable; - -import java.io.File; -import java.io.FileReader; -import java.io.IOException; - - -/** - * Class implementing diffnode reader for GATKReports - */ - -// TODO Version check to be added at the report level - -public class GATKReportDiffableReader implements DiffableReader { - @Override - public String getName() { - return "GATKReport"; - } - - @Override - public DiffElement readFromFile(File file, int maxElementsToRead) { - DiffNode root = DiffNode.rooted(file.getName()); - try { - // one line reads the whole thing into memory - GATKReport report = new GATKReport(file); - - for (GATKReportTable table : report.getTables()) { - root.add(tableToNode(table, root)); - } - - return root.getBinding(); - } catch (Exception e) { - return null; - } - } - - private DiffNode tableToNode(GATKReportTable table, DiffNode root) { - DiffNode tableRoot = DiffNode.empty(table.getTableName(), root); - - tableRoot.add("Description", table.getTableDescription()); - tableRoot.add("NumberOfRows", table.getNumRows()); - - for ( GATKReportColumn column : table.getColumnInfo() ) { - DiffNode columnRoot = DiffNode.empty(column.getColumnName(), tableRoot); - - columnRoot.add("Width", column.getColumnFormat().getWidth()); - // NOTE: as the values are trimmed during parsing left/right alignment is not currently preserved - columnRoot.add("Displayable", true); - - for ( int i = 0; i < table.getNumRows(); i++ ) { - String name = column.getColumnName() + (i+1); - columnRoot.add(name, table.get(i, column.getColumnName()).toString()); - } - - tableRoot.add(columnRoot); - } - - return tableRoot; - } - - @Override - public boolean canRead(File file) { - try { - final String HEADER = GATKReport.GATKREPORT_HEADER_PREFIX; - final char[] buff = new char[HEADER.length()]; - final FileReader FR = new FileReader(file); - FR.read(buff, 0, HEADER.length()); - FR.close(); - String firstLine = new String(buff); - return firstLine.startsWith(HEADER); - } catch (IOException e) { - return false; - } - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java deleted file mode 100644 index 4c1989cdc..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java +++ /dev/null @@ -1,166 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.diffengine; - -import org.apache.log4j.Logger; -import org.broad.tribble.AbstractFeatureReader; -import org.broad.tribble.FeatureReader; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.variant.vcf.*; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.io.*; -import java.util.Iterator; -import java.util.Map; - - -/** - * Created by IntelliJ IDEA. - * User: depristo - * Date: 7/4/11 - * Time: 1:09 PM - * - * Class implementing diffnode reader for VCF - */ -public class VCFDiffableReader implements DiffableReader { - private static Logger logger = Logger.getLogger(VCFDiffableReader.class); - - @Override - public String getName() { return "VCF"; } - - @Override - public DiffElement readFromFile(File file, int maxElementsToRead) { - DiffNode root = DiffNode.rooted(file.getName()); - try { - // read the version line from the file - BufferedReader br = new BufferedReader(new FileReader(file)); - final String version = br.readLine(); - root.add("VERSION", version); - br.close(); - - final VCFCodec vcfCodec = new VCFCodec(); - vcfCodec.disableOnTheFlyModifications(); // must be read as state is stored in reader itself - - FeatureReader reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), vcfCodec, false); - VCFHeader header = (VCFHeader)reader.getHeader(); - for ( VCFHeaderLine headerLine : header.getMetaDataInInputOrder() ) { - String key = headerLine.getKey(); - if ( headerLine instanceof VCFIDHeaderLine) - key += "_" + ((VCFIDHeaderLine) headerLine).getID(); - if ( root.hasElement(key) ) - logger.warn("Skipping duplicate header line: file=" + file + " line=" + headerLine.toString()); - else - root.add(key, headerLine.toString()); - } - - int count = 0, nRecordsAtPos = 1; - String prevName = ""; - Iterator it = reader.iterator(); - while ( it.hasNext() ) { - VariantContext vc = it.next(); - String name = vc.getChr() + ":" + vc.getStart(); - if ( name.equals(prevName) ) { - name += "_" + ++nRecordsAtPos; - } else { - prevName = name; - } - DiffNode vcRoot = DiffNode.empty(name, root); - - // add fields - vcRoot.add("CHROM", vc.getChr()); - vcRoot.add("POS", vc.getStart()); - vcRoot.add("ID", vc.getID()); - vcRoot.add("REF", vc.getReference()); - vcRoot.add("ALT", vc.getAlternateAlleles()); - vcRoot.add("QUAL", vc.hasLog10PError() ? vc.getLog10PError() * -10 : VCFConstants.MISSING_VALUE_v4); - vcRoot.add("FILTER", ! vc.filtersWereApplied() // needs null to differentiate between PASS and . - ? VCFConstants.MISSING_VALUE_v4 - : ( vc.getFilters().isEmpty() ? VCFConstants.PASSES_FILTERS_v4 : vc.getFilters()) ); - - // add info fields - for (Map.Entry attribute : vc.getAttributes().entrySet()) { - if ( ! attribute.getKey().startsWith("_") ) - vcRoot.add(attribute.getKey(), attribute.getValue()); - } - - for (Genotype g : vc.getGenotypes() ) { - DiffNode gRoot = DiffNode.empty(g.getSampleName(), vcRoot); - gRoot.add("GT", g.getGenotypeString()); - if ( g.hasGQ() ) gRoot.add("GQ", g.getGQ() ); - if ( g.hasDP() ) gRoot.add("DP", g.getDP() ); - if ( g.hasAD() ) gRoot.add("AD", Utils.join(",", g.getAD())); - if ( g.hasPL() ) gRoot.add("PL", Utils.join(",", g.getPL())); - if ( g.getFilters() != null ) gRoot.add("FT", g.getFilters()); - - for (Map.Entry attribute : g.getExtendedAttributes().entrySet()) { - if ( ! attribute.getKey().startsWith("_") ) - gRoot.add(attribute.getKey(), attribute.getValue()); - } - - vcRoot.add(gRoot); - } - - root.add(vcRoot); - count += vcRoot.size(); - if ( count > maxElementsToRead && maxElementsToRead != -1) - break; - } - - reader.close(); - } catch ( IOException e ) { - return null; - } - - return root.getBinding(); - } - - @Override - public boolean canRead(File file) { - return AbstractVCFCodec.canDecodeFile(file.getPath(), VCFCodec.VCF4_MAGIC_HEADER); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java deleted file mode 100644 index 3562b3d75..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java +++ /dev/null @@ -1,160 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.fasta; - -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Collections; -import java.util.List; - - -/** - * Generates an alternative reference sequence over the specified interval. - * - *

- * Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). - * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'. - * - * The output format can be partially controlled using the provided command-line arguments. - * Specify intervals with the usual -L argument to output only the reference bases within your intervals. - * Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a - * separate fasta sequence (named numerically in order). - * - * Several important notes: - * 1) if there are multiple variants that start at a site, it chooses one of them randomly. - * 2) when there are overlapping indels (but with different start positions) only the first will be chosen. - * 3) this tool works only for SNPs and for simple indels (but not for things like complex substitutions). - * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order). - * - *

Input

- *

- * The reference, requested intervals, and any number of variant rod files. - *

- * - *

Output

- *

- * A fasta file representing the requested intervals. - *

- * - *

Examples

- * 
- * java -Xmx2g -jar GenomeAnalysisTK.jar \
- *   -R ref.fasta \
- *   -T FastaAlternateReferenceMaker \
- *   -o output.fasta \
- *   -L input.intervals \
- *   --variant input.vcf \
- *   [--snpmask mask.vcf]
- *
- * - */ -@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) -@Reference(window=@Window(start=-1,stop=50)) -@Requires(value={DataSource.REFERENCE}) -public class FastaAlternateReferenceMaker extends FastaReferenceMaker { - - /** - * Variants from these input files are used by this tool to construct an alternate reference. - */ - @Input(fullName = "variant", shortName = "V", doc="variants to model", required=false) - public List> variants = Collections.emptyList(); - - /** - * Snps from this file are used as a mask when constructing the alternate reference. - */ - @Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false) - public RodBinding snpmask; - - private int deletionBasesRemaining = 0; - - public Pair map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - - if (deletionBasesRemaining > 0) { - deletionBasesRemaining--; - return new Pair(context.getLocation(), ""); - } - - String refBase = String.valueOf((char)ref.getBase()); - - // Check to see if we have a called snp - for ( VariantContext vc : tracker.getValues(variants, ref.getLocus()) ) { - if ( vc.isFiltered() ) - continue; - - if ( vc.isSimpleDeletion()) { - deletionBasesRemaining = vc.getReference().length() - 1; - // delete the next n bases, not this one - return new Pair(context.getLocation(), refBase); - } else if ( vc.isSimpleInsertion()) { - return new Pair(context.getLocation(), vc.getAlternateAllele(0).toString()); - } else if (vc.isSNP()) { - return new Pair(context.getLocation(), vc.getAlternateAllele(0).toString()); - } - } - - // if we don't have a called site, and we have a mask at this site, mask it - for ( VariantContext vc : tracker.getValues(snpmask) ) { - if ( vc.isSNP()) { - return new Pair(context.getLocation(), "N"); - } - } - - - // if we got here then we're just ref - return new Pair(context.getLocation(), refBase); - } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java deleted file mode 100644 index 4cac2f119..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.fasta; - -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RefWalker; -import org.broadinstitute.sting.gatk.walkers.WalkerName; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; - -import java.io.PrintStream; - -/** - * Renders a new reference in FASTA format consisting of only those loci provided in the input data set. - * - *

- * The output format can be partially controlled using the provided command-line arguments. - * Specify intervals with the usual -L argument to output only the reference bases within your intervals. - * Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a - * separate fasta sequence (named numerically in order). - * - *

Input

- *

- * The reference and requested intervals. - *

- * - *

Output

- *

- * A fasta file representing the requested intervals. - *

- * - *

Examples

- * 
- * java -Xmx2g -jar GenomeAnalysisTK.jar \
- *   -R ref.fasta \
- *   -T FastaReferenceMaker \
- *   -o output.fasta \
- *   -L input.intervals
- *
- * - */ -@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) -public class FastaReferenceMaker extends RefWalker, GenomeLoc> { - - @Output PrintStream out; - - @Argument(fullName="lineWidth", shortName="lw", doc="Maximum length of sequence to write per line", required=false) - public int fastaLineWidth=60; - - /** - * Please note that when using this argument adjacent intervals will automatically be merged. - */ - @Argument(fullName="rawOnelineSeq", shortName="raw", doc="Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity)", required=false) - public boolean fastaRawSeqs=false; - - protected FastaSequence fasta; - - public void initialize() { - if (fastaRawSeqs) fastaLineWidth = Integer.MAX_VALUE; - fasta = new FastaSequence(out, fastaLineWidth, fastaRawSeqs); - } - - public Pair map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) { - return new Pair(context.getLocation(), String.valueOf((char)ref.getBase())); - } - - public GenomeLoc reduceInit() { - return null; - } - - public GenomeLoc reduce(Pair value, GenomeLoc sum) { - if ( value == null ) - return sum; - - // if there is no interval to the left, then this is the first one - if ( sum == null ) { - sum = value.first; - fasta.append(value.second); - } - // if the intervals don't overlap, print out the leftmost one and start a new one - // (end of contig or new interval) - else if ( value.first.getStart() != sum.getStop() + 1 ) { - fasta.flush(); - sum = value.first; - fasta.append(value.second); - } - // otherwise, merge them - else { - sum = getToolkit().getGenomeLocParser().setStop(sum, value.first.getStop()); - fasta.append(value.second); - } - return sum; - } - - public void onTraversalDone(GenomeLoc sum) { - fasta.flush(); - } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java deleted file mode 100644 index bcdf6c3a6..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java +++ /dev/null @@ -1,122 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.fasta; - -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.io.PrintStream; - -// fasta sequence holder class - -public class FastaSequence { - - private PrintStream out; - private StringBuffer sb = new StringBuffer(); - private long sequenceCounter = 1; - private boolean printedHeader = false; - private String name = null; - private int lineWidth = -1; - private boolean noHeader = false; - - public FastaSequence(PrintStream out, int lineWidth, boolean noHeader) { - this.out = out; - this.lineWidth = lineWidth; - this.noHeader = noHeader; - } - - public void setName(String name) { - if ( printedHeader ) throw new ReviewedStingException("Can not set name for FASTA record: header is already printed."); - this.name = name; - } - - public String getName() { - if ( name != null ) return name; - else return getCurrentID(); - } - - public void append(String s) { - sb.append(s); - printFasta(false); - } - - public void flush() { - printFasta(true); - printedHeader = false; - name = null; - sequenceCounter++; - } - - public long getCurrentCount() { - return sequenceCounter; - } - - public String getCurrentID() { - return String.valueOf(sequenceCounter); - } - - private void printFasta(boolean printAll) { - if ( sb.length() == 0 || (!printAll && sb.length() < lineWidth) ) - return; - if ( !printedHeader && !noHeader) { - if ( name == null ) out.println(">" + sequenceCounter); - else out.println(">" + name); - printedHeader = true; - } - int lines = sb.length() / lineWidth; - int currentStart = 0; - for (int i=0; i < lines; i++) { - out.println(sb.substring(currentStart, currentStart+lineWidth)); - currentStart += lineWidth; - } - if ( printAll ) { - out.println(sb.substring(currentStart)); - sb.setLength(0); - } else { - sb.delete(0, currentStart); - } - } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java deleted file mode 100644 index d73ac9220..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java +++ /dev/null @@ -1,102 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.filters; - -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; - -public class ClusteredSnps { - private GenomeLocParser genomeLocParser; - private int window = 10; - private int snpThreshold = 3; - - public ClusteredSnps(GenomeLocParser genomeLocParser,int snpThreshold, int window) { - this.genomeLocParser = genomeLocParser; - this.window = window; - this.snpThreshold = snpThreshold; - if ( window < 1 || snpThreshold < 1 ) - throw new IllegalArgumentException("Window and threshold values need to be positive values"); - } - - public boolean filter(FiltrationContextWindow contextWindow) { - - FiltrationContext[] variants = contextWindow.getWindow(snpThreshold-1, snpThreshold-1); - for (int i = 0; i < snpThreshold; i++) { - // ignore positions at the beginning or end of the overall interval (where there aren't enough records) - if ( variants[i] == null || variants[i+snpThreshold-1] == null ) - continue; - - // note: the documentation tells users we'll blow up if ref calls are present. - // if we ever get a windowed rod context that isn't a hack, we can actually allow this... - if ( !variants[i].getVariantContext().isVariant() ) - throw new UserException.BadInput("The clustered SNPs filter does not work in the presence of non-variant records; see the documentation for more details"); - - // find the nth variant - GenomeLoc left = GATKVariantContextUtils.getLocation(genomeLocParser, variants[i].getVariantContext()); - GenomeLoc right = null; - int snpsSeen = 1; - - int currentIndex = i; - while ( ++currentIndex < variants.length ) { - if ( variants[currentIndex] != null && variants[currentIndex].getVariantContext() != null && variants[currentIndex].getVariantContext().isVariant() ) { - if ( ++snpsSeen == snpThreshold ) { - right = GATKVariantContextUtils.getLocation(genomeLocParser, variants[currentIndex].getVariantContext()); - break; - } - } - } - - if ( right != null && - left.getContigIndex() == right.getContigIndex() && - Math.abs(right.getStart() - left.getStart()) <= window ) - return true; - } - return false; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java deleted file mode 100644 index 56a5b6289..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.filters; - -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.util.LinkedList; -import java.util.List; -import java.util.ListIterator; - -/** - * A window of variants surrounding the current variant being investigated - * - * @author ebanks - * @version 0.1 - */ - -public class FiltrationContextWindow { - - /** - * The variants. - */ - private LinkedList window = new LinkedList(); - private int currentContext; - - /** - * Contructor for a variant context. - * @param firstVariants the first set of variants, comprising the right half of the window - */ - public FiltrationContextWindow(List firstVariants) { - int windowSize = (firstVariants == null ? 1 : 2 * firstVariants.size() + 1); - currentContext = (firstVariants == null ? 0 : firstVariants.size()); - window.addAll(firstVariants); - while ( window.size() < windowSize ) - window.addFirst(null); - } - - /** - * The context currently being examined. - * @return The current context. - */ - public FiltrationContext getContext() { - return window.get(currentContext); - } - - /** - * The maximum number of elements that can be requested on either end of the current context. - * @return max. - */ - public int maxWindowElements() { - return currentContext; - } - - /** - * The window around the context currently being examined. - * @param elementsToLeft number of earlier contexts to return () - * @param elementsToRight number of later contexts to return () - * @return The current context window. - */ - public FiltrationContext[] getWindow(int elementsToLeft, int elementsToRight) { - if ( elementsToLeft > maxWindowElements() || elementsToRight > maxWindowElements() ) - throw new ReviewedStingException("Too large a window requested"); - if ( elementsToLeft < 0 || elementsToRight < 0 ) - throw new ReviewedStingException("Window size cannot be negative"); - - FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1]; - ListIterator iter = window.listIterator(currentContext - elementsToLeft); - for (int i = 0; i < elementsToLeft + elementsToRight + 1; i++) - array[i] = iter.next(); - return array; - } - - /** - * Move the window along to the next context - * @param context The new rightmost context - */ - public void moveWindow(FiltrationContext context) { - window.removeFirst(); - window.addLast(context); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java index 2257adf6a..ddf47805f 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java @@ -53,6 +53,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.clipping.ReadClipper; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -288,7 +289,7 @@ public class ConsensusAlleleCounter { if (vcs.isEmpty()) return Collections.emptyList(); // nothing else to do, no alleles passed minimum count criterion - final VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false); + final VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(vcs, null, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, GATKVariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false); return mergedVC.getAlleles(); } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java index fc7573f21..2baa89999 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java @@ -47,7 +47,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import net.sf.samtools.SAMUtils; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -425,7 +425,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable { byte qual = p.getQual(); if ( qual > SAMUtils.MAX_PHRED_SCORE ) - throw new UserException.MalformedBAM(p.getRead(), String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s. Perhaps your BAM incorrectly encodes the quality scores in Sanger format; see http://en.wikipedia.org/wiki/FASTQ_format for more details", SAMUtils.MAX_PHRED_SCORE, qual, p.getRead().getReadName())); + throw new UserException.MisencodedBAM(p.getRead(), "we encountered an extremely high quality score (" + (int)qual + ")"); if ( capBaseQualsAtMappingQual ) qual = (byte)Math.min((int)qual, p.getMappingQual()); if ( (int)qual < minBaseQual ) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java index aa117eb3b..14bffbc34 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java @@ -49,9 +49,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import net.sf.samtools.SAMUtils; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java index 9aa8c13ec..9ea027698 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java @@ -77,7 +77,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.*; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.variantcontext.*; import java.util.*; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index b3740bbb7..f48ae81cf 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -51,7 +51,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 84c109c9d..5a1bdf9e5 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Haplotype; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 7dc3e8ee3..0652cc236 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -51,7 +51,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 758d52e68..d16ece4fd 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -176,7 +176,7 @@ public class UnifiedGenotyper extends LocusWalker, Unif /** * A raw, unfiltered, highly sensitive callset in VCF format. */ - @Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer") + //@Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer") @Output(doc="File to which variants should be written",required=true) protected VariantContextWriter writer = null; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 8f6097661..19d218023 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -62,7 +62,7 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java index 131c1284f..d4bb3cab3 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java @@ -70,7 +70,7 @@ public class AFCalcFactory { * the needs of the request (i.e., considering ploidy). */ public enum Calculation { - /** expt. implementation -- for testing only */ + /** default implementation */ EXACT_INDEPENDENT(IndependentAllelesDiploidExactAFCalc.class, 2, -1), /** reference implementation of multi-allelic EXACT model. Extremely slow for many alternate alleles */ diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java index 74a95db37..8d7732a87 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnEdge.java @@ -86,7 +86,7 @@ public class DeBruijnEdge { multiplicity = value; } - public boolean getIsRef() { + public boolean isRef() { return isRef; } @@ -94,10 +94,12 @@ public class DeBruijnEdge { this.isRef = isRef; } + // For use when comparing edges pulled from the same graph public boolean equals( final DefaultDirectedGraph graph, final DeBruijnEdge edge ) { return (graph.getEdgeSource(this).equals(graph.getEdgeSource(edge))) && (graph.getEdgeTarget(this).equals(graph.getEdgeTarget(edge))); } + // For use when comparing edges across graphs! public boolean equals( final DefaultDirectedGraph graph, final DeBruijnEdge edge, final DefaultDirectedGraph graph2 ) { return (graph.getEdgeSource(this).equals(graph2.getEdgeSource(edge))) && (graph.getEdgeTarget(this).equals(graph2.getEdgeTarget(edge))); } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java index 0b898ee8d..c6f23359b 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java @@ -46,6 +46,9 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; +import com.google.java.contract.Ensures; +import com.google.java.contract.Invariant; + import java.util.Arrays; /** @@ -54,6 +57,7 @@ import java.util.Arrays; * Date: Mar 23, 2011 */ // simple node class for storing kmer sequences +@Invariant("kmer > 0") public class DeBruijnVertex { protected final byte[] sequence; @@ -82,10 +86,12 @@ public class DeBruijnVertex { return new String( getSuffix() ); } + @Ensures("result != null") public byte[] getSequence() { return sequence.clone(); } + @Ensures("result != null") public byte[] getSuffix() { return Arrays.copyOfRange( sequence, kmer - 1, sequence.length ); } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java index 27e921432..8b789791d 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java @@ -58,7 +58,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.variantcontext.*; import java.io.PrintStream; @@ -84,7 +84,7 @@ public class GenotypingEngine { final List haplotypes, final List samples, final Map haplotypeReadMap, - final Map> perSampleFilteredReadList, + final Map> perSampleFilteredReadList, final byte[] ref, final GenomeLoc refLoc, final GenomeLoc activeRegionWindow, @@ -124,12 +124,12 @@ public class GenotypingEngine { // Walk along each position in the key set and create each event to be outputted for( final int loc : startPosKeySet ) { if( loc >= activeRegionWindow.getStart() && loc <= activeRegionWindow.getStop() ) { // genotyping an event inside this active region - final ArrayList eventsAtThisLoc = new ArrayList(); // the overlapping events to merge into a common reference view - final ArrayList priorityList = new ArrayList(); // used to merge overlapping events into common reference view + final List eventsAtThisLoc = new ArrayList(); // the overlapping events to merge into a common reference view + final List priorityList = new ArrayList(); // used to merge overlapping events into common reference view if( !in_GGA_mode ) { for( final Haplotype h : haplotypes ) { - final HashMap eventMap = h.getEventMap(); + final Map eventMap = h.getEventMap(); final VariantContext vc = eventMap.get(loc); if( vc != null && !containsVCWithMatchingAlleles(eventsAtThisLoc, vc) ) { eventsAtThisLoc.add(vc); @@ -142,7 +142,7 @@ public class GenotypingEngine { if( compVC.getStart() == loc ) { int alleleCount = 0; for( final Allele compAltAllele : compVC.getAlternateAlleles() ) { - ArrayList alleleSet = new ArrayList(2); + List alleleSet = new ArrayList(2); alleleSet.add(compVC.getReference()); alleleSet.add(compAltAllele); final String vcSourceName = "Comp" + compCount + "Allele" + alleleCount; @@ -174,13 +174,13 @@ public class GenotypingEngine { validatePriorityList( priorityList, eventsAtThisLoc ); // Merge the event to find a common reference representation - final VariantContext mergedVC = VariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false); + final VariantContext mergedVC = GATKVariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false); if( mergedVC == null ) { continue; } if( eventsAtThisLoc.size() != mergedVC.getAlternateAlleles().size() ) { throw new ReviewedStingException("Record size mismatch! Something went wrong in the merging of alleles."); } - final HashMap mergeMap = new HashMap(); + final Map mergeMap = new HashMap(); mergeMap.put(null, mergedVC.getReference()); // the reference event (null) --> the reference allele for(int iii = 0; iii < mergedVC.getAlternateAlleles().size(); iii++) { mergeMap.put(eventsAtThisLoc.get(iii), mergedVC.getAlternateAllele(iii)); // BUGBUG: This is assuming that the order of alleles is the same as the priority list given to simpleMerge function @@ -232,7 +232,7 @@ public class GenotypingEngine { return genotypes; } - private void validatePriorityList( final ArrayList priorityList, final ArrayList eventsAtThisLoc ) { + private void validatePriorityList( final List priorityList, final List eventsAtThisLoc ) { for( final VariantContext vc : eventsAtThisLoc ) { if( !priorityList.contains(vc.getSource()) ) { throw new ReviewedStingException("Event found on haplotype that wasn't added to priority list. Something went wrong in the merging of alleles."); @@ -251,7 +251,7 @@ public class GenotypingEngine { private static Map filterToOnlyOverlappingReads( final GenomeLocParser parser, final Map perSampleReadMap, - final Map> perSampleFilteredReadList, + final Map> perSampleFilteredReadList, final VariantContext call ) { final Map returnMap = new HashMap(); @@ -284,7 +284,7 @@ public class GenotypingEngine { } protected static void cleanUpSymbolicUnassembledEvents( final List haplotypes ) { - final ArrayList haplotypesToRemove = new ArrayList(); + final List haplotypesToRemove = new ArrayList(); for( final Haplotype h : haplotypes ) { for( final VariantContext vc : h.getEventMap().values() ) { if( vc.isSymbolic() ) { @@ -407,7 +407,7 @@ public class GenotypingEngine { // remove the old event from the eventMap on every haplotype and the start pos key set, replace with merged event for( final Haplotype h : haplotypes ) { - final HashMap eventMap = h.getEventMap(); + final Map eventMap = h.getEventMap(); if( eventMap.containsKey(thisStart) && eventMap.containsKey(nextStart) ) { eventMap.remove(thisStart); eventMap.remove(nextStart); @@ -418,7 +418,7 @@ public class GenotypingEngine { boolean containsStart = false; boolean containsNext = false; for( final Haplotype h : haplotypes ) { - final HashMap eventMap = h.getEventMap(); + final Map eventMap = h.getEventMap(); if( eventMap.containsKey(thisStart) ) { containsStart = true; } if( eventMap.containsKey(nextStart) ) { containsNext = true; } } @@ -457,7 +457,7 @@ public class GenotypingEngine { if( refBases.length == altBases.length ) { // insertion + deletion of same length creates an MNP --> trim common prefix bases off the beginning of the allele while( iii < refBases.length && refBases[iii] == altBases[iii] ) { iii++; } } - final ArrayList mergedAlleles = new ArrayList(); + final List mergedAlleles = new ArrayList(); mergedAlleles.add( Allele.create( ArrayUtils.subarray(refBases, iii, refBases.length), true ) ); mergedAlleles.add( Allele.create( ArrayUtils.subarray(altBases, iii, altBases.length), false ) ); return new VariantContextBuilder("merged", thisVC.getChr(), thisVC.getStart() + iii, nextVC.getEnd(), mergedAlleles).make(); @@ -492,10 +492,10 @@ public class GenotypingEngine { eventMapper.put(new Event(vc), new ArrayList()); } - final ArrayList undeterminedHaplotypes = new ArrayList(haplotypes.size()); + final List undeterminedHaplotypes = new ArrayList(haplotypes.size()); for( final Haplotype h : haplotypes ) { if( h.isArtificialHaplotype() && loc == h.getArtificialAllelePosition() ) { - final ArrayList alleles = new ArrayList(2); + final List alleles = new ArrayList(2); alleles.add(h.getArtificialRefAllele()); alleles.add(h.getArtificialAltAllele()); final Event artificialVC = new Event( (new VariantContextBuilder()).source("artificialHaplotype") @@ -572,13 +572,13 @@ public class GenotypingEngine { } @Ensures({"result.size() == haplotypeAllelesForSample.size()"}) - protected static List findEventAllelesInSample( final List eventAlleles, final List haplotypeAlleles, final List haplotypeAllelesForSample, final ArrayList> alleleMapper, final ArrayList haplotypes ) { + protected static List findEventAllelesInSample( final List eventAlleles, final List haplotypeAlleles, final List haplotypeAllelesForSample, final List> alleleMapper, final List haplotypes ) { if( haplotypeAllelesForSample.contains(Allele.NO_CALL) ) { return noCall; } - final ArrayList eventAllelesForSample = new ArrayList(); + final List eventAllelesForSample = new ArrayList(); for( final Allele a : haplotypeAllelesForSample ) { final Haplotype haplotype = haplotypes.get(haplotypeAlleles.indexOf(a)); for( int iii = 0; iii < alleleMapper.size(); iii++ ) { - final ArrayList mappedHaplotypes = alleleMapper.get(iii); + final List mappedHaplotypes = alleleMapper.get(iii); if( mappedHaplotypes.contains(haplotype) ) { eventAllelesForSample.add(eventAlleles.get(iii)); break; @@ -597,8 +597,8 @@ public class GenotypingEngine { return false; } - protected static HashMap generateVCsFromAlignment( final Haplotype haplotype, final int alignmentStartHapwrtRef, final Cigar cigar, final byte[] ref, final byte[] alignment, final GenomeLoc refLoc, final String sourceNameToAdd ) { - final HashMap vcs = new HashMap(); + protected static Map generateVCsFromAlignment( final Haplotype haplotype, final int alignmentStartHapwrtRef, final Cigar cigar, final byte[] ref, final byte[] alignment, final GenomeLoc refLoc, final String sourceNameToAdd ) { + final Map vcs = new HashMap(); int refPos = alignmentStartHapwrtRef; if( refPos < 0 ) { return null; } // Protection against SW failures @@ -609,7 +609,7 @@ public class GenotypingEngine { switch( ce.getOperator() ) { case I: { - final ArrayList insertionAlleles = new ArrayList(); + final List insertionAlleles = new ArrayList(); final int insertionStart = refLoc.getStart() + refPos - 1; final byte refByte = ref[refPos-1]; if( BaseUtils.isRegularBase(refByte) ) { @@ -639,7 +639,7 @@ public class GenotypingEngine { case D: { final byte[] deletionBases = Arrays.copyOfRange( ref, refPos - 1, refPos + elementLength ); // add padding base - final ArrayList deletionAlleles = new ArrayList(); + final List deletionAlleles = new ArrayList(); final int deletionStart = refLoc.getStart() + refPos - 1; // BUGBUG: how often does this symbolic deletion allele case happen? //if( haplotype != null && ( (haplotype.leftBreakPoint + alignmentStartHapwrtRef + refLoc.getStart() + elementLength - 1 >= deletionStart && haplotype.leftBreakPoint + alignmentStartHapwrtRef + refLoc.getStart() + elementLength - 1 < deletionStart + elementLength) @@ -667,7 +667,7 @@ public class GenotypingEngine { final byte altByte = alignment[alignmentPos]; if( refByte != altByte ) { // SNP! if( BaseUtils.isRegularBase(refByte) && BaseUtils.isRegularBase(altByte) ) { - final ArrayList snpAlleles = new ArrayList(); + final List snpAlleles = new ArrayList(); snpAlleles.add( Allele.create( refByte, true ) ); snpAlleles.add( Allele.create( altByte, false ) ); vcs.put(refLoc.getStart() + refPos, new VariantContextBuilder(sourceNameToAdd, refLoc.getContig(), refLoc.getStart() + refPos, refLoc.getStart() + refPos, snpAlleles).make()); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 439a9b3b8..027c62e68 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -47,6 +47,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; import com.google.java.contract.Ensures; +import net.sf.samtools.*; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; @@ -57,6 +58,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.downsampling.DownsampleType; import org.broadinstitute.sting.gatk.filters.BadMateFilter; +import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.iterators.ReadTransformer; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; @@ -67,8 +69,9 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; +import org.broadinstitute.sting.utils.activeregion.ActivityProfileState; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.*; @@ -129,8 +132,8 @@ import java.util.*; @DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) @PartitionBy(PartitionType.LOCUS) @BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN) -@ActiveRegionExtension(extension=65, maxRegion=300) -//@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=5) +@ActiveRegionTraversalParameters(extension=65, maxRegion=300) +@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=20) public class HaplotypeCaller extends ActiveRegionWalker implements AnnotatorCompatible { /** @@ -142,6 +145,17 @@ public class HaplotypeCaller extends ActiveRegionWalker implem @Output(fullName="graphOutput", shortName="graph", doc="File to which debug assembly graph information should be written", required = false) protected PrintStream graphWriter = null; + /** + * The assembled haplotypes will be written as BAM to this file if requested. Really for debugging purposes only. Note that the output here + * does not include uninformative reads so that not every input read is emitted to the bam. + */ + @Hidden + @Output(fullName="bamOutput", shortName="bam", doc="File to which assembled haplotypes should be written", required = false) + protected StingSAMFileWriter bamWriter = null; + private SAMFileHeader bamHeader = null; + private long uniqueNameCounter = 1; + private final static String readGroupId = "ArtificialHaplotype"; + /** * The PairHMM implementation to use for genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime. */ @@ -167,8 +181,15 @@ public class HaplotypeCaller extends ActiveRegionWalker implem @Argument(fullName="minKmer", shortName="minKmer", doc="Minimum kmer length to use in the assembly graph", required = false) protected int minKmer = 11; - @Argument(fullName="downsampleRegion", shortName="dr", doc="coverage, per-sample, to downsample each active region to", required = false) - protected int DOWNSAMPLE_PER_SAMPLE_PER_REGION = 1000; + /** + * If this flag is provided, the haplotype caller will include unmapped reads in the assembly and calling + * when these reads occur in the region being analyzed. Typically, for paired end analyses, one pair of the + * read can map, but if its pair is too divergent then it may be unmapped and placed next to its mate, taking + * the mates contig and alignment start. If this flag is provided the haplotype caller will see such reads, + * and may make use of them in assembly and calling, where possible. + */ + @Argument(fullName="includeUmappedReads", shortName="unmapped", doc="If provided, unmapped reads with chromosomal coordinates (i.e., those placed to their maps) will be included in the assembly and calling", required = false) + protected boolean includeUnmappedReads = false; @Argument(fullName="useAllelesTrigger", shortName="allelesTrigger", doc = "If specified, use additional trigger on variants found in an external alleles file", required=false) protected boolean USE_ALLELES_TRIGGER = false; @@ -242,6 +263,8 @@ public class HaplotypeCaller extends ActiveRegionWalker implem // the genotyping engine private GenotypingEngine genotypingEngine = null; + private VariantAnnotatorEngine annotationEngine = null; + // fasta reference reader to supplement the edges of the reference sequence private CachingIndexedFastaSequenceFile referenceReader; @@ -251,10 +274,10 @@ public class HaplotypeCaller extends ActiveRegionWalker implem // bases with quality less than or equal to this value are trimmed off the tails of the reads private static final byte MIN_TAIL_QUALITY = 20; - private ArrayList samplesList = new ArrayList(); + private List samplesList = new ArrayList(); private final static double LOG_ONE_HALF = -Math.log10(2.0); private final static double LOG_ONE_THIRD = -Math.log10(3.0); - private final ArrayList allelesToGenotype = new ArrayList(); + private final List allelesToGenotype = new ArrayList(); private final static Allele FAKE_REF_ALLELE = Allele.create("N", true); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file private final static Allele FAKE_ALT_ALLELE = Allele.create("", false); // used in isActive function to call into UG Engine. Should never appear anywhere in a VCF file @@ -286,7 +309,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY); // initialize the output VCF header - final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit()); + annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit()); Set headerInfo = new HashSet(); @@ -320,6 +343,9 @@ public class HaplotypeCaller extends ActiveRegionWalker implem assemblyEngine = new SimpleDeBruijnAssembler( DEBUG, graphWriter, minKmer ); likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM ); genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS ); + + if ( bamWriter != null ) + setupBamWriter(); } //--------------------------------------------------------------------------------------------------------------- @@ -335,16 +361,25 @@ public class HaplotypeCaller extends ActiveRegionWalker implem // enable non primary and extended reads in the active region @Override public EnumSet desiredReadStates() { - return EnumSet.of( - ActiveRegionReadState.PRIMARY, - ActiveRegionReadState.NONPRIMARY, - ActiveRegionReadState.EXTENDED - ); + if ( includeUnmappedReads ) { + throw new UserException.BadArgumentValue("includeUmappedReads", "is not yet functional"); +// return EnumSet.of( +// ActiveRegionReadState.PRIMARY, +// ActiveRegionReadState.NONPRIMARY, +// ActiveRegionReadState.EXTENDED, +// ActiveRegionReadState.UNMAPPED +// ); + } else + return EnumSet.of( + ActiveRegionReadState.PRIMARY, + ActiveRegionReadState.NONPRIMARY, + ActiveRegionReadState.EXTENDED + ); } @Override @Ensures({"result.isActiveProb >= 0.0", "result.isActiveProb <= 1.0"}) - public ActivityProfileResult isActive( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) { + public ActivityProfileState isActive( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context ) { if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { for( final VariantContext vc : tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()) ) { @@ -353,15 +388,17 @@ public class HaplotypeCaller extends ActiveRegionWalker implem } } if( tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ) { - return new ActivityProfileResult(ref.getLocus(), 1.0); + return new ActivityProfileState(ref.getLocus(), 1.0); } } if( USE_ALLELES_TRIGGER ) { - return new ActivityProfileResult( ref.getLocus(), tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ? 1.0 : 0.0 ); + return new ActivityProfileState( ref.getLocus(), tracker.getValues(UG_engine.getUAC().alleles, ref.getLocus()).size() > 0 ? 1.0 : 0.0 ); } - if( context == null ) { return new ActivityProfileResult(ref.getLocus(), 0.0); } + if( context == null || context.getBasePileup().isEmpty() ) + // if we don't have any data, just abort early + return new ActivityProfileState(ref.getLocus(), 0.0); final List noCall = new ArrayList(); // used to noCall all genotypes until the exact model is applied noCall.add(Allele.NO_CALL); @@ -392,13 +429,13 @@ public class HaplotypeCaller extends ActiveRegionWalker implem genotypes.add( new GenotypeBuilder(sample.getKey()).alleles(noCall).PL(genotypeLikelihoods).make() ); } - final ArrayList alleles = new ArrayList(); + final List alleles = new ArrayList(); alleles.add( FAKE_REF_ALLELE ); alleles.add( FAKE_ALT_ALLELE ); final VariantCallContext vcOut = UG_engine_simple_genotyper.calculateGenotypes(new VariantContextBuilder("HCisActive!", context.getContig(), context.getLocation().getStart(), context.getLocation().getStop(), alleles).genotypes(genotypes).make(), GenotypeLikelihoodsCalculationModel.Model.INDEL); final double isActiveProb = vcOut == null ? 0.0 : QualityUtils.qualToProb( vcOut.getPhredScaledQual() ); - return new ActivityProfileResult( ref.getLocus(), isActiveProb, averageHQSoftClips.mean() > 6.0 ? ActivityProfileResult.ActivityProfileResultState.HIGH_QUALITY_SOFT_CLIPS : ActivityProfileResult.ActivityProfileResultState.NONE, averageHQSoftClips.mean() ); + return new ActivityProfileState( ref.getLocus(), isActiveProb, averageHQSoftClips.mean() > 6.0 ? ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS : ActivityProfileState.Type.NONE, averageHQSoftClips.mean() ); } //--------------------------------------------------------------------------------------------------------------- @@ -408,12 +445,12 @@ public class HaplotypeCaller extends ActiveRegionWalker implem //--------------------------------------------------------------------------------------------------------------- @Override - public Integer map( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) { + public Integer map( final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) { if ( justDetermineActiveRegions ) // we're benchmarking ART and/or the active region determination code in the HC, just leave without doing any work return 1; - final ArrayList activeAllelesToGenotype = new ArrayList(); + final List activeAllelesToGenotype = new ArrayList(); if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { for( final VariantContext vc : allelesToGenotype ) { @@ -424,16 +461,18 @@ public class HaplotypeCaller extends ActiveRegionWalker implem allelesToGenotype.removeAll( activeAllelesToGenotype ); } - if( !activeRegion.isActive ) { return 0; } // Not active so nothing to do! + if( !activeRegion.isActive() ) { return 0; } // Not active so nothing to do! if( activeRegion.size() == 0 && UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { return 0; } // No reads here so nothing to do! if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES && activeAllelesToGenotype.isEmpty() ) { return 0; } // No alleles found in this region so nothing to do! finalizeActiveRegion( activeRegion ); // merge overlapping fragments, clip adapter and low qual tails - final Haplotype referenceHaplotype = new Haplotype(activeRegion.getActiveRegionReference(referenceReader)); // Create the reference haplotype which is the bases from the reference that make up the active region - referenceHaplotype.setIsReference(true); + + // note this operation must be performed before we clip the reads down, as this must correspond to the full reference region + final GenomeLoc fullSpanBeforeClipping = getPaddedLoc(activeRegion); + + final Haplotype referenceHaplotype = new Haplotype(activeRegion.getActiveRegionReference(referenceReader), true); // Create the reference haplotype which is the bases from the reference that make up the active region final byte[] fullReferenceWithPadding = activeRegion.getFullReference(referenceReader, REFERENCE_PADDING); - //int PRUNE_FACTOR = Math.max(MIN_PRUNE_FACTOR, determinePruneFactorFromCoverage( activeRegion )); - final ArrayList haplotypes = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, getPaddedLoc(activeRegion), MIN_PRUNE_FACTOR, activeAllelesToGenotype ); + final List haplotypes = assemblyEngine.runLocalAssembly( activeRegion, referenceHaplotype, fullReferenceWithPadding, fullSpanBeforeClipping, MIN_PRUNE_FACTOR, activeAllelesToGenotype ); if( haplotypes.size() == 1 ) { return 1; } // only the reference haplotype remains so nothing else to do! activeRegion.hardClipToActiveRegion(); // only evaluate the parts of reads that are overlapping the active region @@ -445,10 +484,10 @@ public class HaplotypeCaller extends ActiveRegionWalker implem // evaluate each sample's reads against all haplotypes final Map stratifiedReadMap = likelihoodCalculationEngine.computeReadLikelihoods( haplotypes, splitReadsBySample( activeRegion.getReads() ) ); - final Map> perSampleFilteredReadList = splitReadsBySample( filteredReads ); + final Map> perSampleFilteredReadList = splitReadsBySample( filteredReads ); // subset down to only the best haplotypes to be genotyped in all samples ( in GGA mode use all discovered haplotypes ) - final ArrayList bestHaplotypes = ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? + final List bestHaplotypes = ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? likelihoodCalculationEngine.selectBestHaplotypes( haplotypes, stratifiedReadMap, maxNumHaplotypesInPopulation ) : haplotypes ); for( final VariantContext call : genotypingEngine.assignGenotypeLikelihoods( UG_engine, @@ -457,13 +496,34 @@ public class HaplotypeCaller extends ActiveRegionWalker implem stratifiedReadMap, perSampleFilteredReadList, fullReferenceWithPadding, - getPaddedLoc(activeRegion), + fullSpanBeforeClipping, activeRegion.getLocation(), getToolkit().getGenomeLocParser(), activeAllelesToGenotype ) ) { + annotationEngine.annotateDBs(metaDataTracker, getToolkit().getGenomeLocParser().createGenomeLoc(call), call); vcfWriter.add( call ); } + if ( bamWriter != null ) { + // write the haplotypes to the bam + for ( Haplotype haplotype : haplotypes ) + writeHaplotype(haplotype, fullSpanBeforeClipping, bestHaplotypes.contains(haplotype)); + + // we need to remap the Alleles back to the Haplotypes; inefficient but unfortunately this is a requirement currently + final Map alleleToHaplotypeMap = new HashMap(haplotypes.size()); + for ( final Haplotype haplotype : haplotypes ) + alleleToHaplotypeMap.put(Allele.create(haplotype.getBases()), haplotype); + + // next, output the interesting reads for each sample aligned against the appropriate haplotype + for ( final PerReadAlleleLikelihoodMap readAlleleLikelihoodMap : stratifiedReadMap.values() ) { + for ( Map.Entry> entry : readAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) { + final Allele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue()); + if ( bestAllele != Allele.NO_CALL ) + writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele), fullSpanBeforeClipping.getStart()); + } + } + } + if( DEBUG ) { System.out.println("----------------------------------------------------------------------------------"); } return 1; // One active region was processed during this map call @@ -498,8 +558,8 @@ public class HaplotypeCaller extends ActiveRegionWalker implem private void finalizeActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) { if( DEBUG ) { System.out.println("\nAssembling " + activeRegion.getLocation() + " with " + activeRegion.size() + " reads: (with overlap region = " + activeRegion.getExtendedLoc() + ")"); } - final ArrayList finalizedReadList = new ArrayList(); - final FragmentCollection fragmentCollection = FragmentUtils.create( ReadUtils.sortReadsByCoordinate(activeRegion.getReads()) ); + final List finalizedReadList = new ArrayList(); + final FragmentCollection fragmentCollection = FragmentUtils.create( activeRegion.getReads() ); activeRegion.clearReads(); // Join overlapping paired reads to create a single longer read @@ -508,24 +568,22 @@ public class HaplotypeCaller extends ActiveRegionWalker implem finalizedReadList.addAll( FragmentUtils.mergeOverlappingPairedFragments(overlappingPair) ); } - Collections.shuffle(finalizedReadList, GenomeAnalysisEngine.getRandomGenerator()); - // Loop through the reads hard clipping the adaptor and low quality tails + final List readsToUse = new ArrayList(finalizedReadList.size()); for( final GATKSAMRecord myRead : finalizedReadList ) { final GATKSAMRecord postAdapterRead = ( myRead.getReadUnmappedFlag() ? myRead : ReadClipper.hardClipAdaptorSequence( myRead ) ); if( postAdapterRead != null && !postAdapterRead.isEmpty() && postAdapterRead.getCigar().getReadLength() > 0 ) { final GATKSAMRecord clippedRead = ReadClipper.hardClipLowQualEnds( postAdapterRead, MIN_TAIL_QUALITY ); - // protect against INTERVALS with abnormally high coverage - // BUGBUG: remove when positional downsampler is hooked up to ART/HC - if( clippedRead.getReadLength() > 0 && activeRegion.size() < samplesList.size() * DOWNSAMPLE_PER_SAMPLE_PER_REGION ) { - activeRegion.add(clippedRead); + if( activeRegion.readOverlapsRegion(clippedRead) && clippedRead.getReadLength() > 0 ) { + readsToUse.add(clippedRead); } } } + activeRegion.addAll(ReadUtils.sortReadsByCoordinate(readsToUse)); } private List filterNonPassingReads( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) { - final ArrayList readsToRemove = new ArrayList(); + final List readsToRemove = new ArrayList(); for( final GATKSAMRecord rec : activeRegion.getReads() ) { if( rec.getReadLength() < 24 || rec.getMappingQuality() < 20 || BadMateFilter.hasBadMate(rec) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) { readsToRemove.add(rec); @@ -536,15 +594,15 @@ public class HaplotypeCaller extends ActiveRegionWalker implem } private GenomeLoc getPaddedLoc( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) { - final int padLeft = Math.max(activeRegion.getReferenceLoc().getStart()-REFERENCE_PADDING, 1); - final int padRight = Math.min(activeRegion.getReferenceLoc().getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(activeRegion.getReferenceLoc().getContig()).getSequenceLength()); - return getToolkit().getGenomeLocParser().createGenomeLoc(activeRegion.getReferenceLoc().getContig(), padLeft, padRight); + final int padLeft = Math.max(activeRegion.getReadSpanLoc().getStart()-REFERENCE_PADDING, 1); + final int padRight = Math.min(activeRegion.getReadSpanLoc().getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(activeRegion.getReadSpanLoc().getContig()).getSequenceLength()); + return getToolkit().getGenomeLocParser().createGenomeLoc(activeRegion.getReadSpanLoc().getContig(), padLeft, padRight); } - private HashMap> splitReadsBySample( final List reads ) { - final HashMap> returnMap = new HashMap>(); + private Map> splitReadsBySample( final List reads ) { + final Map> returnMap = new HashMap>(); for( final String sample : samplesList) { - ArrayList readList = returnMap.get( sample ); + List readList = returnMap.get( sample ); if( readList == null ) { readList = new ArrayList(); returnMap.put(sample, readList); @@ -557,23 +615,92 @@ public class HaplotypeCaller extends ActiveRegionWalker implem return returnMap; } - /* - private int determinePruneFactorFromCoverage( final ActiveRegion activeRegion ) { - final ArrayList readLengthDistribution = new ArrayList(); - for( final GATKSAMRecord read : activeRegion.getReads() ) { - readLengthDistribution.add(read.getReadLength()); - } - final double meanReadLength = MathUtils.average(readLengthDistribution); - final double meanCoveragePerSample = (double) activeRegion.getReads().size() / ((double) activeRegion.getExtendedLoc().size() / meanReadLength) / (double) samplesList.size(); - int PRUNE_FACTOR = 0; - if( meanCoveragePerSample > 8.5 ) { - PRUNE_FACTOR = (int) Math.floor( Math.sqrt( meanCoveragePerSample - 5.0 ) ); - } else if( meanCoveragePerSample > 3.0 ) { - PRUNE_FACTOR = 1; + private void setupBamWriter() { + // prepare the bam header + bamHeader = new SAMFileHeader(); + bamHeader.setSequenceDictionary(getToolkit().getSAMFileHeader().getSequenceDictionary()); + bamHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate); + + // include the original read groups plus a new artificial one for the haplotypes + final List readGroups = new ArrayList(getToolkit().getSAMFileHeader().getReadGroups()); + final SAMReadGroupRecord rg = new SAMReadGroupRecord(readGroupId); + rg.setSample("HC"); + rg.setSequencingCenter("BI"); + readGroups.add(rg); + bamHeader.setReadGroups(readGroups); + + bamWriter.setPresorted(false); + bamWriter.writeHeader(bamHeader); + } + + private void writeHaplotype(final Haplotype haplotype, final GenomeLoc paddedRefLoc, final boolean isAmongBestHaplotypes) { + final GATKSAMRecord record = new GATKSAMRecord(bamHeader); + record.setReadBases(haplotype.getBases()); + record.setAlignmentStart(paddedRefLoc.getStart() + haplotype.getAlignmentStartHapwrtRef()); + record.setBaseQualities(Utils.dupBytes((byte) '!', haplotype.getBases().length)); + record.setCigar(haplotype.getCigar()); + record.setMappingQuality(isAmongBestHaplotypes ? 60 : 0); + record.setReadName("HC" + uniqueNameCounter++); + record.setReadUnmappedFlag(false); + record.setReferenceIndex(paddedRefLoc.getContigIndex()); + record.setAttribute(SAMTag.RG.toString(), readGroupId); + record.setFlags(16); + bamWriter.addAlignment(record); + } + + private void writeReadAgainstHaplotype(final GATKSAMRecord read, final Haplotype haplotype, final int referenceStart) { + + final SWPairwiseAlignment swPairwiseAlignment = new SWPairwiseAlignment(haplotype.getBases(), read.getReadBases(), 5.0, -10.0, -22.0, -1.2); + final int readStartOnHaplotype = swPairwiseAlignment.getAlignmentStart2wrt1(); + final int readStartOnReference = referenceStart + haplotype.getAlignmentStartHapwrtRef() + readStartOnHaplotype; + read.setAlignmentStart(readStartOnReference); + + final Cigar cigar = generateReadCigarFromHaplotype(read, readStartOnHaplotype, haplotype.getCigar()); + read.setCigar(cigar); + + bamWriter.addAlignment(read); + } + + private Cigar generateReadCigarFromHaplotype(final GATKSAMRecord read, final int readStartOnHaplotype, final Cigar haplotypeCigar) { + + int currentReadPos = 0; + int currentHapPos = 0; + final List readCigarElements = new ArrayList(); + + for ( final CigarElement cigarElement : haplotypeCigar.getCigarElements() ) { + + if ( cigarElement.getOperator() == CigarOperator.D ) { + if ( currentReadPos > 0 ) + readCigarElements.add(cigarElement); + } else if ( cigarElement.getOperator() == CigarOperator.M || cigarElement.getOperator() == CigarOperator.I ) { + + final int elementLength = cigarElement.getLength(); + final int nextReadPos = currentReadPos + elementLength; + final int nextHapPos = currentHapPos + elementLength; + + // do we want this element? + if ( currentReadPos > 0 ) { + // do we want the entire element? + if ( nextReadPos < read.getReadLength() ) { + readCigarElements.add(cigarElement); + currentReadPos = nextReadPos; + } + // otherwise, we can finish up and return the cigar + else { + readCigarElements.add(new CigarElement(read.getReadLength() - currentReadPos, cigarElement.getOperator())); + return new Cigar(readCigarElements); + } + } + // do we want part of the element to start? + else if ( currentReadPos == 0 && nextHapPos > readStartOnHaplotype ) { + currentReadPos = Math.min(nextHapPos - readStartOnHaplotype, read.getReadLength()); + readCigarElements.add(new CigarElement(currentReadPos, cigarElement.getOperator())); + } + + currentHapPos = nextHapPos; + } } - if( DEBUG ) { System.out.println(String.format("Mean coverage per sample = %.1f --> prune factor = %d", meanCoveragePerSample, PRUNE_FACTOR)); } - return PRUNE_FACTOR; + return new Cigar(readCigarElements); } - */ } \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java index 7d79edf93..49e926e32 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPaths.java @@ -46,8 +46,15 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; +import net.sf.samtools.Cigar; +import net.sf.samtools.CigarElement; +import net.sf.samtools.CigarOperator; import org.apache.commons.lang.ArrayUtils; +import org.broadinstitute.sting.utils.SWPairwiseAlignment; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.jgrapht.graph.DefaultDirectedGraph; import java.io.Serializable; @@ -55,7 +62,7 @@ import java.util.*; /** * Created by IntelliJ IDEA. - * User: ebanks + * User: ebanks, rpoplin * Date: Mar 23, 2011 */ // Class for finding the K best paths (as determined by the sum of multiplicities of the edges) in a graph. @@ -72,47 +79,85 @@ public class KBestPaths { protected static class Path { // the last vertex seen in the path - private DeBruijnVertex lastVertex; + private final DeBruijnVertex lastVertex; // the list of edges comprising the path - private ArrayList edges; + private final List edges; // the scores for the path - private int totalScore = 0, lowestEdge = -1; + private final int totalScore; - public Path( final DeBruijnVertex initialVertex ) { + // the graph from which this path originated + private final DefaultDirectedGraph graph; + + // used in the bubble state machine to apply Smith-Waterman to the bubble sequence + private final double SW_MATCH = 15.0; + private final double SW_MISMATCH = -15.0; + private final double SW_GAP = -25.0; + private final double SW_GAP_EXTEND = -1.2; + + public Path( final DeBruijnVertex initialVertex, final DefaultDirectedGraph graph ) { lastVertex = initialVertex; edges = new ArrayList(0); + totalScore = 0; + this.graph = graph; } - public Path( final Path p, final DefaultDirectedGraph graph, final DeBruijnEdge edge ) { - lastVertex = graph.getEdgeTarget(edge); + public Path( final Path p, final DeBruijnEdge edge ) { + if( !p.graph.getEdgeSource(edge).equals(p.lastVertex) ) { throw new IllegalStateException("Edges added to path must be contiguous."); } + + graph = p.graph; + lastVertex = p.graph.getEdgeTarget(edge); edges = new ArrayList(p.edges); edges.add(edge); totalScore = p.totalScore + edge.getMultiplicity(); - lowestEdge = ( p.lowestEdge == -1 ) ? edge.getMultiplicity() : Math.min(p.lowestEdge, edge.getMultiplicity()); } - public boolean containsEdge( final DefaultDirectedGraph graph, final DeBruijnEdge edge ) { - final DeBruijnVertex targetVertex = graph.getEdgeTarget(edge); + /** + * Does this path contain the given edge + * @param edge the given edge to test + * @return true if the edge is found in this path + */ + public boolean containsEdge( final DeBruijnEdge edge ) { for( final DeBruijnEdge e : edges ) { - if( e.equals(graph, edge) || graph.getEdgeTarget(e).equals(targetVertex) ) { + if( e.equals(graph, edge) ) { return true; } } - + return false; } - public ArrayList getEdges() { return edges; } + public int numInPath( final DefaultDirectedGraph graph, final DeBruijnEdge edge ) { + int numInPath = 0; + for( final DeBruijnEdge e : edges ) { + if( e.equals(graph, edge) ) { + numInPath++; + } + } + + return numInPath; + } + + + public boolean containsRefEdge() { + for( final DeBruijnEdge e : edges ) { + if( e.isRef() ) { return true; } + } + return false; + } + public List getEdges() { return edges; } public int getScore() { return totalScore; } - public int getLowestEdge() { return lowestEdge; } - public DeBruijnVertex getLastVertexInPath() { return lastVertex; } - public byte[] getBases( final DefaultDirectedGraph graph ) { + /** + * The base sequence for this path. Pull the full sequence for the source of the path and then the suffix for all subsequent nodes + * @return non-null sequence of bases corresponding to this path + */ + @Ensures({"result != null"}) + public byte[] getBases() { if( edges.size() == 0 ) { return lastVertex.getSequence(); } byte[] bases = graph.getEdgeSource( edges.get(0) ).getSequence(); @@ -121,6 +166,157 @@ public class KBestPaths { } return bases; } + + /** + * Pull the added base sequence implied by visiting this node in a path + * @param graph the graph from which the vertex originated + * @param v the vertex whose sequence to grab + * @return non-null sequence of bases corresponding to this node in the graph + */ + @Ensures({"result != null"}) + public byte[] getAdditionalSequence( final DefaultDirectedGraph graph, final DeBruijnVertex v ) { + return ( edges.size()==0 || graph.getEdgeSource(edges.get(0)).equals(v) ? v.getSequence() : v.getSuffix() ); + } + + /** + * Calculate the cigar string for this path using a bubble traversal of the assembly graph and running a Smith-Waterman alignment on each bubble + */ + @Ensures("result != null") + public Cigar calculateCigar() { + + final Cigar cigar = new Cigar(); + // special case for paths that start on reference but not at the reference source node + if( edges.get(0).isRef() && !isRefSource(graph, edges.get(0)) ) { + for( final CigarElement ce : calculateCigarForCompleteBubble(graph, null, null, graph.getEdgeSource(edges.get(0))).getCigarElements() ) { + cigar.add(ce); + } + } + + // reset the bubble state machine + final BubbleStateMachine bsm = new BubbleStateMachine(cigar); + + for( final DeBruijnEdge e : edges ) { + if( e.equals(graph, edges.get(0)) ) { + advanceBubbleStateMachine( bsm, graph, graph.getEdgeSource(e), null ); + } + advanceBubbleStateMachine( bsm, graph, graph.getEdgeTarget(e), e ); + } + + // special case for paths that don't end on reference + if( bsm.inBubble ) { + for( final CigarElement ce : calculateCigarForCompleteBubble(graph, bsm.bubbleBytes, bsm.lastSeenReferenceNode, null).getCigarElements() ) { + bsm.cigar.add(ce); + } + } else if( edges.get(edges.size()-1).isRef() && !isRefSink(graph, edges.get(edges.size()-1)) ) { // special case for paths that end of the reference but haven't completed the entire reference circuit + for( final CigarElement ce : calculateCigarForCompleteBubble(graph, bsm.bubbleBytes, graph.getEdgeTarget(edges.get(edges.size()-1)), null).getCigarElements() ) { + bsm.cigar.add(ce); + } + } + + return AlignmentUtils.consolidateCigar(bsm.cigar); + } + + @Requires({"bsm != null", "graph != null", "node != null"}) + private void advanceBubbleStateMachine( final BubbleStateMachine bsm, final DefaultDirectedGraph graph, final DeBruijnVertex node, final DeBruijnEdge e ) { + if( isReferenceNode( graph, node ) ) { + if( !bsm.inBubble ) { // just add the ref bases as M's in the Cigar string, and don't do anything else + if( e !=null && !e.isRef() ) { + if( referencePathExists( graph, graph.getEdgeSource(e), node) ) { + for( final CigarElement ce : calculateCigarForCompleteBubble(graph, null, graph.getEdgeSource(e), node).getCigarElements() ) { + bsm.cigar.add(ce); + } + bsm.cigar.add( new CigarElement( getAdditionalSequence(graph, node).length, CigarOperator.M) ); + } else if ( graph.getEdgeSource(e).equals(graph.getEdgeTarget(e)) ) { // alt edge at ref node points to itself + bsm.cigar.add( new CigarElement( getAdditionalSequence(graph, node).length, CigarOperator.I) ); + } else { + bsm.inBubble = true; + bsm.bubbleBytes = null; + bsm.lastSeenReferenceNode = graph.getEdgeSource(e); + bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, getAdditionalSequence(graph, node) ); + } + } else { + bsm.cigar.add( new CigarElement( getAdditionalSequence(graph, node).length, CigarOperator.M) ); + } + } else if( bsm.lastSeenReferenceNode != null && !referencePathExists( graph, bsm.lastSeenReferenceNode, node ) ) { // add bases to the bubble string until we get back to the reference path + bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, getAdditionalSequence(graph, node) ); + } else { // close the bubble and use a local SW to determine the Cigar string + for( final CigarElement ce : calculateCigarForCompleteBubble(graph, bsm.bubbleBytes, bsm.lastSeenReferenceNode, node).getCigarElements() ) { + bsm.cigar.add(ce); + } + bsm.inBubble = false; + bsm.bubbleBytes = null; + bsm.lastSeenReferenceNode = null; + bsm.cigar.add( new CigarElement( getAdditionalSequence(graph, node).length, CigarOperator.M) ); + } + } else { // non-ref vertex + if( bsm.inBubble ) { // just keep accumulating until we get back to the reference path + bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, getAdditionalSequence(graph, node) ); + } else { // open up a bubble + bsm.inBubble = true; + bsm.bubbleBytes = null; + bsm.lastSeenReferenceNode = (e != null ? graph.getEdgeSource(e) : null ); + bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, getAdditionalSequence(graph, node) ); + } + } + } + + @Requires({"graph != null"}) + @Ensures({"result != null", "result.getReadLength() == bubbleBytes.length"}) + private Cigar calculateCigarForCompleteBubble( final DefaultDirectedGraph graph, final byte[] bubbleBytes, final DeBruijnVertex fromVertex, final DeBruijnVertex toVertex ) { + final byte[] refBytes = getReferenceBytes(this, graph, fromVertex, toVertex); + + final Cigar cigar = new Cigar(); + + // add padding to anchor ref/alt bases in the SW matrix + byte[] padding = "XXXXXX".getBytes(); + boolean goodAlignment = false; + SWPairwiseAlignment swConsensus = null; + while( !goodAlignment && padding.length < 1000 ) { + padding = ArrayUtils.addAll(padding, padding); // double the size of the padding each time + final byte[] reference = ArrayUtils.addAll( ArrayUtils.addAll(padding, refBytes), padding ); + final byte[] alternate = ArrayUtils.addAll( ArrayUtils.addAll(padding, bubbleBytes), padding ); + swConsensus = new SWPairwiseAlignment( reference, alternate, SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND ); + if( swConsensus.getAlignmentStart2wrt1() == 0 && !swConsensus.getCigar().toString().contains("S") && swConsensus.getCigar().getReferenceLength() == reference.length ) { + goodAlignment = true; + } + } + if( !goodAlignment && swConsensus != null ) { + throw new ReviewedStingException("SmithWaterman offset failure: " + (refBytes == null ? "-" : new String(refBytes)) + " against " + new String(bubbleBytes) + " = " + swConsensus.getCigar()); + } + + if( swConsensus != null ) { + final Cigar swCigar = swConsensus.getCigar(); + for( int iii = 0; iii < swCigar.numCigarElements(); iii++ ) { + // now we need to remove the padding from the cigar string + int length = swCigar.getCigarElement(iii).getLength(); + if( iii == 0 ) { length -= padding.length; } + if( iii == swCigar.numCigarElements() - 1 ) { length -= padding.length; } + if( length > 0 ) { + cigar.add( new CigarElement(length, swCigar.getCigarElement(iii).getOperator()) ); + } + } + if( (refBytes == null && cigar.getReferenceLength() != 0) || ( refBytes != null && cigar.getReferenceLength() != refBytes.length ) ) { + throw new ReviewedStingException("SmithWaterman cigar failure: " + (refBytes == null ? "-" : new String(refBytes)) + " against " + new String(bubbleBytes) + " = " + swConsensus.getCigar()); + } + } + + return cigar; + } + + // class to keep track of the bubble state machine + protected static class BubbleStateMachine { + public boolean inBubble = false; + public byte[] bubbleBytes = null; + public DeBruijnVertex lastSeenReferenceNode = null; + public Cigar cigar = null; + + public BubbleStateMachine( final Cigar initialCigar ) { + inBubble = false; + bubbleBytes = null; + lastSeenReferenceNode = null; + cigar = initialCigar; + } + } } protected static class PathComparatorTotalScore implements Comparator, Serializable { @@ -130,13 +326,6 @@ public class KBestPaths { } } - //protected static class PathComparatorLowestEdge implements Comparator, Serializable { - // @Override - // public int compare(final Path path1, final Path path2) { - // return path2.lowestEdge - path1.lowestEdge; - // } - //} - public static List getKBestPaths( final DefaultDirectedGraph graph, final int k ) { if( k > MAX_PATHS_TO_HOLD/2 ) { throw new ReviewedStingException("Asked for more paths than MAX_PATHS_TO_HOLD!"); } final ArrayList bestPaths = new ArrayList(); @@ -144,7 +333,7 @@ public class KBestPaths { // run a DFS for best paths for( final DeBruijnVertex v : graph.vertexSet() ) { if( graph.inDegreeOf(v) == 0 ) { - findBestPaths(graph, new Path(v), bestPaths); + findBestPaths(new Path(v, graph), bestPaths); } } @@ -153,14 +342,14 @@ public class KBestPaths { return bestPaths.subList(0, Math.min(k, bestPaths.size())); } - private static void findBestPaths( final DefaultDirectedGraph graph, final Path path, final List bestPaths ) { - findBestPaths(graph, path, bestPaths, new MyInt()); + private static void findBestPaths( final Path path, final List bestPaths ) { + findBestPaths(path, bestPaths, new MyInt()); } - private static void findBestPaths( final DefaultDirectedGraph graph, final Path path, final List bestPaths, MyInt n ) { + private static void findBestPaths( final Path path, final List bestPaths, final MyInt n ) { // did we hit the end of a path? - if ( allOutgoingEdgesHaveBeenVisited(graph, path) ) { + if ( allOutgoingEdgesHaveBeenVisited(path) ) { if ( bestPaths.size() >= MAX_PATHS_TO_HOLD ) { // clean out some low scoring paths Collections.sort(bestPaths, new PathComparatorTotalScore() ); @@ -172,27 +361,242 @@ public class KBestPaths { } else { // recursively run DFS final ArrayList edgeArrayList = new ArrayList(); - edgeArrayList.addAll(graph.outgoingEdgesOf(path.lastVertex)); + edgeArrayList.addAll(path.graph.outgoingEdgesOf(path.lastVertex)); Collections.sort(edgeArrayList, new DeBruijnEdge.EdgeWeightComparator()); Collections.reverse(edgeArrayList); for ( final DeBruijnEdge edge : edgeArrayList ) { // make sure the edge is not already in the path - if ( path.containsEdge(graph, edge) ) + if ( path.containsEdge(edge) ) continue; - final Path newPath = new Path(path, graph, edge); + final Path newPath = new Path(path, edge); n.val++; - findBestPaths(graph, newPath, bestPaths, n); + findBestPaths(newPath, bestPaths, n); } } } - private static boolean allOutgoingEdgesHaveBeenVisited( final DefaultDirectedGraph graph, final Path path ) { - for( final DeBruijnEdge edge : graph.outgoingEdgesOf(path.lastVertex) ) { - if( !path.containsEdge(graph, edge) ) { + private static boolean allOutgoingEdgesHaveBeenVisited( final Path path ) { + for( final DeBruijnEdge edge : path.graph.outgoingEdgesOf(path.lastVertex) ) { + if( !path.containsEdge(edge) ) { return false; } } return true; } + + /**************************************************************** + * Collection of graph functions used by KBestPaths * + ***************************************************************/ + + /** + * Test if the vertex is on a reference path in the graph. If so it is referred to as a reference node + * @param graph the graph from which the vertex originated + * @param v the vertex to test + * @return true if the vertex is on the reference path + */ + public static boolean isReferenceNode( final DefaultDirectedGraph graph, final DeBruijnVertex v ) { + for( final DeBruijnEdge e : graph.edgesOf(v) ) { + if( e.isRef() ) { return true; } + } + return false; + } + + /** + * Is this edge a source edge (the source vertex of the edge is a source node in the graph) + * @param graph the graph from which the edge originated + * @param e the edge to test + * @return true if the source vertex of the edge is a source node in the graph + */ + public static boolean isSource( final DefaultDirectedGraph graph, final DeBruijnEdge e ) { + return graph.inDegreeOf(graph.getEdgeSource(e)) == 0; + } + + /** + * Is this vertex a source vertex + * @param graph the graph from which the vertex originated + * @param v the vertex to test + * @return true if the vertex is a source vertex + */ + public static boolean isSource( final DefaultDirectedGraph graph, final DeBruijnVertex v ) { + return graph.inDegreeOf(v) == 0; + } + + /** + * Is this edge both a reference edge and a source edge for the reference path + * @param graph the graph from which the edge originated + * @param e the edge to test + * @return true if the edge is both a reference edge and a reference path source edge + */ + public static boolean isRefSource( final DefaultDirectedGraph graph, final DeBruijnEdge e ) { + for( final DeBruijnEdge edgeToTest : graph.incomingEdgesOf(graph.getEdgeSource(e)) ) { + if( edgeToTest.isRef() ) { return false; } + } + return true; + } + + /** + * Is this vertex both a reference node and a source node for the reference path + * @param graph the graph from which the vertex originated + * @param v the vertex to test + * @return true if the vertex is both a reference node and a reference path source node + */ + public static boolean isRefSource( final DefaultDirectedGraph graph, final DeBruijnVertex v ) { + for( final DeBruijnEdge edgeToTest : graph.incomingEdgesOf(v) ) { + if( edgeToTest.isRef() ) { return false; } + } + return true; + } + + /** + * Is this edge both a reference edge and a sink edge for the reference path + * @param graph the graph from which the edge originated + * @param e the edge to test + * @return true if the edge is both a reference edge and a reference path sink edge + */ + public static boolean isRefSink( final DefaultDirectedGraph graph, final DeBruijnEdge e ) { + for( final DeBruijnEdge edgeToTest : graph.outgoingEdgesOf(graph.getEdgeTarget(e)) ) { + if( edgeToTest.isRef() ) { return false; } + } + return true; + } + + /** + * Is this vertex both a reference node and a sink node for the reference path + * @param graph the graph from which the node originated + * @param v the node to test + * @return true if the vertex is both a reference node and a reference path sink node + */ + public static boolean isRefSink( final DefaultDirectedGraph graph, final DeBruijnVertex v ) { + for( final DeBruijnEdge edgeToTest : graph.outgoingEdgesOf(v) ) { + if( edgeToTest.isRef() ) { return false; } + } + return true; + } + + public static DeBruijnEdge getReferenceSourceEdge( final DefaultDirectedGraph graph ) { + for( final DeBruijnEdge e : graph.edgeSet() ) { + if( e.isRef() && isRefSource(graph, e) ) { + return e; + } + } + throw new ReviewedStingException("All reference graphs should have a source node"); + } + + public static DeBruijnVertex getReferenceSourceVertex( final DefaultDirectedGraph graph ) { + for( final DeBruijnVertex v : graph.vertexSet() ) { + if( isReferenceNode(graph, v) && isRefSource(graph, v) ) { + return v; + } + } + return null; + } + + public static DeBruijnEdge getReferenceSinkEdge( final DefaultDirectedGraph graph ) { + for( final DeBruijnEdge e : graph.edgeSet() ) { + if( e.isRef() && isRefSink(graph, e) ) { + return e; + } + } + throw new ReviewedStingException("All reference graphs should have a sink node"); + } + + public static DeBruijnVertex getReferenceSinkVertex( final DefaultDirectedGraph graph ) { + for( final DeBruijnVertex v : graph.vertexSet() ) { + if( isReferenceNode(graph, v) && isRefSink(graph, v) ) { + return v; + } + } + throw new ReviewedStingException("All reference graphs should have a sink node"); + } + + public static DeBruijnEdge getNextReferenceEdge( final DefaultDirectedGraph graph, final DeBruijnEdge e ) { + if( e == null ) { return null; } + for( final DeBruijnEdge edgeToTest : graph.outgoingEdgesOf(graph.getEdgeTarget(e)) ) { + if( edgeToTest.isRef() ) { + return edgeToTest; + } + } + return null; + } + + public static DeBruijnVertex getNextReferenceVertex( final DefaultDirectedGraph graph, final DeBruijnVertex v ) { + if( v == null ) { return null; } + for( final DeBruijnEdge edgeToTest : graph.outgoingEdgesOf(v) ) { + if( edgeToTest.isRef() ) { + return graph.getEdgeTarget(edgeToTest); + } + } + return null; + } + + public static DeBruijnEdge getPrevReferenceEdge( final DefaultDirectedGraph graph, final DeBruijnEdge e ) { + for( final DeBruijnEdge edgeToTest : graph.incomingEdgesOf(graph.getEdgeSource(e)) ) { + if( edgeToTest.isRef() ) { + return edgeToTest; + } + } + return null; + } + + public static DeBruijnVertex getPrevReferenceVertex( final DefaultDirectedGraph graph, final DeBruijnVertex v ) { + for( final DeBruijnEdge edgeToTest : graph.incomingEdgesOf(v) ) { + if( isReferenceNode(graph, graph.getEdgeSource(edgeToTest)) ) { + return graph.getEdgeSource(edgeToTest); + } + } + return null; + } + + public static boolean referencePathExists(final DefaultDirectedGraph graph, final DeBruijnEdge fromEdge, final DeBruijnEdge toEdge) { + DeBruijnEdge e = fromEdge; + if( e == null ) { + return false; + } + while( !e.equals(graph, toEdge) ) { + e = getNextReferenceEdge(graph, e); + if( e == null ) { + return false; + } + } + return true; + } + + public static boolean referencePathExists(final DefaultDirectedGraph graph, final DeBruijnVertex fromVertex, final DeBruijnVertex toVertex) { + DeBruijnVertex v = fromVertex; + if( v == null ) { + return false; + } + v = getNextReferenceVertex(graph, v); + if( v == null ) { + return false; + } + while( !v.equals(toVertex) ) { + v = getNextReferenceVertex(graph, v); + if( v == null ) { + return false; + } + } + return true; + } + + // fromVertex (exclusive) -> toVertex (exclusive) + public static byte[] getReferenceBytes( final Path path, final DefaultDirectedGraph graph, final DeBruijnVertex fromVertex, final DeBruijnVertex toVertex ) { + byte[] bytes = null; + if( fromVertex != null && toVertex != null && !referencePathExists(graph, fromVertex, toVertex) ) { + throw new ReviewedStingException("Asked for a reference path which doesn't exist. " + fromVertex + " --> " + toVertex); + } + DeBruijnVertex v = fromVertex; + if( v == null ) { + v = getReferenceSourceVertex(graph); + bytes = ArrayUtils.addAll( bytes, path.getAdditionalSequence(graph, v) ); + } + v = getNextReferenceVertex(graph, v); + while( (toVertex != null && !v.equals(toVertex)) || (toVertex == null && v != null) ) { + bytes = ArrayUtils.addAll( bytes, path.getAdditionalSequence(graph, v) ); + // advance along the reference path + v = getNextReferenceVertex(graph, v); + } + return bytes; + } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java index 8b844817d..655b3e529 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java @@ -91,11 +91,11 @@ public class LikelihoodCalculationEngine { DEBUG = debug; } - public Map computeReadLikelihoods( final ArrayList haplotypes, final HashMap> perSampleReadList ) { + public Map computeReadLikelihoods( final List haplotypes, final Map> perSampleReadList ) { final Map stratifiedReadMap = new HashMap(); int X_METRIC_LENGTH = 0; - for( final Map.Entry> sample : perSampleReadList.entrySet() ) { + for( final Map.Entry> sample : perSampleReadList.entrySet() ) { for( final GATKSAMRecord read : sample.getValue() ) { final int readLength = read.getReadLength(); if( readLength > X_METRIC_LENGTH ) { X_METRIC_LENGTH = readLength; } @@ -115,7 +115,7 @@ public class LikelihoodCalculationEngine { pairHMM.initialize(X_METRIC_LENGTH, Y_METRIC_LENGTH); // for each sample's reads - for( final Map.Entry> sampleEntry : perSampleReadList.entrySet() ) { + for( final Map.Entry> sampleEntry : perSampleReadList.entrySet() ) { //if( DEBUG ) { System.out.println("Evaluating sample " + sample + " with " + perSampleReadList.get( sample ).size() + " passing reads"); } // evaluate the likelihood of the reads given those haplotypes stratifiedReadMap.put(sampleEntry.getKey(), computeReadLikelihoods(haplotypes, sampleEntry.getValue())); @@ -123,10 +123,15 @@ public class LikelihoodCalculationEngine { return stratifiedReadMap; } - private PerReadAlleleLikelihoodMap computeReadLikelihoods( final ArrayList haplotypes, final ArrayList reads) { + private PerReadAlleleLikelihoodMap computeReadLikelihoods( final List haplotypes, final List reads) { + // first, a little set up to get copies of the Haplotypes that are Alleles (more efficient than creating them each time) + final int numHaplotypes = haplotypes.size(); + final Map alleleVersions = new HashMap(numHaplotypes); + for ( final Haplotype haplotype : haplotypes ) { + alleleVersions.put(haplotype, Allele.create(haplotype.getBases())); + } final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap(); - final int numHaplotypes = haplotypes.size(); for( final GATKSAMRecord read : reads ) { final byte[] overallGCP = new byte[read.getReadLength()]; Arrays.fill( overallGCP, constantGCP ); // Is there a way to derive empirical estimates for this from the data? @@ -138,20 +143,17 @@ public class LikelihoodCalculationEngine { readQuals[kkk] = ( readQuals[kkk] > (byte) read.getMappingQuality() ? (byte) read.getMappingQuality() : readQuals[kkk] ); // cap base quality by mapping quality //readQuals[kkk] = ( readQuals[kkk] > readInsQuals[kkk] ? readInsQuals[kkk] : readQuals[kkk] ); // cap base quality by base insertion quality, needs to be evaluated //readQuals[kkk] = ( readQuals[kkk] > readDelQuals[kkk] ? readDelQuals[kkk] : readQuals[kkk] ); // cap base quality by base deletion quality, needs to be evaluated + // TODO -- why is Q18 hard-coded here??? readQuals[kkk] = ( readQuals[kkk] < (byte) 18 ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] ); } for( int jjj = 0; jjj < numHaplotypes; jjj++ ) { final Haplotype haplotype = haplotypes.get(jjj); - // TODO -- need to test against a reference/position with non-standard bases - //if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) ) - // continue; - final int haplotypeStart = ( previousHaplotypeSeen == null ? 0 : computeFirstDifferingPosition(haplotype.getBases(), previousHaplotypeSeen.getBases()) ); previousHaplotypeSeen = haplotype; - perReadAlleleLikelihoodMap.add(read, Allele.create(haplotype.getBases()), + perReadAlleleLikelihoodMap.add(read, alleleVersions.get(haplotype), pairHMM.computeReadLikelihoodGivenHaplotypeLog10(haplotype.getBases(), read.getReadBases(), readQuals, readInsQuals, readDelQuals, overallGCP, haplotypeStart, jjj == 0)); } @@ -233,72 +235,13 @@ public class LikelihoodCalculationEngine { return likelihoodMatrix; } - /* @Requires({"haplotypes.size() > 0"}) @Ensures({"result.size() <= haplotypes.size()"}) - public ArrayList selectBestHaplotypes( final ArrayList haplotypes ) { - - // BUGBUG: This function needs a lot of work. Need to use 4-gamete test or Tajima's D to decide to break up events into separate pieces for genotyping - - final int numHaplotypes = haplotypes.size(); - final Set sampleKeySet = haplotypes.get(0).getSampleKeySet(); // BUGBUG: assume all haplotypes saw the same samples - final ArrayList bestHaplotypesIndexList = new ArrayList(); - bestHaplotypesIndexList.add(0); // always start with the reference haplotype - final double[][][] haplotypeLikelihoodMatrix = new double[sampleKeySet.size()][numHaplotypes][numHaplotypes]; - - int sampleCount = 0; - for( final String sample : sampleKeySet ) { - haplotypeLikelihoodMatrix[sampleCount++] = computeDiploidHaplotypeLikelihoods( haplotypes, sample ); - } - - int hap1 = 0; - int hap2 = 0; - int chosenSample = 0; - //double bestElement = Double.NEGATIVE_INFINITY; - final int maxChosenHaplotypes = Math.min( 15, sampleKeySet.size() * 2 + 1 ); - while( bestHaplotypesIndexList.size() < maxChosenHaplotypes ) { - double maxElement = Double.NEGATIVE_INFINITY; - for( int kkk = 0; kkk < sampleCount; kkk++ ) { - for( int iii = 0; iii < numHaplotypes; iii++ ) { - for( int jjj = 0; jjj <= iii; jjj++ ) { - if( haplotypeLikelihoodMatrix[kkk][iii][jjj] > maxElement ) { - maxElement = haplotypeLikelihoodMatrix[kkk][iii][jjj]; - hap1 = iii; - hap2 = jjj; - chosenSample = kkk; - } - } - } - } - if( maxElement == Double.NEGATIVE_INFINITY ) { break; } - - if( !bestHaplotypesIndexList.contains(hap1) ) { bestHaplotypesIndexList.add(hap1); } - if( !bestHaplotypesIndexList.contains(hap2) ) { bestHaplotypesIndexList.add(hap2); } - - for( int iii = 0; iii < numHaplotypes; iii++ ) { - for( int jjj = 0; jjj <= iii; jjj++ ) { - haplotypeLikelihoodMatrix[chosenSample][iii][jjj] = Double.NEGATIVE_INFINITY; - } - } - } - - if( DEBUG ) { System.out.println("Chose " + (bestHaplotypesIndexList.size() - 1) + " alternate haplotypes to genotype in all samples."); } - - final ArrayList bestHaplotypes = new ArrayList(); - for( final int hIndex : bestHaplotypesIndexList ) { - bestHaplotypes.add( haplotypes.get(hIndex) ); - } - return bestHaplotypes; - } - */ - - @Requires({"haplotypes.size() > 0"}) - @Ensures({"result.size() <= haplotypes.size()"}) - public ArrayList selectBestHaplotypes( final ArrayList haplotypes, final Map stratifiedReadMap, final int maxNumHaplotypesInPopulation ) { + public List selectBestHaplotypes( final List haplotypes, final Map stratifiedReadMap, final int maxNumHaplotypesInPopulation ) { final int numHaplotypes = haplotypes.size(); final Set sampleKeySet = stratifiedReadMap.keySet(); - final ArrayList bestHaplotypesIndexList = new ArrayList(); + final List bestHaplotypesIndexList = new ArrayList(); bestHaplotypesIndexList.add( findReferenceIndex(haplotypes) ); // always start with the reference haplotype final List haplotypesAsAlleles = new ArrayList(); for( final Haplotype h : haplotypes ) { haplotypesAsAlleles.add(Allele.create(h.getBases())); } @@ -330,7 +273,7 @@ public class LikelihoodCalculationEngine { if( DEBUG ) { System.out.println("Chose " + (bestHaplotypesIndexList.size() - 1) + " alternate haplotypes to genotype in all samples."); } - final ArrayList bestHaplotypes = new ArrayList(); + final List bestHaplotypes = new ArrayList(); for( final int hIndex : bestHaplotypesIndexList ) { bestHaplotypes.add( haplotypes.get(hIndex) ); } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java index b0e340dc2..3efa342b1 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java @@ -51,7 +51,7 @@ import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.variant.variantcontext.VariantContext; -import java.util.ArrayList; +import java.util.List; /** * Created by IntelliJ IDEA. @@ -67,5 +67,5 @@ public abstract class LocalAssemblyEngine { protected LocalAssemblyEngine() { } - public abstract ArrayList runLocalAssembly(ActiveRegion activeRegion, Haplotype refHaplotype, byte[] fullReferenceWithPadding, GenomeLoc refLoc, int PRUNE_FACTOR, ArrayList activeAllelesToGenotype); + public abstract List runLocalAssembly(ActiveRegion activeRegion, Haplotype refHaplotype, byte[] fullReferenceWithPadding, GenomeLoc refLoc, int PRUNE_FACTOR, List activeAllelesToGenotype); } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java index e1a94eee7..a007bfa0c 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java @@ -84,7 +84,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { private final boolean DEBUG; private final PrintStream GRAPH_WRITER; - private final ArrayList> graphs = new ArrayList>(); + private final List> graphs = new ArrayList>(); private final int MIN_KMER; private int PRUNE_FACTOR = 2; @@ -96,7 +96,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { MIN_KMER = minKmer; } - public ArrayList runLocalAssembly( final ActiveRegion activeRegion, final Haplotype refHaplotype, final byte[] fullReferenceWithPadding, final GenomeLoc refLoc, final int PRUNE_FACTOR, final ArrayList activeAllelesToGenotype ) { + public List runLocalAssembly( final ActiveRegion activeRegion, final Haplotype refHaplotype, final byte[] fullReferenceWithPadding, final GenomeLoc refLoc, final int PRUNE_FACTOR, final List activeAllelesToGenotype ) { this.PRUNE_FACTOR = PRUNE_FACTOR; // create the graphs @@ -152,10 +152,10 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { final DeBruijnVertex addedVertex = new DeBruijnVertex( ArrayUtils.addAll(incomingVertex.getSequence(), outgoingVertex.getSuffix()), outgoingVertex.kmer ); graph.addVertex(addedVertex); for( final DeBruijnEdge edge : outEdges ) { - graph.addEdge(addedVertex, graph.getEdgeTarget(edge), new DeBruijnEdge(edge.getIsRef(), edge.getMultiplicity())); + graph.addEdge(addedVertex, graph.getEdgeTarget(edge), new DeBruijnEdge(edge.isRef(), edge.getMultiplicity())); } for( final DeBruijnEdge edge : inEdges ) { - graph.addEdge(graph.getEdgeSource(edge), addedVertex, new DeBruijnEdge(edge.getIsRef(), edge.getMultiplicity())); + graph.addEdge(graph.getEdgeSource(edge), addedVertex, new DeBruijnEdge(edge.isRef(), edge.getMultiplicity())); } graph.removeVertex( incomingVertex ); @@ -168,16 +168,16 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { } protected static void pruneGraph( final DefaultDirectedGraph graph, final int pruneFactor ) { - final ArrayList edgesToRemove = new ArrayList(); + final List edgesToRemove = new ArrayList(); for( final DeBruijnEdge e : graph.edgeSet() ) { - if( e.getMultiplicity() <= pruneFactor && !e.getIsRef() ) { // remove non-reference edges with weight less than or equal to the pruning factor + if( e.getMultiplicity() <= pruneFactor && !e.isRef() ) { // remove non-reference edges with weight less than or equal to the pruning factor edgesToRemove.add(e); } } graph.removeAllEdges(edgesToRemove); // Run through the graph and clean up singular orphaned nodes - final ArrayList verticesToRemove = new ArrayList(); + final List verticesToRemove = new ArrayList(); for( final DeBruijnVertex v : graph.vertexSet() ) { if( graph.inDegreeOf(v) == 0 && graph.outDegreeOf(v) == 0 ) { verticesToRemove.add(v); @@ -187,7 +187,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { } protected static void eliminateNonRefPaths( final DefaultDirectedGraph graph ) { - final ArrayList verticesToRemove = new ArrayList(); + final List verticesToRemove = new ArrayList(); boolean done = false; while( !done ) { done = true; @@ -195,7 +195,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { if( graph.inDegreeOf(v) == 0 || graph.outDegreeOf(v) == 0 ) { boolean isRefNode = false; for( final DeBruijnEdge e : graph.edgesOf(v) ) { - if( e.getIsRef() ) { + if( e.isRef() ) { isRefNode = true; break; } @@ -299,10 +299,10 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { if( edge.getMultiplicity() > PRUNE_FACTOR ) { GRAPH_WRITER.println("\t" + graph.getEdgeSource(edge).toString() + " -> " + graph.getEdgeTarget(edge).toString() + " [" + (edge.getMultiplicity() <= PRUNE_FACTOR ? "style=dotted,color=grey" : "label=\""+ edge.getMultiplicity() +"\"") + "];"); } - if( edge.getIsRef() ) { + if( edge.isRef() ) { GRAPH_WRITER.println("\t" + graph.getEdgeSource(edge).toString() + " -> " + graph.getEdgeTarget(edge).toString() + " [color=red];"); } - if( !edge.getIsRef() && edge.getMultiplicity() <= PRUNE_FACTOR ) { System.out.println("Graph pruning warning!"); } + if( !edge.isRef() && edge.getMultiplicity() <= PRUNE_FACTOR ) { System.out.println("Graph pruning warning!"); } } for( final DeBruijnVertex v : graph.vertexSet() ) { final String label = ( graph.inDegreeOf(v) == 0 ? v.toString() : v.getSuffixString() ); @@ -313,8 +313,8 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { } @Ensures({"result.contains(refHaplotype)"}) - private ArrayList findBestPaths( final Haplotype refHaplotype, final byte[] fullReferenceWithPadding, final GenomeLoc refLoc, final ArrayList activeAllelesToGenotype, final GenomeLoc activeRegionWindow ) { - final ArrayList returnHaplotypes = new ArrayList(); + private List findBestPaths( final Haplotype refHaplotype, final byte[] fullReferenceWithPadding, final GenomeLoc refLoc, final List activeAllelesToGenotype, final GenomeLoc activeRegionWindow ) { + final List returnHaplotypes = new ArrayList(); // add the reference haplotype separately from all the others final SWPairwiseAlignment swConsensus = new SWPairwiseAlignment( fullReferenceWithPadding, refHaplotype.getBases(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND ); @@ -338,12 +338,12 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { for( final DefaultDirectedGraph graph : graphs ) { for ( final KBestPaths.Path path : KBestPaths.getKBestPaths(graph, NUM_BEST_PATHS_PER_KMER_GRAPH) ) { - final Haplotype h = new Haplotype( path.getBases( graph ), path.getScore() ); + final Haplotype h = new Haplotype( path.getBases() ); if( addHaplotype( h, fullReferenceWithPadding, returnHaplotypes, activeRegionStart, activeRegionStop, false ) ) { // for GGA mode, add the desired allele into the haplotype if it isn't already present if( !activeAllelesToGenotype.isEmpty() ) { - final HashMap eventMap = GenotypingEngine.generateVCsFromAlignment( h, h.getAlignmentStartHapwrtRef(), h.getCigar(), fullReferenceWithPadding, h.getBases(), refLoc, "HCassembly" ); // BUGBUG: need to put this function in a shared place + final Map eventMap = GenotypingEngine.generateVCsFromAlignment( h, h.getAlignmentStartHapwrtRef(), h.getCigar(), fullReferenceWithPadding, h.getBases(), refLoc, "HCassembly" ); // BUGBUG: need to put this function in a shared place for( final VariantContext compVC : activeAllelesToGenotype ) { // for GGA mode, add the desired allele into the haplotype if it isn't already present final VariantContext vcOnHaplotype = eventMap.get(compVC.getStart()); @@ -378,7 +378,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { return returnHaplotypes; } - private boolean addHaplotype( final Haplotype haplotype, final byte[] ref, final ArrayList haplotypeList, final int activeRegionStart, final int activeRegionStop, final boolean FORCE_INCLUSION_FOR_GGA_MODE ) { + private boolean addHaplotype( final Haplotype haplotype, final byte[] ref, final List haplotypeList, final int activeRegionStart, final int activeRegionStop, final boolean FORCE_INCLUSION_FOR_GGA_MODE ) { if( haplotype == null ) { return false; } final SWPairwiseAlignment swConsensus = new SWPairwiseAlignment( ref, haplotype.getBases(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND ); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 851703648..ad554a130 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -75,7 +75,7 @@ import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.File; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java index de91765b7..cbc6a1f94 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import java.util.Arrays; import java.util.LinkedList; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index 4510dfe55..80c49ff19 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -59,6 +59,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; @@ -444,7 +445,7 @@ public class PhaseByTransmission extends RodWalker, HashMa ArrayList rodNames = new ArrayList(); rodNames.add(variantCollection.variants.getName()); Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); - Set vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); + Set vcfSamples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); //Get the trios from the families passed as ped setTrios(); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java index f2ba027f8..a04789f61 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index aa42ebfa3..2722e396c 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -59,7 +59,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.HasGenomeLocation; import org.broadinstitute.sting.utils.SampleUtils; @@ -323,7 +323,7 @@ public class ReadBackedPhasing extends RodWalker { public void initialize() { // Get list of samples to include in the output Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit()); - TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); + TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); Collection samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles); Collection samplesFromExpressions = SampleUtils.matchSamplesExpressions(vcfSamples, sampleExpressions); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java deleted file mode 100644 index dc11b1032..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +++ /dev/null @@ -1,130 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; 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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.sting.gatk.walkers.varianteval.evaluators; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; - -/** - * The Broad Institute - * SOFTWARE COPYRIGHT NOTICE AGREEMENT - * This software and its documentation are copyright 2009 by the - * Broad Institute/Massachusetts Institute of Technology. All rights are reserved. - *

- * This software is supplied without any warranty or guaranteed support whatsoever. Neither - * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. - */ -@Analysis(description = "The overlap between eval and comp sites") -public class CompOverlap extends VariantEvaluator implements StandardEval { - @DataPoint(description = "number of eval variant sites", format = "%d") - public long nEvalVariants = 0; - - @DataPoint(description = "number of eval sites outside of comp sites", format = "%d") - public long novelSites = 0; - - @DataPoint(description = "number of eval sites at comp sites", format = "%d") - public long nVariantsAtComp = 0; - - @DataPoint(description = "percentage of eval sites at comp sites", format = "%.2f" ) - public double compRate = 0.0; - - @DataPoint(description = "number of concordant sites", format = "%d") - public long nConcordant = 0; - - @DataPoint(description = "the concordance rate", format = "%.2f") - public double concordantRate = 0.0; - - public int getComparisonOrder() { - return 2; // we need to see each eval track and each comp track - } - - public long nNovelSites() { return nEvalVariants - nVariantsAtComp; } - public double compRate() { return rate(nVariantsAtComp, nEvalVariants); } - public double concordanceRate() { return rate(nConcordant, nVariantsAtComp); } - - public void finalizeEvaluation() { - compRate = 100 * compRate(); - concordantRate = 100 * concordanceRate(); - novelSites = nNovelSites(); - } - - /** - * Returns true if every allele in eval is also in comp - * - * @param eval eval context - * @param comp db context - * @return true if eval and db are discordant - */ - public boolean discordantP(VariantContext eval, VariantContext comp) { - for (Allele a : eval.getAlleles()) { - if (!comp.hasAllele(a, true)) - return true; - } - - return false; - } - - public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - boolean evalIsGood = eval != null && eval.isPolymorphicInSamples(); - boolean compIsGood = comp != null && comp.isNotFiltered(); - - if (evalIsGood) nEvalVariants++; // count the number of eval events - - if (compIsGood && evalIsGood) { - nVariantsAtComp++; - - if (!discordantP(eval, comp)) { // count whether we're concordant or not with the comp value - nConcordant++; - } - } - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java deleted file mode 100644 index 2392f4901..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ /dev/null @@ -1,238 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; - -@Analysis(description = "Counts different classes of variants in the sample") -public class CountVariants extends VariantEvaluator implements StandardEval { - // the following fields are in output order: - - // basic counts on various rates found - @DataPoint(description = "Number of processed loci", format = "%d") - public long nProcessedLoci = 0; - @DataPoint(description = "Number of called loci", format = "%d") - public long nCalledLoci = 0; - @DataPoint(description = "Number of reference loci", format = "%d") - public long nRefLoci = 0; - @DataPoint(description = "Number of variant loci", format = "%d") - public long nVariantLoci = 0; - - // the following two calculations get set in the finalizeEvaluation - @DataPoint(description = "Variants per loci rate", format = "%.8f") - public double variantRate = 0; - @DataPoint(description = "Number of variants per base", format = "%.8f") - public double variantRatePerBp = 0; - - @DataPoint(description = "Number of snp loci", format = "%d") - public long nSNPs = 0; - @DataPoint(description = "Number of mnp loci", format = "%d") - public long nMNPs = 0; - @DataPoint(description = "Number of insertions", format = "%d") - public long nInsertions = 0; - @DataPoint(description = "Number of deletions", format = "%d") - public long nDeletions = 0; - @DataPoint(description = "Number of complex indels", format = "%d") - public long nComplex = 0; - @DataPoint(description = "Number of symbolic events", format = "%d") - public long nSymbolic = 0; - - @DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)", format = "%d") - public long nMixed = 0; - - @DataPoint(description = "Number of no calls loci", format = "%d") - public long nNoCalls = 0; - @DataPoint(description = "Number of het loci", format = "%d") - public long nHets = 0; - @DataPoint(description = "Number of hom ref loci", format = "%d") - public long nHomRef = 0; - @DataPoint(description = "Number of hom var loci", format = "%d") - public long nHomVar = 0; - @DataPoint(description = "Number of singletons", format = "%d") - public long nSingletons = 0; - @DataPoint(description = "Number of derived homozygotes", format = "%d") - public long nHomDerived = 0; - - // calculations that get set in the finalizeEvaluation method - @DataPoint(description = "heterozygosity per locus rate", format = "%.2e") - public double heterozygosity = 0; - @DataPoint(description = "heterozygosity per base pair", format = "%.2f") - public double heterozygosityPerBp = 0; - @DataPoint(description = "heterozygosity to homozygosity ratio", format = "%.2f") - public double hetHomRatio = 0; - @DataPoint(description = "indel rate (insertion count + deletion count)", format = "%.2e") - public double indelRate = 0; - @DataPoint(description = "indel rate per base pair", format = "%.2f") - public double indelRatePerBp = 0; - @DataPoint(description = "insertion to deletion ratio", format = "%.2f") - public double insertionDeletionRatio = 0; - - private double perLocusRate(long n) { - return rate(n, nProcessedLoci); - } - - private long perLocusRInverseRate(long n) { - return inverseRate(n, nProcessedLoci); - } - - - public int getComparisonOrder() { - return 1; // we only need to see each eval track - } - - public void update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - nCalledLoci++; - - // Note from Eric: - // This is really not correct. What we really want here is a polymorphic vs. monomorphic count (i.e. on the Genotypes). - // So in order to maintain consistency with the previous implementation (and the intention of the original author), I've - // added in a proxy check for monomorphic status here. - // Protect against case when vc only as no-calls too - can happen if we strafity by sample and sample as a single no-call. - if ( getWalker().ignoreAC0Sites() && vc1.isMonomorphicInSamples() ) { - nRefLoci++; - } else { - switch (vc1.getType()) { - case NO_VARIATION: - // shouldn't get here - break; - case SNP: - nVariantLoci++; - nSNPs++; - if (variantWasSingleton(vc1)) nSingletons++; - break; - case MNP: - nVariantLoci++; - nMNPs++; - if (variantWasSingleton(vc1)) nSingletons++; - break; - case INDEL: - nVariantLoci++; - if (vc1.isSimpleInsertion()) - nInsertions++; - else if (vc1.isSimpleDeletion()) - nDeletions++; - else - nComplex++; - break; - case MIXED: - nVariantLoci++; - nMixed++; - break; - case SYMBOLIC: - nSymbolic++; - break; - default: - throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType()); - } - } - - // these operations are ordered to ensure that we don't get the base string of the ref unless we need it - final String aaStr = vc1.hasAttribute("ANCESTRALALLELE") ? vc1.getAttributeAsString("ANCESTRALALLELE", null).toUpperCase() : null; - final String refStr = aaStr != null ? vc1.getReference().getBaseString().toUpperCase() : null; - - // ref aa alt class - // A C A der homozygote - // A C C anc homozygote - - // A A A ref homozygote - // A A C - // A C A - // A C C - - for (final Genotype g : vc1.getGenotypes()) { - final String altStr = vc1.getAlternateAlleles().size() > 0 ? vc1.getAlternateAllele(0).getBaseString().toUpperCase() : null; - - switch (g.getType()) { - case NO_CALL: - nNoCalls++; - break; - case HOM_REF: - nHomRef++; - - if ( aaStr != null && altStr != null && !refStr.equalsIgnoreCase(aaStr) ) { - nHomDerived++; - } - - break; - case HET: - nHets++; - break; - case HOM_VAR: - nHomVar++; - - if ( aaStr != null && altStr != null && !altStr.equalsIgnoreCase(aaStr) ) { - nHomDerived++; - } - - break; - case MIXED: - break; - default: - throw new ReviewedStingException("BUG: Unexpected genotype type: " + g); - } - } - } - - public void finalizeEvaluation() { - nProcessedLoci = getWalker().getnProcessedLoci(); - variantRate = perLocusRate(nVariantLoci); - variantRatePerBp = perLocusRInverseRate(nVariantLoci); - heterozygosity = perLocusRate(nHets); - heterozygosityPerBp = perLocusRInverseRate(nHets); - hetHomRatio = ratio(nHets, nHomVar); - indelRate = perLocusRate(nDeletions + nInsertions + nComplex); - indelRatePerBp = perLocusRInverseRate(nDeletions + nInsertions + nComplex); - insertionDeletionRatio = ratio(nInsertions, nDeletions); - } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java deleted file mode 100644 index bc38a63f7..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java +++ /dev/null @@ -1,273 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeType; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.*; - -/* - * Copyright (c) 2010 The Broad Institute - * - * 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. - */ - -/** - * a table of sample names to genotype concordance figures - */ -@Analysis(name = "Genotype Concordance Detailed", description = "Determine the genotype concordance between the genotypes in difference tracks, and concordance statistics") -public class GenotypeConcordance extends VariantEvaluator { - protected final static Logger logger = Logger.getLogger(GenotypeConcordance.class); - - @Molten(variableFormat = "%s", valueFormat = "%s") - public final Map map = new TreeMap(); - - // concordance counts - private final long[][] truthByCalledGenotypeCounts; - - /** - * Initialize this object - */ - public GenotypeConcordance() { - final int nGenotypeTypes = GenotypeType.values().length; - truthByCalledGenotypeCounts = new long[nGenotypeTypes][nGenotypeTypes]; - } - - @Override - public int getComparisonOrder() { - return 2; - } - - @Override - public void update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - // sanity check that we at least have either eval or validation data - if ( (validation != null && !validation.hasGenotypes()) || eval == null && !isValidVC(validation)) { - return; - } else { - final boolean validationIsValidVC = isValidVC(validation); - - // determine concordance for eval data - if (eval != null) { - for (final Genotype g : eval.getGenotypes() ) { - final String sample = g.getSampleName(); - final GenotypeType called = g.getType(); - final GenotypeType truth; - - if (!validationIsValidVC || !validation.hasGenotype(sample)) { - truth = GenotypeType.NO_CALL; - } else { - truth = validation.getGenotype(sample).getType(); - } - - incrValue(truth, called); - } - } - - // otherwise, mark no-calls for all samples - else { - final GenotypeType called = GenotypeType.NO_CALL; - - for (final Genotype g : validation.getGenotypes()) { - final GenotypeType truth = g.getType(); - incrValue(truth, called); - - // print out interesting sites - /* - if ( PRINT_INTERESTING_SITES && super.getVEWalker().gcLog != null ) { - if ( (truth == GenotypeType.HOM_VAR || truth == GenotypeType.HET) && called == GenotypeType.NO_CALL ) { - super.getVEWalker().gcLog.printf("%s FN %s%n", group, validation); - } - if ( (called == GenotypeType.HOM_VAR || called == GenotypeType.HET) && truth == GenotypeType.HOM_REF ) { - super.getVEWalker().gcLog.printf("%s FP %s%n", group, validation); - } - } - */ - } - } - } - } - - private static boolean isValidVC(final VariantContext vc) { - return (vc != null && !vc.isFiltered()); - } - - /** - * increment the specified value - * @param truth the truth type - * @param called the called type - */ - private void incrValue(final GenotypeType truth, final GenotypeType called) { - truthByCalledGenotypeCounts[truth.ordinal()][called.ordinal()]++; - } - - private long count(final GenotypeType truth, final GenotypeType called) { - return truthByCalledGenotypeCounts[truth.ordinal()][called.ordinal()]; - } - - private long count(final EnumSet truth, final GenotypeType called) { - return count(truth, EnumSet.of(called)); - } - - private long count(final GenotypeType truth, final EnumSet called) { - return count(EnumSet.of(truth), called); - } - - private long count(final EnumSet truth, final EnumSet called) { - long sum = 0; - for ( final GenotypeType truth1 : truth ) { - for ( final GenotypeType called1 : called ) { - sum += count(truth1, called1); - } - } - return sum; - } - - private long countDiag( final EnumSet d1 ) { - long sum = 0; - - for(final GenotypeType e1 : d1 ) { - sum += truthByCalledGenotypeCounts[e1.ordinal()][e1.ordinal()]; - } - - return sum; - } - - @Override - public void finalizeEvaluation() { - final EnumSet allVariantGenotypes = EnumSet.of(GenotypeType.HOM_VAR, GenotypeType.HET); - final EnumSet allCalledGenotypes = EnumSet.of(GenotypeType.HOM_VAR, GenotypeType.HET, GenotypeType.HOM_REF); - final EnumSet allGenotypes = EnumSet.allOf(GenotypeType.class); - - // exact values of the table - for ( final GenotypeType truth : GenotypeType.values() ) { - for ( final GenotypeType called : GenotypeType.values() ) { - final String field = String.format("n_true_%s_called_%s", truth, called); - final Long value = count(truth, called); - map.put(field, value.toString()); - } - } - - // counts of called genotypes - for ( final GenotypeType called : GenotypeType.values() ) { - final String field = String.format("total_called_%s", called); - final Long value = count(allGenotypes, called); - map.put(field, value.toString()); - } - - // counts of true genotypes - for ( final GenotypeType truth : GenotypeType.values() ) { - final String field = String.format("total_true_%s", truth); - final Long value = count(truth, allGenotypes); - map.put(field, value.toString()); - } - - for ( final GenotypeType genotype : GenotypeType.values() ) { - final String field = String.format("percent_%s_called_%s", genotype, genotype); - long numer = count(genotype, genotype); - long denom = count(EnumSet.of(genotype), allGenotypes); - map.put(field, Utils.formattedPercent(numer, denom)); - } - - { - // % non-ref called as non-ref - // MAD: this is known as the non-reference sensitivity (# non-ref according to comp found in eval / # non-ref in comp) - final String field = "percent_non_reference_sensitivity"; - long numer = count(allVariantGenotypes, allVariantGenotypes); - long denom = count(allVariantGenotypes, allGenotypes); - map.put(field, Utils.formattedPercent(numer, denom)); - } - - { - // overall genotype concordance of sites called in eval track - // MAD: this is the tradition genotype concordance - final String field = "percent_overall_genotype_concordance"; - long numer = countDiag(allCalledGenotypes); - long denom = count(allCalledGenotypes, allCalledGenotypes); - map.put(field, Utils.formattedPercent(numer, denom)); - } - - { - // overall genotype concordance of sites called non-ref in eval track - // MAD: this is the non-reference discrepancy rate - final String field = "percent_non_reference_discrepancy_rate"; - long homrefConcords = count(GenotypeType.HOM_REF, GenotypeType.HOM_REF); - long allNoHomRef = count(allCalledGenotypes, allCalledGenotypes) - homrefConcords; - long numer = allNoHomRef - countDiag(allVariantGenotypes); - long denom = count(allCalledGenotypes, allCalledGenotypes) - homrefConcords; - map.put(field, Utils.formattedPercent(numer, denom)); - } - } -} - diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java deleted file mode 100644 index 548b0ab42..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ /dev/null @@ -1,144 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.*; - -/** - * Simple utility for histogramming indel lengths - * - * Based on code from chartl - * - * @author Mark DePristo - * @since 3/21/12 - */ -@Analysis(description = "Indel length histogram", molten = true) -public class IndelLengthHistogram extends VariantEvaluator implements StandardEval { - private final Map counts = new HashMap(); - private final static boolean asFrequencies = true; - int nIndels = 0; - - @Molten(variableName = "Length", valueName = "Freq", variableFormat = "%d", valueFormat = "%.2f") - public TreeMap results; - - public final static int MAX_SIZE_FOR_HISTOGRAM = 10; - private final static boolean INCLUDE_LONG_EVENTS_AT_MAX_SIZE = false; - - public IndelLengthHistogram() { - initializeCounts(MAX_SIZE_FOR_HISTOGRAM); - } - - private void initializeCounts(int size) { - for ( int i = -size; i <= size; i++ ) { - if ( i != 0 ) counts.put(i, 0); - } - } - - @Override - public void finalizeEvaluation() { - if ( asFrequencies ) { - results = new TreeMap(); - for ( final int len : counts.keySet() ) { - final double value = nIndels == 0 ? 0.0 : counts.get(len) / (1.0 * nIndels); - results.put(len, value); - } - } else { - results = new TreeMap(results); - } - } - - @Override - public int getComparisonOrder() { - return 1; - } - - @Override - public void update1(final VariantContext eval, final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { - if ( eval.isIndel() && ! eval.isComplexIndel() ) { - if ( ! ( getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples() )) { - // only if we are actually polymorphic in the subsetted samples should we count the allele - for ( Allele alt : eval.getAlternateAlleles() ) { - final int alleleSize = alt.length() - eval.getReference().length(); - if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference()); - updateLengthHistogram(eval.getReference(), alt); - } - } - } - } - - /** - * Update the histogram with the implied length of the indel allele between ref and alt (alt.len - ref.len). - * - * If this size is outside of MAX_SIZE_FOR_HISTOGRAM, the size is capped to MAX_SIZE_FOR_HISTOGRAM, - * if INCLUDE_LONG_EVENTS_AT_MAX_SIZE is set. - * - * @param ref - * @param alt - */ - public void updateLengthHistogram(final Allele ref, final Allele alt) { - int len = alt.length() - ref.length(); - if ( INCLUDE_LONG_EVENTS_AT_MAX_SIZE ) { - if ( len > MAX_SIZE_FOR_HISTOGRAM ) len = MAX_SIZE_FOR_HISTOGRAM; - if ( len < -MAX_SIZE_FOR_HISTOGRAM ) len = -MAX_SIZE_FOR_HISTOGRAM; - } - - if ( Math.abs(len) > MAX_SIZE_FOR_HISTOGRAM ) - return; - - nIndels++; - counts.put(len, counts.get(len) + 1); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java deleted file mode 100644 index 0ad5c8c31..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ /dev/null @@ -1,208 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.samples.Sample; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.MendelianViolation; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Map; -import java.util.Set; - -/** - * Mendelian violation detection and counting - *

- * a violation looks like: - * Suppose dad = A/B and mom = C/D - * The child can be [A or B] / [C or D]. - * If the child doesn't match this, the site is a violation - *

- * Some examples: - *

- * mom = A/A, dad = C/C - * child can be A/C only - *

- * mom = A/C, dad = C/C - * child can be A/C or C/C - *

- * mom = A/C, dad = A/C - * child can be A/A, A/C, C/C - *

- * The easiest way to do this calculation is to: - *

- * Get alleles for mom => A/B - * Get alleles for dad => C/D - * Make allowed genotypes for child: A/C, A/D, B/C, B/D - * Check that the child is one of these. - */ -@Analysis(name = "Mendelian Violation Evaluator", description = "Mendelian Violation Evaluator") -public class MendelianViolationEvaluator extends VariantEvaluator { - - @DataPoint(description = "Number of variants found with at least one family having genotypes", format = "%d") - public long nVariants; - @DataPoint(description = "Number of variants found with no family having genotypes -- these sites do not count in the nNoCall", format = "%d") - public long nSkipped; - @DataPoint(description="Number of variants x families called (no missing genotype or lowqual)", format = "%d") - public long nFamCalled; - @DataPoint(description="Number of variants x families called (no missing genotype or lowqual) that contain at least one var allele.", format = "%d") - public long nVarFamCalled; - @DataPoint(description="Number of variants x families discarded as low quality", format = "%d") - public long nLowQual; - @DataPoint(description="Number of variants x families discarded as no call", format = "%d") - public long nNoCall; - @DataPoint(description="Number of loci with mendelian violations", format = "%d") - public long nLociViolations; - @DataPoint(description = "Number of mendelian violations found", format = "%d") - public long nViolations; - - @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_REF -> HOM_VAR", format = "%d") - public long mvRefRef_Var; - @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_REF -> HET", format = "%d") - public long mvRefRef_Het; - @DataPoint(description="Number of mendelian violations of the type HOM_REF/HET -> HOM_VAR", format = "%d") - public long mvRefHet_Var; - @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_VAR -> HOM_VAR", format = "%d") - public long mvRefVar_Var; - @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_VAR -> HOM_REF", format = "%d") - public long mvRefVar_Ref; - @DataPoint(description="Number of mendelian violations of the type HOM_VAR/HET -> HOM_REF", format = "%d") - public long mvVarHet_Ref; - @DataPoint(description="Number of mendelian violations of the type HOM_VAR/HOM_VAR -> HOM_REF", format = "%d") - public long mvVarVar_Ref; - @DataPoint(description="Number of mendelian violations of the type HOM_VAR/HOM_VAR -> HET", format = "%d") - public long mvVarVar_Het; - - @DataPoint(description="Number of HomRef/HomRef/HomRef trios", format = "%d") - public long HomRefHomRef_HomRef; - @DataPoint(description="Number of Het/Het/Het trios", format = "%d") - public long HetHet_Het; - @DataPoint(description="Number of Het/Het/HomRef trios", format = "%d") - public long HetHet_HomRef; - @DataPoint(description="Number of Het/Het/HomVar trios", format = "%d") - public long HetHet_HomVar; - @DataPoint(description="Number of HomVar/HomVar/HomVar trios", format = "%d") - public long HomVarHomVar_HomVar; - @DataPoint(description="Number of HomRef/HomVar/Het trios", format = "%d") - public long HomRefHomVAR_Het; - @DataPoint(description="Number of ref alleles inherited from het/het parents", format = "%d") - public long HetHet_inheritedRef; - @DataPoint(description="Number of var alleles inherited from het/het parents", format = "%d") - public long HetHet_inheritedVar; - @DataPoint(description="Number of ref alleles inherited from homRef/het parents", format = "%d") - public long HomRefHet_inheritedRef; - @DataPoint(description="Number of var alleles inherited from homRef/het parents", format = "%d") - public long HomRefHet_inheritedVar; - @DataPoint(description="Number of ref alleles inherited from homVar/het parents", format = "%d") - public long HomVarHet_inheritedRef; - @DataPoint(description="Number of var alleles inherited from homVar/het parents", format = "%d") - public long HomVarHet_inheritedVar; - - MendelianViolation mv; - Map> families; - - public void initialize(VariantEval walker) { - super.initialize(walker); - mv = new MendelianViolation(walker.getMendelianViolationQualThreshold(),false); - families = walker.getSampleDB().getFamilies(); - } - - public String getName() { - return "mendelian_violations"; - } - - public int getComparisonOrder() { - return 1; // we only need to see each eval track - } - - public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if (vc.isBiallelic() && vc.hasGenotypes()) { // todo -- currently limited to biallelic loci - - if(mv.countViolations(families,vc)>0){ - nLociViolations++; - nViolations += mv.getViolationsCount(); - mvRefRef_Var += mv.getParentsRefRefChildVar(); - mvRefRef_Het += mv.getParentsRefRefChildHet(); - mvRefHet_Var += mv.getParentsRefHetChildVar(); - mvRefVar_Var += mv.getParentsRefVarChildVar(); - mvRefVar_Ref += mv.getParentsRefVarChildRef(); - mvVarHet_Ref += mv.getParentsVarHetChildRef(); - mvVarVar_Ref += mv.getParentsVarVarChildRef(); - mvVarVar_Het += mv.getParentsVarVarChildHet(); - - } - HomRefHomRef_HomRef += mv.getRefRefRef(); - HetHet_Het += mv.getHetHetHet(); - HetHet_HomRef += mv.getHetHetHomRef(); - HetHet_HomVar += mv.getHetHetHomVar(); - HomVarHomVar_HomVar += mv.getVarVarVar(); - HomRefHomVAR_Het += mv.getRefVarHet(); - HetHet_inheritedRef += mv.getParentsHetHetInheritedRef(); - HetHet_inheritedVar += mv.getParentsHetHetInheritedVar(); - HomRefHet_inheritedRef += mv.getParentsRefHetInheritedRef(); - HomRefHet_inheritedVar += mv.getParentsRefHetInheritedVar(); - HomVarHet_inheritedRef += mv.getParentsVarHetInheritedRef(); - HomVarHet_inheritedVar += mv.getParentsVarHetInheritedVar(); - - if(mv.getFamilyCalledCount()>0){ - nVariants++; - nFamCalled += mv.getFamilyCalledCount(); - nLowQual += mv.getFamilyLowQualsCount(); - nNoCall += mv.getFamilyNoCallCount(); - nVarFamCalled += mv.getVarFamilyCalledCount(); - } - else{ - nSkipped++; - } - } - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java deleted file mode 100644 index e839d73b8..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java +++ /dev/null @@ -1,185 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; - -@Analysis(description = "Evaluation summary for multi-allelic variants") -public class MultiallelicSummary extends VariantEvaluator implements StandardEval { - final protected static Logger logger = Logger.getLogger(MultiallelicSummary.class); - - public enum Type { - SNP, INDEL - } - - // basic counts on various rates found - @DataPoint(description = "Number of processed loci", format = "%d") - public long nProcessedLoci = 0; - - @DataPoint(description = "Number of SNPs", format = "%d") - public int nSNPs = 0; - @DataPoint(description = "Number of multi-allelic SNPs", format = "%d") - public int nMultiSNPs = 0; - @DataPoint(description = "% processed sites that are multi-allelic SNPs", format = "%.5f") - public double processedMultiSnpRatio = 0; - @DataPoint(description = "% SNP sites that are multi-allelic", format = "%.3f") - public double variantMultiSnpRatio = 0; - - @DataPoint(description = "Number of Indels", format = "%d") - public int nIndels = 0; - @DataPoint(description = "Number of multi-allelic Indels", format = "%d") - public int nMultiIndels = 0; - @DataPoint(description = "% processed sites that are multi-allelic Indels", format = "%.5f") - public double processedMultiIndelRatio = 0; - @DataPoint(description = "% Indel sites that are multi-allelic", format = "%.3f") - public double variantMultiIndelRatio = 0; - - @DataPoint(description = "Number of Transitions", format = "%d") - public int nTi = 0; - @DataPoint(description = "Number of Transversions", format = "%d") - public int nTv = 0; - @DataPoint(description = "Overall TiTv ratio", format = "%.2f") - public double TiTvRatio = 0; - - @DataPoint(description = "Multi-allelic SNPs partially known", format = "%d") - public int knownSNPsPartial = 0; - @DataPoint(description = "Multi-allelic SNPs completely known", format = "%d") - public int knownSNPsComplete = 0; - @DataPoint(description = "Multi-allelic SNP Novelty Rate") - public String SNPNoveltyRate = "NA"; - - //TODO -- implement me - //@DataPoint(description = "Multi-allelic Indels partially known", format = "%d") - public int knownIndelsPartial = 0; - //@DataPoint(description = "Multi-allelic Indels completely known", format = "%d") - public int knownIndelsComplete = 0; - //@DataPoint(description = "Multi-allelic Indel Novelty Rate") - public String indelNoveltyRate = "NA"; - - - @Override public int getComparisonOrder() { return 2; } - - public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( eval == null || (getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples()) ) - return; - - // update counts - switch ( eval.getType() ) { - case SNP: - nSNPs++; - if ( !eval.isBiallelic() ) { - nMultiSNPs++; - calculatePairwiseTiTv(eval); - calculateSNPPairwiseNovelty(eval, comp); - } - break; - case INDEL: - nIndels++; - if ( !eval.isBiallelic() ) { - nMultiIndels++; - calculateIndelPairwiseNovelty(eval, comp); - } - break; - default: - //throw new UserException.BadInput("Unexpected variant context type: " + eval); - break; - } - - return; - } - - private void calculatePairwiseTiTv(VariantContext vc) { - for ( Allele alt : vc.getAlternateAlleles() ) { - if ( VariantContextUtils.isTransition(vc.getReference(), alt) ) - nTi++; - else - nTv++; - } - } - - private void calculateSNPPairwiseNovelty(VariantContext eval, VariantContext comp) { - if ( comp == null ) - return; - - int knownAlleles = 0; - for ( Allele alt : eval.getAlternateAlleles() ) { - if ( comp.getAlternateAlleles().contains(alt) ) - knownAlleles++; - } - - if ( knownAlleles == eval.getAlternateAlleles().size() ) - knownSNPsComplete++; - else if ( knownAlleles > 0 ) - knownSNPsPartial++; - } - - private void calculateIndelPairwiseNovelty(VariantContext eval, VariantContext comp) { - // TODO -- implement me - } - - public void finalizeEvaluation() { - nProcessedLoci = getWalker().getnProcessedLoci(); - processedMultiSnpRatio = (double)nMultiSNPs / (double)nProcessedLoci; - variantMultiSnpRatio = (double)nMultiSNPs / (double)nSNPs; - processedMultiIndelRatio = (double)nMultiIndels / (double)nProcessedLoci; - variantMultiIndelRatio = (double)nMultiIndels / (double)nIndels; - - TiTvRatio = (double)nTi / (double)nTv; - - SNPNoveltyRate = Utils.formattedNoveltyRate(knownSNPsPartial + knownSNPsComplete, nMultiSNPs); - indelNoveltyRate = Utils.formattedNoveltyRate(knownIndelsPartial + knownIndelsComplete, nMultiSNPs); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java deleted file mode 100644 index 55712772e..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java +++ /dev/null @@ -1,49 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -public interface StandardEval {} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java deleted file mode 100644 index 54cccb52c..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ /dev/null @@ -1,164 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.concurrent.ConcurrentHashMap; -import java.util.concurrent.ConcurrentMap; - -@Analysis(description = "Computes different estimates of theta based on variant sites and genotypes") -public class ThetaVariantEvaluator extends VariantEvaluator { - @DataPoint(description = "Average heterozygosity at variant sites; note that missing genotypes are ignored when computing this value", format = "%.8f") - public double avgHet = 0.0; - @DataPoint(description = "Average pairwise differences at aligned sequences; averaged over both number of sequeneces and number of variant sites; note that missing genotypes are ignored when computing this value", format = "%.8f") - public double avgAvgDiffs = 0.0; - @DataPoint(description = "Sum of heterozygosity over all variant sites; divide this by total target to get estimate of per base theta", format = "%.8f") - public double totalHet = 0.0; - @DataPoint(description = "Sum of pairwise diffs over all variant sites; divide this by total target to get estimate of per base theta", format = "%.8f") - public double totalAvgDiffs = 0.0; - @DataPoint(description = "Theta for entire region estimated based on number of segregating sites; divide ths by total target to get estimate of per base theta", format = "%.8f") - public double thetaRegionNumSites = 0.0; - - //helper variables - double numSites = 0; - - public int getComparisonOrder() { - return 1; - } - - public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if (vc == null || !vc.isSNP() || (getWalker().ignoreAC0Sites() && vc.isMonomorphicInSamples())) { - return; - } - - //this maps allele to a count - ConcurrentMap alleleCounts = new ConcurrentHashMap(); - - int numHetsHere = 0; - int numGenosHere = 0; - int numIndsHere = 0; - - for (final Genotype genotype : vc.getGenotypes()) { - numIndsHere++; - if (!genotype.isNoCall()) { - //increment stats for heterozygosity - if (genotype.isHet()) { - numHetsHere++; - } - - numGenosHere++; - //increment stats for pairwise mismatches - - for (Allele allele : genotype.getAlleles()) { - if (allele.isCalled()) { - String alleleString = allele.toString(); - alleleCounts.putIfAbsent(alleleString, 0); - alleleCounts.put(alleleString, alleleCounts.get(alleleString) + 1); - } - } - } - } - if (numGenosHere > 0) { - //only if have one called genotype at least - this.numSites++; - - this.totalHet += numHetsHere / (double)numGenosHere; - - //compute based on num sites - float harmonicFactor = 0; - for (int i = 1; i <= numIndsHere; i++) { - harmonicFactor += 1.0 / i; - } - this.thetaRegionNumSites += 1.0 / harmonicFactor; - - //now compute pairwise mismatches - float numPairwise = 0; - int numDiffs = 0; - for (String allele1 : alleleCounts.keySet()) { - int allele1Count = alleleCounts.get(allele1); - - for (String allele2 : alleleCounts.keySet()) { - if (allele1.compareTo(allele2) < 0) { - continue; - } - if (allele1 .compareTo(allele2) == 0) { - numPairwise += allele1Count * (allele1Count - 1) * .5; - - } - else { - int allele2Count = alleleCounts.get(allele2); - numPairwise += allele1Count * allele2Count; - numDiffs += allele1Count * allele2Count; - } - } - } - - if (numPairwise > 0) { - this.totalAvgDiffs += numDiffs / numPairwise; - } - } - } - - @Override - public void finalizeEvaluation() { - - if (this.numSites > 0) { - - this.avgHet = this.totalHet / this.numSites; - this.avgAvgDiffs = this.totalAvgDiffs / this.numSites; - - } - } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java deleted file mode 100644 index 129b67e81..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.variant.utils.BaseUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; - -@Analysis(description = "Ti/Tv Variant Evaluator") -public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval { - @DataPoint(description = "number of transition loci", format = "%d") - public long nTi = 0; - @DataPoint(description = "number of transversion loci", format = "%d") - public long nTv = 0; - @DataPoint(description = "the transition to transversion ratio", format = "%.2f") - public double tiTvRatio = 0.0; - @DataPoint(description = "number of comp transition sites", format = "%d") - public long nTiInComp = 0; - @DataPoint(description = "number of comp transversion sites", format = "%d") - public long nTvInComp = 0; - @DataPoint(description = "the transition to transversion ratio for comp sites", format = "%.2f") - public double TiTvRatioStandard = 0.0; - @DataPoint(description = "number of derived transition loci", format = "%d") - public long nTiDerived = 0; - @DataPoint(description = "number of derived transversion loci", format = "%d") - public long nTvDerived = 0; - @DataPoint(description = "the derived transition to transversion ratio", format = "%.2f") - public double tiTvDerivedRatio = 0.0; - - public int getComparisonOrder() { - return 2; // we only need to see each eval track - } - - public void updateTiTv(VariantContext vc, boolean updateStandard) { - if (vc != null && vc.isSNP() && vc.isBiallelic() && vc.isPolymorphicInSamples()) { - if (VariantContextUtils.isTransition(vc)) { - if (updateStandard) nTiInComp++; - else nTi++; - } else { - if (updateStandard) nTvInComp++; - else nTv++; - } - - if (vc.hasAttribute("ANCESTRALALLELE")) { - final String aaStr = vc.getAttributeAsString("ANCESTRALALLELE", "null").toUpperCase(); - if ( ! aaStr.equals(".") ) { - switch ( BaseUtils.SNPSubstitutionType(aaStr.getBytes()[0], vc.getAlternateAllele(0).getBases()[0] ) ) { - case TRANSITION: nTiDerived++; break; - case TRANSVERSION: nTvDerived++; break; - default: break; - } - } - } - } - } - - @Override - public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if (eval != null) - updateTiTv(eval, false); - if (comp != null) - updateTiTv(comp, true); - } - - @Override - public void finalizeEvaluation() { - // the ti/tv ratio needs to be set (it's not calculated per-variant). - this.tiTvRatio = rate(nTi,nTv); - this.tiTvDerivedRatio = rate(nTiDerived,nTvDerived); - this.TiTvRatioStandard = rate(nTiInComp, nTvInComp); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java deleted file mode 100644 index 92a1c6c43..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ /dev/null @@ -1,204 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Collection; -import java.util.Set; - -/** - * The Broad Institute - * SOFTWARE COPYRIGHT NOTICE AGREEMENT - * This software and its documentation are copyright 2009 by the - * Broad Institute/Massachusetts Institute of Technology. All rights are reserved. - *

- * This software is supplied without any warranty or guaranteed support whatsoever. Neither - * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. - */ -@Analysis(description = "Assess site accuracy and sensitivity of callset against follow-up validation assay") -public class ValidationReport extends VariantEvaluator implements StandardEval { - // todo -- note this isn't strictly allele away. It's really focused on sites. A/T call at a validated A/G site is currently counted as a TP - @DataPoint(description = "nComp", format = "%d") public int nComp = 0; - @DataPoint(description = "TP", format = "%d") public int TP = 0; - @DataPoint(description = "FP", format = "%d") public int FP = 0; - @DataPoint(description = "FN", format = "%d") public int FN = 0; - @DataPoint(description = "TN", format = "%d") public int TN = 0; - - @DataPoint(description = "Sensitivity", format = "%.2f") public double sensitivity = 0; - @DataPoint(description = "Specificity", format = "%.2f") public double specificity = 0; - @DataPoint(description = "PPV", format = "%.2f") public double PPV = 0; - @DataPoint(description = "FDR", format = "%.2f") public double FDR = 0; - - @DataPoint(description = "CompMonoEvalNoCall", format = "%d") public int CompMonoEvalNoCall = 0; - @DataPoint(description = "CompMonoEvalFiltered", format = "%d") public int CompMonoEvalFiltered = 0; - @DataPoint(description = "CompMonoEvalMono", format = "%d") public int CompMonoEvalMono = 0; - @DataPoint(description = "CompMonoEvalPoly", format = "%d") public int CompMonoEvalPoly = 0; - - @DataPoint(description = "CompPolyEvalNoCall", format = "%d") public int CompPolyEvalNoCall = 0; - @DataPoint(description = "CompPolyEvalFiltered", format = "%d") public int CompPolyEvalFiltered = 0; - @DataPoint(description = "CompPolyEvalMono", format = "%d") public int CompPolyEvalMono = 0; - @DataPoint(description = "CompPolyEvalPoly", format = "%d") public int CompPolyEvalPoly = 0; - - @DataPoint(description = "CompFiltered", format = "%d") public int CompFiltered = 0; - @DataPoint(description = "Eval and comp have different alleles", format = "%d") public int nDifferentAlleleSites = 0; - - private static final boolean TREAT_ALL_SITES_IN_EVAL_VCF_AS_CALLED = true; - private static final boolean REQUIRE_IDENTICAL_ALLELES = false; - - private enum SiteStatus { NO_CALL, FILTERED, MONO, POLY } - - // Counts of ValidationSiteStatus x CallSiteStatus - final int[][] counts = new int[SiteStatus.values().length][SiteStatus.values().length]; - - @Override public int getComparisonOrder() { return 2; } - - @Override - public void finalizeEvaluation() { - for ( SiteStatus x : SiteStatus.values() ) - CompFiltered += getCounts(SiteStatus.FILTERED, x); - - CompMonoEvalNoCall = getCounts(SiteStatus.MONO, SiteStatus.NO_CALL); - CompMonoEvalFiltered = getCounts(SiteStatus.MONO, SiteStatus.FILTERED); - CompMonoEvalMono = getCounts(SiteStatus.MONO, SiteStatus.MONO); - CompMonoEvalPoly = getCounts(SiteStatus.MONO, SiteStatus.POLY); - - CompPolyEvalNoCall = getCounts(SiteStatus.POLY, SiteStatus.NO_CALL); - CompPolyEvalFiltered = getCounts(SiteStatus.POLY, SiteStatus.FILTERED); - CompPolyEvalMono = getCounts(SiteStatus.POLY, SiteStatus.MONO); - CompPolyEvalPoly = getCounts(SiteStatus.POLY, SiteStatus.POLY); - - TP = CompPolyEvalPoly; - FN = CompPolyEvalNoCall + CompPolyEvalFiltered + CompPolyEvalMono; - FP = CompMonoEvalPoly; - TN = CompMonoEvalNoCall + CompMonoEvalFiltered + CompMonoEvalMono; - - for ( SiteStatus x : SiteStatus.values() ) - for ( SiteStatus y : SiteStatus.values() ) - nComp += getCounts(x, y); - - if ( nComp != TP + FN + FP + TN + CompFiltered ) - throw new ReviewedStingException("BUG: nComp != TP + FN + FP + TN + CompFiltered!"); - - sensitivity = (100.0 * TP) / (TP + FN); - specificity = (TN+FP > 0) ? (100.0 * TN) / (TN + FP) : 100.0; - PPV = (100.0 * TP) / (TP + FP); - FDR = (100.0 * FP) / (FP + TP); - } - - private int getCounts(SiteStatus comp, SiteStatus eval) { - return counts[comp.ordinal()][eval.ordinal()]; - } - - @Override - public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( comp != null ) { // we only need to consider sites in comp - if ( REQUIRE_IDENTICAL_ALLELES && (eval != null && haveDifferentAltAlleles(eval, comp))) - nDifferentAlleleSites++; - else { - SiteStatus evalStatus = calcSiteStatus(eval); - final Set evalSamples = getWalker().getSampleNamesForEvaluation(); - if ( comp.hasGenotypes() && ! evalSamples.isEmpty() && comp.hasGenotypes(evalSamples) ) - // if we have genotypes in both eval and comp, subset comp down just the samples in eval - comp = comp.subContextFromSamples(evalSamples, false); - SiteStatus compStatus = calcSiteStatus(comp); - counts[compStatus.ordinal()][evalStatus.ordinal()]++; - } - } - } - - // - // helper routines - // - private SiteStatus calcSiteStatus(VariantContext vc) { - if ( vc == null ) return SiteStatus.NO_CALL; - if ( vc.isFiltered() ) return SiteStatus.FILTERED; - if ( vc.isMonomorphicInSamples() ) return SiteStatus.MONO; - if ( vc.hasGenotypes() ) return SiteStatus.POLY; // must be polymorphic if isMonomorphicInSamples was false and there are genotypes - - if ( vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) { - int ac = 0; - if ( vc.getNAlleles() > 2 ) { - return SiteStatus.POLY; - } - else - ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0); - return ac > 0 ? SiteStatus.POLY : SiteStatus.MONO; - } else { - return TREAT_ALL_SITES_IN_EVAL_VCF_AS_CALLED ? SiteStatus.POLY : SiteStatus.NO_CALL; // we can't figure out what to do - } - } - - - - private boolean haveDifferentAltAlleles(VariantContext eval, VariantContext comp) { - Collection evalAlts = eval.getAlternateAlleles(); - Collection compAlts = comp.getAlternateAlleles(); - if ( evalAlts.size() != compAlts.size() ) { - return true; - } else { - // same size => every alt from eval must be in comp - for ( Allele a : evalAlts ) { - if ( ! compAlts.contains(a) ) { -// System.out.printf("Different alleles: %s:%d eval=%s comp=%s\n\t\teval=%s\n\t\tcomp=%s%n", -// eval.getChr(), eval.getStart(), eval.getAlleles(), comp.getAlleles(), eval, comp); - return true; - } - } - - return false; - } - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java deleted file mode 100644 index d3660cf32..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java +++ /dev/null @@ -1,154 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.evaluators; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.VariantContext; - -public abstract class VariantEvaluator implements Comparable { - private VariantEval walker; - private final String simpleName; - - protected VariantEvaluator() { - this.simpleName = getClass().getSimpleName(); - } - - public void initialize(VariantEval walker) { - this.walker = walker; - } - - public VariantEval getWalker() { - return walker; - } - - // Should return the number of VariantContexts expected as inputs to update. Can be 1 or 2 - public abstract int getComparisonOrder(); - - // called at all sites, regardless of eval context itself; useful for counting processed bases - // No longer available. The processed bp is kept in VEW itself for performance reasons - // public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - - public void update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - } - - public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - } - - public void finalizeEvaluation() {} - - protected double rate(long n, long d) { - return n / (1.0 * Math.max(d, 1)); - } - - protected long inverseRate(long n, long d) { - return n == 0 ? 0 : d / Math.max(n, 1); - } - - protected double ratio(long num, long denom) { - return ((double)num) / (Math.max(denom, 1)); - } - - /** - * Returns true if the variant in vc was a singleton in the original input evaluation - * set, regardless of variant context subsetting that has occurred. - * @param eval the VariantContext being assessed for this previous status as a singleton - * @return true if eval was originally a singleton site - */ - protected static boolean variantWasSingleton(final VariantContext eval) { - return eval.getAttributeAsBoolean(VariantEval.IS_SINGLETON_KEY, false); - } - - public final String getSimpleName() { - return simpleName; - } - - @Override - public int compareTo(final VariantEvaluator variantEvaluator) { - return getSimpleName().compareTo(variantEvaluator.getSimpleName()); - } - - /** - * Evaluation modules that override this function to indicate that they support - * combining the results of two independent collections of eval data into - * a single meaningful result. The purpose of this interface is to - * allow us to cut up the input data into many independent stratifications, and then - * at the end of the eval run decide which stratifications to combine. This is - * important in the case of AC, where you may have thousands of distinct AC - * values that chop up the number of variants to too small a number of variants, - * and you'd like to combine the AC values into ranges containing some percent - * of the data. - * - * For example, suppose you have an eval that - * counts variants in a variable nVariants. If you want to be able to combine - * multiple evaluations of this type, overload the combine function - * with a function that sets this.nVariants += other.nVariants. - * - * Add in the appropriate fields of the VariantEvaluator T - * (of the same type as this object) to the values of this object. - * - * The values in this and other are implicitly independent, so that - * the values can be added together. - * - * @param other a VariantEvaluator of the same type of this object - */ - public void combine(final VariantEvaluator other) { - throw new ReviewedStingException(getSimpleName() + " doesn't support combining results, sorry"); - } - - /** - * Must be overloaded to return true for evaluation modules that support the combine operation - * - * @return - */ - public boolean supportsCombine() { - return false; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java deleted file mode 100644 index fdd4b1ef4..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +++ /dev/null @@ -1,135 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; -import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.*; - -/** - * Stratifies the eval RODs by the allele count of the alternate allele - * - * Looks first at the MLEAC value in the INFO field, and uses that value if present. - * If not present, it then looks for the AC value in the INFO field. If both are absent, - * it computes the AC from the genotypes themselves. If no AC can be computed, 0 is used. - */ -public class AlleleCount extends VariantStratifier { - int nchrom; - - @Override - public void initialize() { - // we can only work with a single eval VCF, and it must have genotypes - if ( getVariantEvalWalker().getEvals().size() != 1 && !getVariantEvalWalker().mergeEvals ) - throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification only works with a single eval vcf"); - - // There are ploidy x n sample chromosomes - // TODO -- generalize to handle multiple ploidy - nchrom = getVariantEvalWalker().getNumberOfSamplesForEvaluation() * getVariantEvalWalker().getSamplePloidy(); - if ( nchrom < 2 ) - throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample"); - - // create an array containing each of the allele counts - for( int ac = 0; ac <= nchrom; ac++ ) { - states.add(ac); - } - - getVariantEvalWalker().getLogger().info("AlleleCount using " + nchrom + " chromosomes"); - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - if (eval != null) { - int AC = 0; // by default, the site is considered monomorphic - - try { - if ( eval.isBiallelic() ) { - if ( eval.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) ) { - // the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1) - AC = Math.min(eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0), nchrom); - } else if ( eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) { - AC = eval.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0); - } - } - } catch ( ClassCastException e ) { - // protect ourselves from bad inputs - // TODO -- fully decode VC - } - - if ( AC == 0 && eval.isVariant() ) { - // fall back to the direct calculation - for (Allele allele : eval.getAlternateAlleles()) - AC = Math.max(AC, eval.getCalledChrCount(allele)); - } - - // make sure that the AC isn't invalid - if ( AC > nchrom ) - throw new UserException.MalformedVCF(String.format("The AC value (%d) at position %s:%d " + - "is larger than the number of chromosomes over all samples (%d)", AC, - eval.getChr(), eval.getStart(), nchrom)); - - return Collections.singletonList((Object) AC); - } else { - return Collections.emptyList(); - } - } - - @Override - public Set> getIncompatibleEvaluators() { - return new HashSet>(Arrays.asList(VariantSummary.class)); - } - - @Override - public String getFormat() { - return "%d"; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java deleted file mode 100644 index 1d8b05fce..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java +++ /dev/null @@ -1,82 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Collections; -import java.util.List; - -/** - * Stratifies the eval RODs by the allele frequency of the alternate allele - * - * Uses a constant 0.005 frequency grid, and projects the AF INFO field value. Requires - * that AF be present in every ROD, otherwise this stratification throws an exception - */ -public class AlleleFrequency extends VariantStratifier { - @Override - public void initialize() { - for( double a = 0.000; a <= 1.005; a += 0.005 ) { - states.add(String.format("%.3f", a)); - } - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - if (eval != null) { - try { - return Collections.singletonList((Object)String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF", 0.0) / 5.0, 3)))); - } catch (Exception e) { - return Collections.emptyList(); - } - } - - return Collections.emptyList(); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java deleted file mode 100644 index f0cb84930..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java +++ /dev/null @@ -1,75 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.Collections; -import java.util.List; - -/** - * Stratifies the evaluation by each contig in the reference sequence - */ -public class Contig extends VariantStratifier { - @Override - public void initialize() { - states.addAll(getVariantEvalWalker().getContigNames()); - states.add("all"); - } - - @Override - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - if (eval != null) { - return Arrays.asList((Object)"all", eval.getChr()); - } else { - return Collections.emptyList(); - } - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java deleted file mode 100644 index e3457cad1..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java +++ /dev/null @@ -1,97 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.ArrayList; -import java.util.List; - -/** - * CpG is a stratification module for VariantEval that divides the input data by within/not within a CpG site - * - *

- * It is a three-state stratification: - *

    - *
  • The locus is a CpG site ("CpG") - *
  • The locus is not a CpG site ("non_CpG") - *
  • The locus is either a CpG or not a CpG site ("all") - *
- * A CpG site is defined as a site where the reference base at a locus is a C and the adjacent reference base in the 3' direction is a G. - */ -public class CpG extends VariantStratifier { - @Override - public void initialize() { - states.add("all"); - states.add("CpG"); - states.add("non_CpG"); - } - - @Override - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - boolean isCpG = false; - if (ref != null && ref.getBases() != null) { - String fwRefBases = new String(ref.getBases()); - - //String leftFlank = fwRefBases.substring((fwRefBases.length()/2) - 1, (fwRefBases.length()/2) + 1); - String rightFlank = fwRefBases.substring((fwRefBases.length()/2), (fwRefBases.length()/2) + 2); - - //if (leftFlank.equalsIgnoreCase("CG") || leftFlank.equalsIgnoreCase("GC") || rightFlank.equalsIgnoreCase("CG") || rightFlank.equalsIgnoreCase("GC")) { - if (rightFlank.equalsIgnoreCase("CG")) { - isCpG = true; - } - } - - ArrayList relevantStates = new ArrayList(2); - relevantStates.add("all"); - relevantStates.add(isCpG ? "CpG" : "non_CpG"); - - return relevantStates; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java deleted file mode 100644 index 02c306c43..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java +++ /dev/null @@ -1,179 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.HashSet; -import java.util.List; - -/** - * Experimental stratification by the degeneracy of an amino acid, according to VCF annotation. Not safe - */ -public class Degeneracy extends VariantStratifier { - private HashMap> degeneracies; - - @Override - public void initialize() { - states.add("1-fold"); - states.add("2-fold"); - states.add("3-fold"); - states.add("4-fold"); - states.add("6-fold"); - states.add("all"); - - HashMap aminoAcids = new HashMap(); - aminoAcids.put("Ile", new String[]{"ATT", "ATC", "ATA"}); - aminoAcids.put("Leu", new String[]{"CTT", "CTC", "CTA", "CTG", "TTA", "TTG"}); - aminoAcids.put("Val", new String[]{"GTT", "GTC", "GTA", "GTG"}); - aminoAcids.put("Phe", new String[]{"TTT", "TTC"}); - aminoAcids.put("Met", new String[]{"ATG"}); - aminoAcids.put("Cys", new String[]{"TGT", "TGC"}); - aminoAcids.put("Ala", new String[]{"GCT", "GCC", "GCA", "GCG"}); - aminoAcids.put("Gly", new String[]{"GGT", "GGC", "GGA", "GGG"}); - aminoAcids.put("Pro", new String[]{"CCT", "CCC", "CCA", "CCG"}); - aminoAcids.put("Thr", new String[]{"ACT", "ACC", "ACA", "ACG"}); - aminoAcids.put("Ser", new String[]{"TCT", "TCC", "TCA", "TCG", "AGT", "AGC"}); - aminoAcids.put("Tyr", new String[]{"TAT", "TAC"}); - aminoAcids.put("Trp", new String[]{"TGG"}); - aminoAcids.put("Glu", new String[]{"CAA", "CAG"}); - aminoAcids.put("Asn", new String[]{"AAT", "AAC"}); - aminoAcids.put("His", new String[]{"CAT", "CAC"}); - aminoAcids.put("Gln", new String[]{"GAA", "GAG"}); - aminoAcids.put("Asp", new String[]{"GAT", "GAC"}); - aminoAcids.put("Lys", new String[]{"AAA", "AAG"}); - aminoAcids.put("Arg", new String[]{"CGT", "CGC", "CGA", "CGG", "AGA", "AGG"}); - aminoAcids.put("Stop", new String[]{"TAA", "TAG", "TGA"}); - - degeneracies = new HashMap>(); - - for (String aminoAcid : aminoAcids.keySet()) { - String[] codons = aminoAcids.get(aminoAcid); - - for (int pos = 0; pos < 3; pos++) { - HashSet alleles = new HashSet(); - - for (String codon : codons) { - alleles.add(codon.charAt(pos)); - } - - String degeneracy; - switch (alleles.size()) { - case 1: degeneracy = "1-fold"; break; - case 2: degeneracy = "2-fold"; break; - case 3: degeneracy = "3-fold"; break; - case 4: degeneracy = "4-fold"; break; - case 6: degeneracy = "6-fold"; break; - default: degeneracy = "1-fold"; break; - } - - if (!degeneracies.containsKey(aminoAcid)) { - degeneracies.put(aminoAcid, new HashMap()); - } - - degeneracies.get(aminoAcid).put(pos, degeneracy); - } - } - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - ArrayList relevantStates = new ArrayList(); - - relevantStates.add("all"); - - if (eval != null && eval.isVariant()) { - String type = null; - String aa = null; - Integer frame = null; - - if (eval.hasAttribute("refseq.functionalClass")) { - aa = eval.getAttributeAsString("refseq.variantAA", null); - frame = eval.getAttributeAsInt("refseq.frame", 0); - } else if (eval.hasAttribute("refseq.functionalClass_1")) { - int annotationId = 1; - String key; - - do { - key = String.format("refseq.functionalClass_%d", annotationId); - - String newtype = eval.getAttributeAsString(key, null); - - if ( newtype != null && - ( type == null || - ( type.equals("silent") && !newtype.equals("silent") ) || - ( type.equals("missense") && newtype.equals("nonsense") ) ) - ) { - type = newtype; - - String aakey = String.format("refseq.variantAA_%d", annotationId); - aa = eval.getAttributeAsString(aakey, null); - - if (aa != null) { - String framekey = String.format("refseq.frame_%d", annotationId); - - if (eval.hasAttribute(framekey)) { - frame = eval.getAttributeAsInt(framekey, 0); - } - } - } - - annotationId++; - } while (eval.hasAttribute(key)); - } - - if (aa != null && degeneracies.containsKey(aa) && frame != null) { - relevantStates.add(degeneracies.get(aa).get(frame)); - } - } - - return relevantStates; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java deleted file mode 100644 index 6e03f2bce..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java +++ /dev/null @@ -1,87 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.variant.variantcontext.VariantContext; - -/** - * Tag this stratification as dynamically determining the final strat based on the input data - * - * The paradigm here is simple. We upfront create a strat with N states that reflect the finest grained - * possible division of the data. The data is processed, and statistics collected for each of the N states. - * An update call is made to the stratification for evaluation VariantContext during each map call, - * allowing the strat to collect data about the usage of each state. A final call requests that - * the stratification map down the N states into M states (typically less than N, not necessarily - * a subset of N). This is provided by returning a map from each of M state -> N states and - * the VariantEval walker will combine all of the evaluations for N into a single value for - * each M. - * - * For example, suppose I have a dynamic strat called AC, adopting 7 possible values 0,1,2,3,4,5,6. This - * strats tracks the number of eval vcs for each state, with final counts 0=1, 1=100, 2=10, 3=5, 4=3, 5=2, 6=1. - * The stratification attempts to combine the strats down to so that each state has approximately the same - * fraction of the data in each bin. Overall there is 1+100+10+5+3+2+1=124 observations and 7 bins so we really - * want ~ 18 observations in each bin. So we merge 3-6 with 5+3+2+1 = 11 and keep 2, 1, and 0 as distinct bins. We - * return a map from 0 -> 0, 1 -> 1, 2 -> 2, 3-6 -> {3,4,5,6}. - * - * TODO - some open implementation questions - * -- We should only create one stratifier overall. How do we track this? When we create the stratifiers - * perhaps we can look at them and create a tracker? - * -- How do we create a new stratifier based on the finalStratifications() given the framework? Conceptually - * this new thing is itself a stratifier, just like before, but it's states are determined at the end. We'd - * then like to call not getRelevantStates but a different function that accepts an old state and returns - * the new state. Perhaps the process should look like: - * finalizeStratification -> new Stratifier whose states are the final ones - * getNewState(old state) -> new state (one of those in getFinalStratification) - * - * @author Mark DePristo - * @since 4/9/12 - */ -public interface DynamicStratification { - public void update(final VariantContext eval); - public VariantStratifier finalizeStratification(); - public Object getFinalState(final Object oldState); -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java deleted file mode 100644 index e1a0f9ea4..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java +++ /dev/null @@ -1,73 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.List; - -/** - * Required stratification grouping output by each eval ROD - */ -public class EvalRod extends VariantStratifier implements RequiredStratification { - @Override - public void initialize() { - for ( RodBinding rod : getVariantEvalWalker().getEvals() ) { - states.add(rod.getName()); - if ( getVariantEvalWalker().mergeEvals ) - break; - } - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - return Arrays.asList((Object)evalName); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java deleted file mode 100644 index 60b05c966..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +++ /dev/null @@ -1,131 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.ArrayList; -import java.util.List; - -/** - * Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation. - */ -public class FunctionalClass extends VariantStratifier { - - public enum FunctionalType { - silent, - missense, - nonsense - } - - - @Override - public void initialize() { - states.add("all"); - for ( FunctionalType type : FunctionalType.values() ) - states.add(type.name()); - } - - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - ArrayList relevantStates = new ArrayList(); - - relevantStates.add("all"); - - if (eval != null && eval.isVariant()) { - FunctionalType type = null; - - if (eval.hasAttribute("refseq.functionalClass")) { - try { - type = FunctionalType.valueOf(eval.getAttributeAsString("refseq.functionalClass", null)); - } catch ( Exception e ) {} // don't error out if the type isn't supported - } else if (eval.hasAttribute("refseq.functionalClass_1")) { - int annotationId = 1; - String key; - - do { - key = String.format("refseq.functionalClass_%d", annotationId); - - String newtypeStr = eval.getAttributeAsString(key, null); - if ( newtypeStr != null && !newtypeStr.equalsIgnoreCase("null") ) { - try { - FunctionalType newType = FunctionalType.valueOf(newtypeStr); - if ( type == null || - ( type == FunctionalType.silent && newType != FunctionalType.silent ) || - ( type == FunctionalType.missense && newType == FunctionalType.nonsense ) ) { - type = newType; - } - } catch ( Exception e ) {} // don't error out if the type isn't supported - } - - annotationId++; - } while (eval.hasAttribute(key)); - - } else if ( eval.hasAttribute(SnpEff.InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName()) ) { - try { - SnpEff.EffectFunctionalClass snpEffFunctionalClass = SnpEff.EffectFunctionalClass.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName()).toString()); - if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.NONSENSE ) - type = FunctionalType.nonsense; - else if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.MISSENSE ) - type = FunctionalType.missense; - else if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.SILENT ) - type = FunctionalType.silent; - } - catch ( Exception e ) {} // don't error out if the type isn't supported - } - - if ( type != null ) { - relevantStates.add(type.name()); - } - } - - return relevantStates; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java deleted file mode 100644 index 18d7ed3f8..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java +++ /dev/null @@ -1,99 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Collections; -import java.util.List; - -/** - * Stratifies the eval RODs by the indel size - * - * Indel sizes are stratified from sizes -100 to +100. Sizes greater than this are lumped in the +/- 100 bin - * This stratification ignores multi-allelic indels (whose size is not defined uniquely) - */ -public class IndelSize extends VariantStratifier { - static final int MAX_INDEL_SIZE = 100; - - @Override - public void initialize() { - for( int a=-MAX_INDEL_SIZE; a <=MAX_INDEL_SIZE; a++ ) { - states.add(a); - } - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - if (eval != null && eval.isIndel() && eval.isBiallelic()) { - try { - int eventLength = 0; - if ( eval.isSimpleInsertion() ) { - eventLength = eval.getAlternateAllele(0).length(); - } else if ( eval.isSimpleDeletion() ) { - eventLength = -eval.getReference().length(); - } - - if (eventLength > MAX_INDEL_SIZE) - eventLength = MAX_INDEL_SIZE; - else if (eventLength < -MAX_INDEL_SIZE) - eventLength = -MAX_INDEL_SIZE; - - return Collections.singletonList((Object)eventLength); - } catch (Exception e) { - return Collections.emptyList(); - } - } - - return Collections.emptyList(); - } - @Override - public String getFormat() { - return "%d"; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java deleted file mode 100644 index c2555b3c9..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java +++ /dev/null @@ -1,113 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import net.sf.picard.util.IntervalTree; -import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.*; - -/** - * Stratifies the variants by whether they overlap an interval in the set provided on the command line. - * - * The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up - * by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring - * in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like: - * - * -T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification - * - * Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to - * safely use this module you should provide entire contigs worth of variants, and let the interval strat decide - * overlap, as opposed to using -L which will not properly work with symbolic variants. - */ -public class IntervalStratification extends VariantStratifier { - final protected static Logger logger = Logger.getLogger(IntervalStratification.class); - Map> intervalTreeByContig = null; - - final List OVERLAPPING = Arrays.asList((Object)"all", (Object)"overlaps.intervals"); - final List NOT_OVERLAPPING = Arrays.asList((Object)"all", (Object)"outside.intervals"); - - - @Override - public void initialize() { - if ( getVariantEvalWalker().intervalsFile == null ) - throw new UserException.MissingArgument("stratIntervals", "Must be provided when IntervalStratification is enabled"); - - final List locs = getVariantEvalWalker().intervalsFile.getIntervals(getVariantEvalWalker().getToolkit()); - - if ( locs.isEmpty() ) - throw new UserException.BadArgumentValue("stratIntervals", "Contains no intervals. Perhaps the file is malformed or empty?"); - - intervalTreeByContig = getVariantEvalWalker().createIntervalTreeByContig(getVariantEvalWalker().intervalsFile); - - logger.info(String.format("Creating IntervalStratification %s containing %d intervals covering %d bp", - getVariantEvalWalker().intervalsFile.getSource(), locs.size(), IntervalUtils.intervalSize(locs))); - - states.addAll(Arrays.asList("all", "overlaps.intervals", "outside.intervals")); - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - if (eval != null) { - final GenomeLoc loc = getVariantEvalWalker().getToolkit().getGenomeLocParser().createGenomeLoc(eval, true); - IntervalTree intervalTree = intervalTreeByContig.get(loc.getContig()); - IntervalTree.Node node = intervalTree.minOverlapper(loc.getStart(), loc.getStop()); - //logger.info(String.format("Overlap %s found %s", loc, node)); - if ( node != null ) - return OVERLAPPING; - else - return NOT_OVERLAPPING; - } - - return Collections.emptyList(); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java deleted file mode 100644 index a83c2941c..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java +++ /dev/null @@ -1,90 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; - -import java.util.List; -import java.util.ArrayList; -import java.util.Set; - -/** - * Stratifies the eval RODs by user-supplied JEXL expressions - * - * See http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk for more details - */ -public class JexlExpression extends VariantStratifier implements StandardStratification { - // needs to know the jexl expressions - private Set jexlExpressions; - - @Override - public void initialize() { - jexlExpressions = getVariantEvalWalker().getJexlExpressions(); - - states.add("none"); - for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) { - states.add(jexlExpression.name); - } - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - ArrayList relevantStates = new ArrayList(); - relevantStates.add("none"); - - for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) { - if (eval != null && VariantContextUtils.match(eval, jexlExpression)) { - relevantStates.add(jexlExpression.name); - } - } - - return relevantStates; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java deleted file mode 100644 index 2be5c350b..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.*; - -/** - * Stratifies by whether a site in in the list of known RODs (e.g., dbsnp by default) - */ -public class Novelty extends VariantStratifier implements StandardStratification { - // needs the variant contexts and known names - private List> knowns; - - private final static List KNOWN_STATES = Arrays.asList((Object)"all", (Object)"known"); - private final static List NOVEL_STATES = Arrays.asList((Object)"all", (Object)"novel"); - - @Override - public void initialize() { - states.addAll(Arrays.asList("all", "known", "novel")); - knowns = getVariantEvalWalker().getKnowns(); - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - if (tracker != null && eval != null) { - final Collection knownComps = tracker.getValues(knowns, ref.getLocus()); - for ( final VariantContext c : knownComps ) { - // loop over sites, looking for something that matches the type eval - if ( eval.getType() == c.getType() || eval.getType() == VariantContext.Type.NO_VARIATION ) { - return KNOWN_STATES; - } - } - } - - return NOVEL_STATES; - } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java deleted file mode 100644 index 6eb607879..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java +++ /dev/null @@ -1,80 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.List; - -/** - * Stratifies the eval RODs into sites where the indel is 1 bp in length and those where the event is 2+. - * all non indel events go into all bins, so that SNP counts can be used as contrasts in eval modules. - */ -public class OneBPIndel extends VariantStratifier { - private final static List ALL = Arrays.asList((Object)"all", (Object)"one.bp", (Object)"two.plus.bp"); - private final static List ONE_BP = Arrays.asList((Object)"all", (Object)"one.bp"); - private final static List TWO_PLUS_BP = Arrays.asList((Object)"all", (Object)"two.plus.bp"); - - @Override - public void initialize() { - states.addAll(ALL); - } - - @Override - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - if (eval != null && eval.isIndel()) { - for ( int l : eval.getIndelLengths() ) - if ( Math.abs(l) > 1 ) - return TWO_PLUS_BP; // someone is too long - return ONE_BP; // all lengths are one - } else - return ALL; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java deleted file mode 100644 index 5a1f51f05..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java +++ /dev/null @@ -1,49 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -public interface RequiredStratification {} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java deleted file mode 100644 index 144eeb841..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java +++ /dev/null @@ -1,78 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; -import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.*; - -/** - * Stratifies the eval RODs by each sample in the eval ROD. - * - * This allows the system to analyze each sample separately. Since many evaluations - * only consider non-reference sites, stratifying by sample results in meaningful - * calculations for CompOverlap - */ -public class Sample extends VariantStratifier { - @Override - public void initialize() { - states.addAll(getVariantEvalWalker().getSampleNamesForStratification()); - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - return Collections.singletonList((Object) sampleName); - } - - @Override - public Set> getIncompatibleEvaluators() { - return new HashSet>(Arrays.asList(VariantSummary.class)); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java deleted file mode 100644 index 06fc29e16..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java +++ /dev/null @@ -1,50 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -public interface StandardStratification { -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java deleted file mode 100644 index 621644df8..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java +++ /dev/null @@ -1,88 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Arrays; -import java.util.List; - -/** - * Stratifies the eval RODs into sites that are tandem repeats - */ -public class TandemRepeat extends VariantStratifier { - private final static List JUST_ALL = Arrays.asList((Object)"all"); - private final static List ALL = Arrays.asList((Object)"all", (Object)"is.repeat", (Object)"not.repeat"); - private final static List REPEAT = Arrays.asList((Object)"all", (Object)"is.repeat"); - private final static List NOT_REPEAT = Arrays.asList((Object)"all", (Object)"not.repeat"); - - @Override - public void initialize() { - states.addAll(ALL); - } - - @Override - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - if ( eval == null || ! eval.isIndel() ) - return ALL; - else if ( GATKVariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) { - print("REPEAT", eval, ref); - return REPEAT; - } else { - print("NOT A REPEAT", eval, ref); - return NOT_REPEAT; - } - } - - private final void print(String prefix, VariantContext eval, ReferenceContext ref) { -// String alleles = ParsingUtils.sortList(eval.getAlleles()).toString(); -// this.getVariantEvalWalker().getLogger().info(prefix + ": " + "pos=" + eval.getStart() + " alleles=" + alleles + " ref=" + new String(ref.getForwardBases())); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java deleted file mode 100644 index 91005e3c3..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java +++ /dev/null @@ -1,131 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; -import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; -import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.Stratifier; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.ArrayList; -import java.util.Collections; -import java.util.List; -import java.util.Set; - -public abstract class VariantStratifier implements Comparable, Stratifier { - private VariantEval variantEvalWalker; - final private String name; - final protected ArrayList states = new ArrayList(); - - protected VariantStratifier() { - name = this.getClass().getSimpleName(); - } - - // ------------------------------------------------------------------------------------- - // - // to be overloaded - // - // ------------------------------------------------------------------------------------- - - public abstract void initialize(); - - public abstract List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName); - - // ------------------------------------------------------------------------------------- - // - // final capabilities - // - // ------------------------------------------------------------------------------------- - - /** - * @return a reference to the parent VariantEvalWalker running this stratification - */ - public final VariantEval getVariantEvalWalker() { - return variantEvalWalker; - } - - /** - * Should only be called by VariantEvalWalker itself - * @param variantEvalWalker - */ - public final void setVariantEvalWalker(VariantEval variantEvalWalker) { - this.variantEvalWalker = variantEvalWalker; - } - - public final int compareTo(VariantStratifier o1) { - return this.getName().compareTo(o1.getName()); - } - - @Override - public String toString() { - return getName(); - } - - public final String getName() { - return name; - } - - public String getFormat() { return "%s"; } - - public final ArrayList getAllStates() { - return states; - } - - - /** - * The way for a stratifier to specify that it's incompatible with specific evaluations. For - * example, VariantSummary includes a per-sample metric, and so cannot be used safely with Sample - * or AlleleCount stratifications as this introduces an O(n^2) memory and cpu cost. - * - * @return the set of VariantEvaluators that cannot be active with this Stratification - */ - public Set> getIncompatibleEvaluators() { - return Collections.emptySet(); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java deleted file mode 100644 index ecca7aecb..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java +++ /dev/null @@ -1,70 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications; - -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Collections; -import java.util.List; - -/** - * Stratifies the eval variants by their type (SNP, INDEL, ETC) - */ -public class VariantType extends VariantStratifier { - @Override - public void initialize() { - for (VariantContext.Type t : VariantContext.Type.values()) - states.add(t.toString()); - } - - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType().toString()); - } - -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java deleted file mode 100644 index 256a7b7ff..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications.manager; - -import com.google.java.contract.Ensures; -import com.google.java.contract.Invariant; -import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.util.*; - -/** - * Helper class representing a tree of stratification splits, where leaf nodes - * are given a unique integer key starting at 0 and incrementing up to the - * number of leaves in the tree. This allows you to use this tree to produce - * a key to map into an array index mapped data structure. - * - * Suppose I have to strats, each with two values: A = 1, 2 and B = 3, 4 - * - * This data structure creates a tree such as: - * - * root -> A -> 1 -> B -> 3 : 0 - * |- B -> 4 : 1 - * |- A -> 2 -> B -> 3 : 2 - * |- B -> 4 : 3 - * - * This code allows us to efficiently look up a state key (A=2, B=3) and map it - * to a specific key (an integer) that's unique over the tree - * - * Note the structure of this tree is that the keys are -1 for all internal nodes, and - * leafs are the only nodes with meaningful keys. So for a tree with 2N nodes N of these - * will be internal, with no keys, and meaningful maps from states -> subtrees. The - * other N nodes are leafs, with meaningful keys, empty maps, and null stratification objects - * - * @author Mark DePristo - * @since 3/27/12 - */ -@Invariant({ - "(isLeaf() && stratifier == null && subnodes.isEmpty()) || (!isLeaf() && stratifier != null && !subnodes.isEmpty())"}) -class StratNode implements Iterable> { - int key = -1; - final T stratifier; - final Map> subnodes; // NOTE, because we don't iterate our best option is a HashMap - - protected StratNode() { - this.subnodes = Collections.emptyMap(); - this.stratifier = null; - } - - protected StratNode(final T stratifier, final Map> subnodes) { - this.stratifier = stratifier; - // important to reallocate an unmodififable hashmap with this specific size for space and safety - this.subnodes = Collections.unmodifiableMap(new HashMap>(subnodes)); - } - - @Requires("key >= 0") - public void setKey(final int key) { - if ( ! isLeaf() ) - throw new ReviewedStingException("Cannot set key of non-leaf node"); - this.key = key; - } - - @Requires({ - "states != null", - "offset >= 0", - "offset <= states.size()" - }) - public int find(final List states, int offset) { - if ( isLeaf() ) // we're here! - return key; - else { - final Object state = states.get(offset); - StratNode subnode = subnodes.get(state); - if ( subnode == null ) - return -1; - else - return subnode.find(states, offset+1); - } - } - - @Requires({ - "multipleStates != null", - "offset >= 0", - "offset <= multipleStates.size()", - "keys != null", - "offset == multipleStates.size() || multipleStates.get(offset) != null"}) - public void find(final List> multipleStates, final int offset, final HashSet keys) { - if ( isLeaf() ) // we're here! - keys.add(key); - else { - for ( final Object state : multipleStates.get(offset) ) { - // loop over all of the states at this offset - final StratNode subnode = subnodes.get(state); - if ( subnode == null ) - throw new ReviewedStingException("Couldn't find state for " + state + " at node " + this); - else - subnode.find(multipleStates, offset+1, keys); - } - } - } - - @Ensures("result >= 0") - public int getKey() { - if ( ! isLeaf() ) - throw new ReviewedStingException("Cannot get key of non-leaf node"); - else - return key; - } - - protected Map> getSubnodes() { - return subnodes; - } - - @Ensures("result >= 0") - public int size() { - if ( isLeaf() ) - return 1; - else { - return subnodes.values().iterator().next().size() * subnodes.size(); - } - } - - public T getSetOfStates() { - return stratifier; - } - - /** - * @return true if this node is a leaf - */ - public boolean isLeaf() { - return stratifier == null; - } - - /** - * Returns an iterator over this node and all subnodes including internal and leaf nodes - * @return - */ - @Override - @Ensures("result != null") - public Iterator> iterator() { - return new StratNodeIterator(this); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java deleted file mode 100644 index 7bda94916..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java +++ /dev/null @@ -1,90 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications.manager; - -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.util.*; - -/** - * Helper class for creating iterators over all nodes in the stratification tree - * - * @author Mark DePristo - * @since 3/27/12 - */ -class StratNodeIterator implements Iterator> { - Queue>> iterators = new LinkedList>>(); - Iterator> currentIterator; - - StratNodeIterator(final StratNode root) { - currentIterator = Collections.singleton(root).iterator(); - for ( final StratNode subNode : root.subnodes.values() ) - iterators.add(new StratNodeIterator(subNode)); - } - - @Override - public boolean hasNext() { - return currentIterator.hasNext() || ! iterators.isEmpty(); - } - - @Override - public StratNode next() { - if ( currentIterator.hasNext() ) - return currentIterator.next(); - else if ( ! iterators.isEmpty() ) { - currentIterator = iterators.poll(); - return next(); - } else { - throw new IllegalStateException("Next called on empty iterator"); - } - } - - @Override - public void remove() { - throw new ReviewedStingException("Cannot remove from StratNode iterator"); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java deleted file mode 100644 index be2a0dad5..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java +++ /dev/null @@ -1,62 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.stratifications.manager; - -import java.util.List; - -/** - * A basic interface for a class to be used with the StratificationManager system - * - * @author Mark DePristo - * @since 3/28/12 - */ -public interface Stratifier { - /** - * @return a list of all objects states that may be provided by this States provider - */ - public List getAllStates(); -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java deleted file mode 100644 index 9cc7e88de..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java +++ /dev/null @@ -1,57 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.util; - -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; - -@Retention(RetentionPolicy.RUNTIME) -public @interface Analysis { - String name() default ""; // its description, required - String description(); // its description, required - boolean molten() default false; // if true we'll look for a @Molten map -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java deleted file mode 100644 index 4394e17a8..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java +++ /dev/null @@ -1,175 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.util; - -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.lang.annotation.Annotation; -import java.lang.reflect.Field; -import java.util.HashMap; -import java.util.LinkedHashMap; -import java.util.Map; - - -/** - * @author aaron - *

- * Class AnalysisModuleScanner - *

- * Given an analysis, find the annotated fields and methods. Given this module and - * the object, a Mashalling object can serialize or deserialize a analysis module. - */ -public class AnalysisModuleScanner { - final private static Map annotationCache = new HashMap(); - - // what we extracted from the class - private Map datums = new LinkedHashMap(); // the data we've discovered - private Analysis analysis; // the analysis annotation - - private Field moltenField = null; - private Molten moltenAnnotation = null; - - // private storage of the class type - private final Class cls; - - /** - * create a report scanner from the passed in class - * @param cls the target class, annotated with the @Analysis annotation - */ - public AnalysisModuleScanner(Class cls) { - this.cls = cls; - scan(); // scan the passed in class - } - - /** - * create a report scanner from the passed in class - * @param obj the target object, annotated with the @Analysis annotation - */ - public AnalysisModuleScanner(Object obj) { - this.cls = obj.getClass(); - scan(); // scan the passed in class - } - - /** scan the class and find all appropriate fields and tables */ - public void scan() { - if (cls == null || !cls.isAnnotationPresent(Analysis.class)) - throw new ReviewedStingException("The class passed in cannot be null, " + "" + - "and must contain the @Analysis annotation, class " + cls + " was the input"); - - // get the annotation off of the class - analysis = (Analysis) cls.getAnnotation(Analysis.class); - scanFields(); - } - - /** - * scan the fields of the class, extracting parameters and table annotations and their associated fields - */ - private void scanFields() { - // get the fields from the class, and extract - for ( Class superCls = cls; superCls != null; superCls=superCls.getSuperclass() ) { - for (Field f : superCls.getDeclaredFields()) { - for (Annotation annotation : getAnnotations(f)) { - if (annotation.annotationType().equals(DataPoint.class)) - datums.put(f,(DataPoint) annotation); - if ( annotation.annotationType().equals(Molten.class)) { - if ( hasMoltenField() ) - throw new ReviewedStingException("Analysis " + analysis.name() + " has multiple @Molten fields, which is forbidden"); - moltenField = f; - moltenAnnotation = (Molten)annotation; - } - } - } - } - - if ( hasMoltenField() ) { - if ( datums.size() > 0 ) - throw new ReviewedStingException("Analysis " + analysis.name() + " has an @Molten field as well as @DataPoint fields, which is forbidden"); - } - } - - public Field getMoltenField() { - return moltenField; - } - - public Molten getMoltenAnnotation() { - return moltenAnnotation; - } - - public boolean hasMoltenField() { - return getMoltenField() != null; - } - - private Annotation[] getAnnotations(final Field field) { - final String fieldName = field.toString(); - Annotation[] annotations = annotationCache.get(fieldName); - if ( annotations == null ) { - annotations = field.getAnnotations(); - annotationCache.put(fieldName, annotations); - } - return annotations; - } - - /** - * - * @return a map of the datum annotations found - */ - public Map getData() { - return datums; - } - - /** - * - * @return the analysis annotation found - */ - public Analysis getAnalysis() { - return analysis; - } - - public Class getModuleClass() { - return cls; - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java deleted file mode 100644 index aacbb29e5..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java +++ /dev/null @@ -1,56 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.util; - -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; - -@Retention(RetentionPolicy.RUNTIME) -public @interface DataPoint { - String description() default ""; // the description, optional - String format() default ""; -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java deleted file mode 100644 index 3059de37b..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java +++ /dev/null @@ -1,136 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.util; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; -import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; -import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.ArrayList; -import java.util.Set; -import java.util.TreeSet; - -public final class EvaluationContext { - // NOTE: must be hashset to avoid O(log n) cost of iteration in the very frequently called apply function - final VariantEval walker; - private final ArrayList evaluationInstances; - private final Set> evaluationClasses; - - public EvaluationContext(final VariantEval walker, final Set> evaluationClasses) { - this(walker, evaluationClasses, true); - } - - private EvaluationContext(final VariantEval walker, final Set> evaluationClasses, final boolean doInitialize) { - this.walker = walker; - this.evaluationClasses = evaluationClasses; - this.evaluationInstances = new ArrayList(evaluationClasses.size()); - - for ( final Class c : evaluationClasses ) { - try { - final VariantEvaluator eval = c.newInstance(); - if ( doInitialize ) eval.initialize(walker); - evaluationInstances.add(eval); - } catch (InstantiationException e) { - throw new ReviewedStingException("Unable to instantiate eval module '" + c.getSimpleName() + "'", e); - } catch (IllegalAccessException e) { - throw new ReviewedStingException("Illegal access error when trying to instantiate eval module '" + c.getSimpleName() + "'", e); - } - } - } - - /** - * Returns a sorted set of VariantEvaluators - * - * @return - */ - public final TreeSet getVariantEvaluators() { - return new TreeSet(evaluationInstances); - } - - public final void apply(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext comp, VariantContext eval) { - for ( final VariantEvaluator evaluation : evaluationInstances ) { - // the other updateN methods don't see a null context - if ( tracker == null ) - continue; - - // now call the single or paired update function - switch ( evaluation.getComparisonOrder() ) { - case 1: - if (eval != null) { - evaluation.update1(eval, tracker, ref, context); - } - break; - case 2: - evaluation.update2(eval, comp, tracker, ref, context); - break; - default: - throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation); - } - } - } - - public void combine(final EvaluationContext rhs) { - for ( int i = 0; i < evaluationInstances.size(); i++ ) - evaluationInstances.get(i).combine(rhs.evaluationInstances.get(i)); - } - - public final static EvaluationContextCombiner COMBINER = new EvaluationContext.EvaluationContextCombiner(); - private static class EvaluationContextCombiner implements StratificationManager.Combiner { - @Override - public EvaluationContext combine(EvaluationContext lhs, final EvaluationContext rhs) { - if ( lhs == null ) - lhs = new EvaluationContext(rhs.walker, rhs.evaluationClasses, false); - lhs.combine(rhs); - return lhs; - } - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java deleted file mode 100644 index a2f3acb4e..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.varianteval.util; - -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; - -/** - * Molten for @Analysis modules. - * - * If you are flagged as a molten analysis, then there must be one and - * only one annotation in that evaluation module: @Molten which - * must have time Map. This data set will then - * be represented in the VE output as: - * - * variable value - * key1 value1 - * key2 value1 - * ... - * keyN valueN - * - * in the output table. The names of these two fields can be override via annotation values. - */ -@Retention(RetentionPolicy.RUNTIME) -public @interface Molten { - String description() default ""; // the description, optional - - /** - * The name to use for the molten variable field in the output table. - * @return - */ - String variableName() default "variable"; - String variableFormat() default ""; - - /** - * The name to use for the molten value field in the output table. - * @return - */ - String valueName() default "value"; - String valueFormat() default ""; -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java deleted file mode 100644 index d3a79221e..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java +++ /dev/null @@ -1,181 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.variantrecalibration; - -import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.io.File; -import java.io.FileNotFoundException; -import java.util.ArrayList; -import java.util.List; - -/** - * Created by IntelliJ IDEA. - * User: depristo - * Date: 3/11/11 - * Time: 10:33 AM - * To change this template use File | Settings | File Templates. - */ -public class VQSRCalibrationCurve { - private final static boolean DEBUG = false; - List points; - public static final double CERTAIN_FALSE_POSITIVE = -1; - - private static class VQSRRange { - double start, stop, truePositiveRate; - - public double getStart() { - return start; - } - - public double getStop() { - return stop; - } - - public double getTruePositiveRate() { - return truePositiveRate; - } - - private VQSRRange(double start, double stop, double truePositiveRate) { - this.start = start; - this.stop = stop; - this.truePositiveRate = truePositiveRate; - } - } - - public static VQSRCalibrationCurve readFromFile(File source) { - List points = new ArrayList(); - - try { - for ( String line : new XReadLines(source).readLines() ) { - if ( ! line.trim().isEmpty() ) { - String[] parts = line.split("\\s+"); - double fpRate = Double.parseDouble(parts[2]); - double tpRate = fpRate >= 1.0 ? CERTAIN_FALSE_POSITIVE : 1.0 - fpRate; - points.add(new VQSRRange(Double.parseDouble(parts[0]), Double.parseDouble(parts[1]), tpRate)); - } - } - } catch ( FileNotFoundException e ) { - throw new UserException.CouldNotReadInputFile(source, e); - } - - // ensure that the entire range gets caught - points.get(0).start = Double.POSITIVE_INFINITY; - points.get(points.size()-1).stop = Double.NEGATIVE_INFINITY; - - return new VQSRCalibrationCurve(points); - } - - protected VQSRCalibrationCurve(List points) { - this.points = points; - } - - public boolean certainFalsePositive(String VQSRQualKey, VariantContext vc) { - return probTrueVariant(VQSRQualKey, vc) == CERTAIN_FALSE_POSITIVE; - } - - - public double probTrueVariant(double VQSRqual) { - for ( VQSRRange r : points ) { - if ( VQSRqual <= r.getStart() && VQSRqual > r.getStop() ) - return r.getTruePositiveRate(); - } - - throw new ReviewedStingException("BUG: should not be able to reach this code"); - } - - public double probTrueVariant(String VQSRQualKey, VariantContext vc) { - if ( vc.isFiltered() ) - return 0.0; - else if ( vc.hasAttribute(VQSRQualKey) ) { - double qual = vc.getAttributeAsDouble(VQSRQualKey, 0.0); - return probTrueVariant(qual); - } else { - throw new UserException.VariantContextMissingRequiredField(VQSRQualKey, vc); - } - } - - /** - * Returns a likelihoods vector adjusted by the probability that the site is an error. Returns a - * null vector if the probability of the site being real is 0.0 - * @param VQSRQualKey - * @param vc - * @param log10Likelihoods - * @return - */ - public double[] includeErrorRateInLikelihoods(String VQSRQualKey, VariantContext vc, double[] log10Likelihoods) { - double[] updated = new double[log10Likelihoods.length]; - - double alpha = probTrueVariant(VQSRQualKey, vc); - - if ( alpha == CERTAIN_FALSE_POSITIVE ) - return null; - else { - double noInfoPr = 1.0 / 3; - if ( DEBUG ) System.out.printf("------------------------------%n"); - for ( int i = 0; i < log10Likelihoods.length; i++) { - double p = Math.pow(10, log10Likelihoods[i]); - double q = alpha * p + (1-alpha) * noInfoPr; - if ( DEBUG ) System.out.printf(" vqslod = %.2f, p = %.2e, alpha = %.2e, q = %.2e%n", vc.getAttributeAsDouble(VQSRQualKey, 0.0), p, alpha, q); - updated[i] = Math.log10(q); - } - - return updated; - } - } - - - public void printInfo(Logger logger) { - for ( VQSRRange r : points ) { - logger.info(String.format(" start=%f stop=%f TPrate=%.6e", r.getStart(), r.getStop(), r.getTruePositiveRate())); - } - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index 433900d02..d8d79e26c 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -59,6 +59,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.R.RScriptExecutor; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; @@ -66,7 +67,6 @@ import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.io.Resource; import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.File; @@ -274,7 +274,7 @@ public class VariantRecalibrator extends RodWalker,ConcordanceMetrics> { - - @Input(fullName="eval",shortName="eval",doc="The variants and genotypes to evaluate",required=true) - RodBinding evalBinding; - - @Input(fullName="comp",shortName="comp",doc="The variants and genotypes to compare against",required=true) - RodBinding compBinding; - - @Argument(fullName="ignoreFilters",doc="Filters will be ignored",required=false) - boolean ignoreFilters = false; - - @Output - PrintStream out; - - List evalSamples; - List compSamples; - - // todo -- integration test coverage - // todo -- deal with occurrences like: - // Eval: 20 4000 A C - // Eval: 20 4000 A AC - // Comp: 20 4000 A C - // currently this results in a warning and skipping - // todo -- extend to multiple eval, multiple comp - // todo -- table with "proportion of overlapping sites" (not just eval/comp margins) - - - public ConcordanceMetrics reduceInit() { - Map headerMap = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(evalBinding,compBinding)); - VCFHeader evalHeader = headerMap.get(evalBinding.getName()); - evalSamples = evalHeader.getGenotypeSamples(); - VCFHeader compHeader = headerMap.get(compBinding.getName()); - compSamples = compHeader.getGenotypeSamples(); - return new ConcordanceMetrics(evalHeader,compHeader); - } - - - public Pair map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - Pair evalCompPair = null; - if ( tracker != null && ( - tracker.getValues(evalBinding,ref.getLocus()).size() > 0 || - tracker.getValues(compBinding,ref.getLocus()).size() > 0 ) ) { - - List eval = tracker.getValues(evalBinding,ref.getLocus()); - List comp = tracker.getValues(compBinding,ref.getLocus()); - if ( eval.size() > 1 || comp.size() > 1 ) { - logger.warn("Eval or Comp Rod at position "+ref.getLocus().toString()+" has multiple records. Site will be skipped."); - return evalCompPair; - } - // if a rod is missing, explicitly create a variant context with 'missing' genotypes. Slow, but correct. - // note that if there is no eval rod there must be a comp rod, and also the reverse - VariantContext evalContext = eval.size() == 1 ? eval.get(0) : createEmptyContext(ref,comp.get(0),evalSamples); - VariantContext compContext = comp.size() == 1 ? comp.get(0) : createEmptyContext(ref,eval.get(0),compSamples); - evalContext = filterGenotypes(evalContext,ignoreFilters); - compContext = filterGenotypes(compContext,ignoreFilters); - evalCompPair = new Pair(evalContext,compContext); - } - - return evalCompPair; - } - - public ConcordanceMetrics reduce(Pair evalComp, ConcordanceMetrics metrics) { - if ( evalComp != null ) - metrics.update(evalComp.getFirst(),evalComp.getSecond()); - return metrics; - } - - public void onTraversalDone(ConcordanceMetrics metrics) { - GATKReport report = new GATKReport(); - GATKReportTable concordanceCounts = new GATKReportTable("GenotypeConcordance_Counts","Per-sample concordance tables: comparison counts",2+GenotypeType.values().length*GenotypeType.values().length); - GATKReportTable concordanceEvalProportions = new GATKReportTable("GenotypeConcordance_EvalProportions", "Per-sample concordance tables: proportions of genotypes called in eval",2+GenotypeType.values().length*GenotypeType.values().length); - GATKReportTable concordanceCompProportions = new GATKReportTable("GenotypeConcordance_CompProportions", "Per-sample concordance tables: proportions of genotypes called in comp",2+GenotypeType.values().length*GenotypeType.values().length); - GATKReportTable concordanceSummary = new GATKReportTable("GenotypeConcordance_Summary","Per-sample summary statistics: NRS and NRD",2); - GATKReportTable siteConcordance = new GATKReportTable("SiteConcordance_Summary","Site-level summary statistics",ConcordanceMetrics.SiteConcordanceType.values().length); - concordanceCompProportions.addColumn("Sample","%s"); - concordanceCounts.addColumn("Sample","%s"); - concordanceEvalProportions.addColumn("Sample","%s"); - concordanceSummary.addColumn("Sample","%s"); - for ( GenotypeType evalType : GenotypeType.values() ) { - for ( GenotypeType compType : GenotypeType.values() ) { - String colKey = String.format("%s_%s", evalType.toString(), compType.toString()); - concordanceCounts.addColumn(colKey,"%d"); - if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) - concordanceEvalProportions.addColumn(colKey,"%.3f"); - if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) - concordanceCompProportions.addColumn(colKey,"%.3f"); - } - } - concordanceEvalProportions.addColumn("Mismatching_Alleles","%.3f"); - concordanceCompProportions.addColumn("Mismatching_Alleles","%.3f"); - concordanceCounts.addColumn("Mismatching_Alleles","%d"); - concordanceSummary.addColumn("Non-Reference Sensitivity","%.3f"); - concordanceSummary.addColumn("Non-Reference Discrepancy","%.3f"); - for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) { - siteConcordance.addColumn(type.toString(),"%d"); - } - - for ( Map.Entry entry : metrics.getPerSampleGenotypeConcordance().entrySet() ) { - ConcordanceMetrics.GenotypeConcordanceTable table = entry.getValue(); - concordanceEvalProportions.set(entry.getKey(),"Sample",entry.getKey()); - concordanceCompProportions.set(entry.getKey(),"Sample",entry.getKey()); - concordanceCounts.set(entry.getKey(),"Sample",entry.getKey()); - for ( GenotypeType evalType : GenotypeType.values() ) { - for ( GenotypeType compType : GenotypeType.values() ) { - String colKey = String.format("%s_%s",evalType.toString(),compType.toString()); - int count = table.get(evalType, compType); - concordanceCounts.set(entry.getKey(),colKey,count); - if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) - concordanceEvalProportions.set(entry.getKey(),colKey,( (double) count)/table.getnEvalGenotypes(evalType)); - if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) - concordanceCompProportions.set(entry.getKey(),colKey,( (double) count)/table.getnCompGenotypes(compType)); - } - } - concordanceEvalProportions.set(entry.getKey(),"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()); - concordanceCompProportions.set(entry.getKey(),"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()); - concordanceCounts.set(entry.getKey(),"Mismatching_Alleles",table.getnMismatchingAlt()); - } - - String rowKey = "ALL"; - concordanceCompProportions.set(rowKey,"Sample",rowKey); - concordanceEvalProportions.set(rowKey,"Sample",rowKey); - concordanceCounts.set(rowKey,"Sample",rowKey); - ConcordanceMetrics.GenotypeConcordanceTable table = metrics.getOverallGenotypeConcordance(); - for ( GenotypeType evalType : GenotypeType.values() ) { - for ( GenotypeType compType : GenotypeType.values() ) { - String colKey = String.format("%s_%s",evalType.toString(),compType.toString()); - int count = table.get(evalType,compType); - concordanceCounts.set(rowKey,colKey,count); - if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) - concordanceEvalProportions.set(rowKey,colKey,( (double) count)/table.getnEvalGenotypes(evalType)); - if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) - concordanceCompProportions.set(rowKey,colKey,( (double) count)/table.getnCompGenotypes(compType)); - } - } - concordanceEvalProportions.set(rowKey,"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes()); - concordanceCompProportions.set(rowKey,"Mismatching_Alleles", ( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes()); - concordanceCounts.set(rowKey,"Mismatching_Alleles",table.getnMismatchingAlt()); - - for ( Map.Entry nrsEntry : metrics.getPerSampleNRS().entrySet() ) { - concordanceSummary.set(nrsEntry.getKey(),"Sample",nrsEntry.getKey()); - concordanceSummary.set(nrsEntry.getKey(),"Non-Reference Sensitivity",nrsEntry.getValue()); - } - for ( Map.Entry nrdEntry : metrics.getPerSampleNRD().entrySet() ) { - concordanceSummary.set(nrdEntry.getKey(),"Non-Reference Discrepancy",nrdEntry.getValue()); - } - concordanceSummary.set("ALL","Sample","ALL"); - concordanceSummary.set("ALL","Non-Reference Sensitivity",metrics.getOverallNRS()); - concordanceSummary.set("ALL","Non-Reference Discrepancy",metrics.getOverallNRD()); - - for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) { - siteConcordance.set("Comparison",type.toString(),metrics.getOverallSiteConcordance().get(type)); - } - - report.addTable(concordanceCompProportions); - report.addTable(concordanceEvalProportions); - report.addTable(concordanceCounts); - report.addTable(concordanceSummary); - report.addTable(siteConcordance); - - report.print(out); - } - - public VariantContext createEmptyContext(ReferenceContext ref, VariantContext other, List samples) { - VariantContextBuilder builder = new VariantContextBuilder(); - // set the alleles to be the same - builder.alleles(other.getAlleles()); - builder.loc(other.getChr(),other.getStart(),other.getEnd()); - // set all genotypes to empty - List genotypes = new ArrayList(samples.size()); - for ( String sample : samples ) - genotypes.add(GenotypeBuilder.create(sample, new ArrayList(0))); - builder.genotypes(genotypes); - return builder.make(); - } - - public VariantContext filterGenotypes(VariantContext context, boolean ignoreSiteFilter) { - // placeholder method for genotype-level filtering. However if the site itself is filtered, - // and such filters are not ignored, the genotype-level data should be altered to reflect this - if ( ! context.isFiltered() || ignoreSiteFilter ) { - // todo -- add genotype-level jexl filtering here - return context; - } - VariantContextBuilder builder = new VariantContextBuilder(); - builder.alleles(Arrays.asList(context.getReference())); - builder.loc(context.getChr(),context.getStart(),context.getEnd()); - List newGeno = new ArrayList(context.getNSamples()); - for ( Genotype g : context.getGenotypes().iterateInSampleNameOrder() ) { - newGeno.add(GenotypeBuilder.create(g.getSampleName(),new ArrayList())); - } - builder.genotypes(newGeno); - return builder.make(); - } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java deleted file mode 100644 index 940f2faf4..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ /dev/null @@ -1,189 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.variantutils; - -import net.sf.picard.liftover.LiftOver; -import net.sf.picard.util.Interval; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileReader; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.*; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; - -import java.io.File; -import java.util.*; - -/** - * Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted. - */ -@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) -public class LiftoverVariants extends RodWalker { - - @ArgumentCollection - protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); - - @Output(doc="File to which variants should be written",required=true) - protected File file = null; - protected VariantContextWriter writer = null; - - @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true) - protected File CHAIN = null; - - @Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true) - protected File NEW_SEQ_DICT = null; - - @Argument(fullName="recordOriginalLocation", shortName="recordOriginalLocation", doc="Should we record what the original location was in the INFO field?", required=false) - protected Boolean RECORD_ORIGINAL_LOCATION = false; - - private LiftOver liftOver; - - private long successfulIntervals = 0, failedIntervals = 0; - - public void initialize() { - try { - liftOver = new LiftOver(CHAIN); - } catch (RuntimeException e) { - throw new UserException.BadInput("there is a problem with the chain file you are using: " + e.getMessage()); - } - - liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH); - - try { - final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader(); - liftOver.validateToSequences(toHeader.getSequenceDictionary()); - } catch (RuntimeException e) { - throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference"); - } - - String trackName = variantCollection.variants.getName(); - Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)); - Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); - - Set metaData = new HashSet(); - if ( vcfHeaders.containsKey(trackName) ) - metaData.addAll(vcfHeaders.get(trackName).getMetaDataInSortedOrder()); - if ( RECORD_ORIGINAL_LOCATION ) { - metaData.add(new VCFInfoHeaderLine("OriginalChr", 1, VCFHeaderLineType.String, "Original contig name for the record")); - metaData.add(new VCFInfoHeaderLine("OriginalStart", 1, VCFHeaderLineType.Integer, "Original start position for the record")); - } - - - final VCFHeader vcfHeader = new VCFHeader(metaData, samples); - writer = VariantContextWriterFactory.create(file, getMasterSequenceDictionary(), VariantContextWriterFactory.NO_OPTIONS); - writer.writeHeader(vcfHeader); - } - - private void convertAndWrite(VariantContext vc, ReferenceContext ref) { - - final Interval fromInterval = new Interval(vc.getChr(), vc.getStart(), vc.getStart(), false, String.format("%s:%d", vc.getChr(), vc.getStart())); - final int length = vc.getEnd() - vc.getStart(); - final Interval toInterval = liftOver.liftOver(fromInterval); - VariantContext originalVC = vc; - - if ( toInterval != null ) { - // check whether the strand flips, and if so reverse complement everything - if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && vc.isPointEvent() ) { - vc = VariantContextUtils.reverseComplement(vc); - } - - vc = new VariantContextBuilder(vc).loc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length).make(); - - if ( RECORD_ORIGINAL_LOCATION ) { - vc = new VariantContextBuilder(vc) - .attribute("OriginalChr", fromInterval.getSequence()) - .attribute("OriginalStart", fromInterval.getStart()).make(); - } - - if ( originalVC.isSNP() && originalVC.isBiallelic() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(vc) ) { - logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s", - originalVC.getChr(), originalVC.getStart(), vc.getChr(), vc.getStart(), - originalVC.getReference(), originalVC.getAlternateAllele(0), vc.getReference(), vc.getAlternateAllele(0))); - } - - writer.add(vc); - successfulIntervals++; - } else { - failedIntervals++; - } - } - - public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( tracker == null ) - return 0; - - Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation()); - for ( VariantContext vc : VCs ) - convertAndWrite(vc, ref); - - return 0; - } - - public Integer reduceInit() { return 0; } - - public Integer reduce(Integer value, Integer sum) { return 0; } - - public void onTraversalDone(Integer result) { - System.out.println("Converted " + successfulIntervals + " records; failed to convert " + failedIntervals + " records."); - writer.close(); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java similarity index 72% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java index 23516b5ed..c8fc27e6a 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java @@ -46,65 +46,83 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.gatk.walkers.TreeReducible; +import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; +import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; +import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper; +import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.variantcontext.*; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; +import org.broadinstitute.variant.vcf.*; -import java.io.File; import java.util.*; /** - * Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results. + * Regenotypes the variants from a VCF. VCF records must contain PLs or GLs. + * + *

+ * This tool triggers re-genotyping of the samples through the Exact Allele Frequency calculation model. Note that this is truly the + * mathematically correct way to select samples from a larger set (especially when calls were generated from low coverage sequencing data); + * using the hard genotypes to select (i.e. the default mode of SelectVariants) can lead to false positives when errors are confused for + * variants in the original genotyping. This functionality used to comprise the --regenotype option in SelectVariants but we pulled it out + * into its own tool for technical purposes. + * + *

Input

+ *

+ * A variant set to regenotype. + *

+ * + *

Output

+ *

+ * A re-genotyped VCF. + *

+ * + *

Examples

+ * 
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T RegenotypeVariants \
+ *   --variant input.vcf \
+ *   -o output.vcf
+ *
+ * */ @DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) -public class RandomlySplitVariants extends RodWalker { +public class RegenotypeVariants extends RodWalker implements TreeReducible { - @ArgumentCollection - protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); - @Output(fullName="out1", shortName="o1", doc="File #1 to which variants should be written", required=true) - protected VariantContextWriter vcfWriter1 = null; + @Output(doc="File to which variants should be written",required=true) + protected VariantContextWriter vcfWriter = null; - @Output(fullName="out2", shortName="o2", doc="File #2 to which variants should be written", required=true) - // there's a reported bug in the GATK where we can't have 2 @Output writers - protected File file2 = null; - protected VariantContextWriter vcfWriter2 = null; + private UnifiedGenotyperEngine UG_engine = null; - @Argument(fullName="fractionToOut1", shortName="fraction", doc="Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2", required=false) - protected double fraction = 0.5; - - /** - * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher - */ public void initialize() { - if ( fraction < 0.0 || fraction > 1.0 ) - throw new UserException.BadArgumentValue("fractionToOut1", "this value needs to be a number between 0 and 1"); + final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection(); + UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH; + UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES; + UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES; - // setup the header info - final List inputNames = Arrays.asList(variantCollection.variants.getName()); - Set samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames); - Set hInfo = new HashSet(); - hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames)); + String trackName = variantCollection.variants.getName(); + Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)); + UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY); - vcfWriter1.writeHeader(new VCFHeader(hInfo, samples)); - vcfWriter2 = VariantContextWriterFactory.create(file2, getMasterSequenceDictionary()); - vcfWriter2.writeHeader(new VCFHeader(hInfo, samples)); + final Set hInfo = new HashSet(); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(trackName))); + hInfo.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null)); + + vcfWriter.writeHeader(new VCFHeader(hInfo, samples)); } /** @@ -115,28 +133,53 @@ public class RandomlySplitVariants extends RodWalker { * @param context alignment info * @return 1 if the record was printed to the output file, 0 if otherwise */ + @Override public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { if ( tracker == null ) return 0; Collection vcs = tracker.getValues(variantCollection.variants, context.getLocation()); - for ( VariantContext vc : vcs ) { - double random = GenomeAnalysisEngine.getRandomGenerator().nextDouble(); - if ( random < fraction ) - vcfWriter1.add(vc); - else - vcfWriter2.add(vc); + + if ( vcs == null || vcs.size() == 0) { + return 0; + } + + for (VariantContext vc : vcs) { + + if ( vc.isPolymorphicInSamples() && hasPLs(vc) ) { + synchronized (UG_engine) { + final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(vc)).filters(vc.getFiltersMaybeNull()); + VariantContextUtils.calculateChromosomeCounts(builder, false); + vc = builder.make(); + } + } + + vcfWriter.add(vc); } return 1; } + private boolean hasPLs(final VariantContext vc) { + for ( Genotype g : vc.getGenotypes() ) { + if ( g.hasLikelihoods() ) + return true; + } + return false; + } + + @Override public Integer reduceInit() { return 0; } + @Override public Integer reduce(Integer value, Integer sum) { return value + sum; } + @Override + public Integer treeReduce(Integer lhs, Integer rhs) { + return lhs + rhs; + } + public void onTraversalDone(Integer result) { logger.info(result + " records processed."); - vcfWriter2.close(); } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java deleted file mode 100644 index 81a17b6ae..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java +++ /dev/null @@ -1,267 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; 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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.sting.gatk.walkers.variantutils; - -import org.apache.commons.io.FilenameUtils; -import org.broad.tribble.Feature; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.*; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.text.ListFileUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; - -import java.io.File; -import java.util.*; - -/** - * Selects headers from a VCF source. - *

- *

- * Often, a VCF containing many headers will need to be subset in order to facilitate certain formatting guidelines. - * SelectHeaders can be used for this purpose. Given a single VCF file, one or more headers can be extracted from the - * file (based on a complete header name or a pattern match). - *

- *

Input

- *

- * A set of VCFs. - *

- *

- *

Output

- *

- * A header selected VCF. - *

- *

- *

Examples

- * 
- * Select only the FILTER, FORMAT, and INFO headers:
- * java -Xmx2g -jar GenomeAnalysisTK.jar \
- *   -R ref.fasta \
- *   -T SelectHeaders \
- *   --variant input.vcf \
- *   -o output.vcf \
- *   -hn FILTER \
- *   -hn FORMAT \
- *   -hn INFO
- *
- * Select only the FILTER, FORMAT, and INFO headers and add in the reference file names:
- * java -Xmx2g -jar GenomeAnalysisTK.jar \
- *   -R ref.fasta \
- *   -T SelectHeaders \
- *   --variant input.vcf \
- *   -o output.vcf \
- *   -hn FILTER \
- *   -hn FORMAT \
- *   -hn INFO \
- *   -irn \
- *   -iln
- *
- * Select only the FILTER, FORMAT, and INFO headers, plus any headers with SnpEff:
- * java -Xmx2g -jar GenomeAnalysisTK.jar \
- *   -R ref.fasta \
- *   -T SelectHeaders \
- *   --variant input.vcf \
- *   -o output.vcf \
- *   -hn FILTER \
- *   -hn FORMAT \
- *   -hn INFO \
- *   -he '.*SnpEff.*'
- *
- */ -@SuppressWarnings("unused") -@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) -public class SelectHeaders extends RodWalker implements TreeReducible { - @ArgumentCollection - protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); - - @Output(doc = "File to which variants should be written", required = true) - protected VariantContextWriter vcfWriter; - - @Argument(fullName = "header_name", shortName = "hn", doc = "Include header. Can be specified multiple times", required = false) - public Set headerNames; - - @Argument(fullName = "header_expression", shortName = "he", doc = "Regular expression to select many headers from the tracks provided. Can be specified multiple times", required = false) - public Set headerExpressions; - - /** - * Note that header exclusion takes precedence over inclusion, so that if a header is in both lists it will be excluded. - */ - @Argument(fullName = "exclude_header_name", shortName = "xl_hn", doc = "Exclude header. Can be specified multiple times", required = false) - public Set XLheaderNames; - - /** - * Note that interval name inclusion takes precedence over other header matching. If set other interval lines may be excluded but the intervals will still be added. - */ - @Argument(fullName = "include_interval_names", shortName = "iln", doc = "If set the interval file name minus the file extension, or the command line intervals, will be added to the headers", required = false) - public boolean includeIntervals; - - /** - * Note that engine header inclusion takes precedence over other header matching. If set other engine lines may be excluded but the intervals will still be added. - */ - @Hidden // TODO: Determine if others find this valuable and either remove @Hidden or remove -ieh. - @Argument(fullName = "include_engine_headers", shortName = "ieh", doc = "If set the headers normally output by the engine will be added to the headers", required = false) - public boolean includeEngineHeaders; - - private static final ListFileUtils.StringConverter headerKey = new ListFileUtils.StringConverter() { - @Override - public String convert(VCFHeaderLine value) { - return value.getKey(); - } - }; - - /** - * Set up the VCF writer, the header expressions and regexps - */ - @Override - public void initialize() { - // Get list of samples to include in the output - List rodNames = Arrays.asList(variantCollection.variants.getName()); - - Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); - Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger); - - headerLines.add(new VCFHeaderLine(VCFHeader.SOURCE_KEY, "SelectHeaders")); - - // Select only the headers requested by name or expression. - headerLines = new LinkedHashSet(getSelectedHeaders(headerLines)); - - // Optionally add in the intervals. - if (includeIntervals && getToolkit().getArguments().intervals != null) { - for (IntervalBinding intervalBinding : getToolkit().getArguments().intervals) { - String source = intervalBinding.getSource(); - if (source == null) - continue; - File file = new File(source); - if (file.exists()) { - headerLines.add(new VCFHeaderLine(VCFHeader.INTERVALS_KEY, FilenameUtils.getBaseName(file.getName()))); - } else { - headerLines.add(new VCFHeaderLine(VCFHeader.INTERVALS_KEY, source)); - } - } - } - - TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); - VCFHeader vcfHeader = new VCFHeader(headerLines, vcfSamples); - vcfHeader.setWriteEngineHeaders(includeEngineHeaders); - vcfWriter.writeHeader(vcfHeader); - } - - private Set getSelectedHeaders(Set headerLines) { - Set selectedHeaders = new TreeSet(); - if (headerNames == null && headerExpressions == null) { - // Include everything if nothing was explicitly included. - selectedHeaders.addAll(headerLines); - } else { - // Only include the selected headers. - if (headerNames != null) - selectedHeaders.addAll(ListFileUtils.includeMatching(headerLines, headerKey, headerNames, true)); - if (headerExpressions != null) - selectedHeaders.addAll(ListFileUtils.includeMatching(headerLines, headerKey, headerExpressions, false)); - } - - // Remove any excluded headers. - if (XLheaderNames != null) - selectedHeaders = ListFileUtils.excludeMatching(selectedHeaders, headerKey, XLheaderNames, true); - - // always include the contig lines - selectedHeaders = VCFUtils.withUpdatedContigsAsLines(selectedHeaders, getToolkit().getArguments().referenceFile, getToolkit().getMasterSequenceDictionary(), true); - return selectedHeaders; - } - - /** - * Pass through the VC record - * - * @param tracker the ROD tracker - * @param ref reference information - * @param context alignment info - * @return number of records processed - */ - @Override - public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - int count = 0; - if (tracker != null) { - Collection vcs = tracker.getValues(variantCollection.variants, context.getLocation()); - if (vcs != null) { - for (VariantContext vc : vcs) { - vcfWriter.add(vc); - count++; - } - } - } - return count; - } - - @Override - public Integer reduceInit() { - return 0; - } - - @Override - public Integer reduce(Integer value, Integer sum) { - return value + sum; - } - - @Override - public Integer treeReduce(Integer lhs, Integer rhs) { - return lhs + rhs; - } - - @Override - public void onTraversalDone(Integer result) { - logger.info(result + " records processed."); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java deleted file mode 100644 index f3e8167df..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ /dev/null @@ -1,205 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.gatk.walkers.variantutils; - -import org.broad.tribble.TribbleException; -import org.broadinstitute.sting.commandline.*; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; -import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.io.File; -import java.util.Arrays; -import java.util.Collection; -import java.util.HashSet; -import java.util.Set; - - -/** - * Validates a VCF file with an extra strict set of criteria. - * - *

- * ValidateVariants is a GATK tool that takes a VCF file and validates much of the information inside it. - * In addition to standard adherence to the VCF specification, this tool performs extra checks to make ensure - * the information contained within the file is correct. Checks include the correctness of the reference base(s), - * accuracy of AC & AN values, tests against rsIDs when a dbSNP file is provided, and that all alternate alleles - * are present in at least one sample. - * - * If you are looking simply to test the adherence to the VCF specification, use --validationType NONE. - * - *

Input

- *

- * A variant set to validate. - *

- * - *

Examples

- * 
- * java -Xmx2g -jar GenomeAnalysisTK.jar \
- *   -R ref.fasta \
- *   -T ValidateVariants \
- *   --variant input.vcf \
- *   --dbsnp dbsnp.vcf
- *
- * - */ -@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) -@Reference(window=@Window(start=0,stop=100)) -public class ValidateVariants extends RodWalker { - - @ArgumentCollection - protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); - - @ArgumentCollection - protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection(); - - public enum ValidationType { - ALL, REF, IDS, ALLELES, CHR_COUNTS, NONE - } - - @Argument(fullName = "validationType", shortName = "type", doc = "which validation type to run", required = false) - protected ValidationType type = ValidationType.ALL; - - /** - * By default, even filtered records are validated. - */ - @Argument(fullName = "doNotValidateFilteredRecords", shortName = "doNotValidateFilteredRecords", doc = "skip validation on filtered records", required = false) - 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; - - private long numErrors = 0; - - private File file = null; - - public void initialize() { - file = new File(variantCollection.variants.getSource()); - } - - public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( tracker == null ) - return 0; - - Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation()); - for ( VariantContext vc : VCs ) - validate(vc, tracker, ref); - - return VCs.size(); - } - - public Integer reduceInit() { return 0; } - - public Integer reduce(Integer value, Integer sum) { return sum+value; } - - public void onTraversalDone(Integer result) { - if ( numErrors == 0 ) - System.out.println("Successfully validated the input file. Checked " + result + " records with no failures."); - else - System.out.println("Found " + numErrors + " records with failures."); - } - - private void validate(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref) { - if ( DO_NOT_VALIDATE_FILTERED && vc.isFiltered() ) - return; - - // get the true reference allele - final Allele reportedRefAllele = vc.getReference(); - final int refLength = reportedRefAllele.length(); - if ( refLength > 100 ) { - logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", refLength, vc.getChr(), vc.getStart())); - return; - } - - final byte[] observedRefBases = new byte[refLength]; - System.arraycopy(ref.getBases(), 0, observedRefBases, 0, refLength); - final Allele observedRefAllele = Allele.create(observedRefBases); - - // get the RS IDs - Set rsIDs = null; - if ( tracker.hasValues(dbsnp.dbsnp) ) { - rsIDs = new HashSet(); - for ( VariantContext rsID : tracker.getValues(dbsnp.dbsnp, ref.getLocus()) ) - rsIDs.addAll(Arrays.asList(rsID.getID().split(VCFConstants.ID_FIELD_SEPARATOR))); - } - - try { - switch( type ) { - case ALL: - vc.extraStrictValidation(reportedRefAllele, observedRefAllele, rsIDs); - break; - case REF: - vc.validateReferenceBases(reportedRefAllele, observedRefAllele); - break; - case IDS: - vc.validateRSIDs(rsIDs); - break; - case ALLELES: - vc.validateAlternateAlleles(); - break; - case CHR_COUNTS: - vc.validateChromosomeCounts(); - break; - } - } catch (TribbleException e) { - if ( WARN_ON_ERROR ) { - numErrors++; - logger.warn("***** " + e.getMessage() + " *****"); - } else { - throw new UserException.FailsStrictValidation(file, e.getMessage()); - } - } - } -} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java deleted file mode 100644 index 28c20921e..000000000 --- a/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java +++ /dev/null @@ -1,180 +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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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.sting.utils.genotyper; - - -import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; - -import java.io.PrintStream; -import java.util.*; - -public class PerReadAlleleLikelihoodMap { - - public static final double INFORMATIVE_LIKELIHOOD_THRESHOLD = 0.2; - - protected List alleles; - protected Map> likelihoodReadMap; - - public PerReadAlleleLikelihoodMap() { - likelihoodReadMap = new LinkedHashMap>(); - alleles = new ArrayList(); - } - - public void add(GATKSAMRecord read, Allele a, Double likelihood) { - Map likelihoodMap; - if (likelihoodReadMap.containsKey(read)){ - // seen pileup element before - likelihoodMap = likelihoodReadMap.get(read); - } - else { - likelihoodMap = new HashMap(); - likelihoodReadMap.put(read,likelihoodMap); - } - likelihoodMap.put(a,likelihood); - - if (!alleles.contains(a)) - alleles.add(a); - - } - - public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { - return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log); - } - - public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) { - // special case removal of all or no reads - if ( downsamplingFraction <= 0.0 ) - return; - if ( downsamplingFraction >= 1.0 ) { - likelihoodReadMap.clear(); - return; - } - - // start by stratifying the reads by the alleles they represent at this position - final Map> alleleReadMap = new HashMap>(alleles.size()); - for ( Allele allele : alleles ) - alleleReadMap.put(allele, new ArrayList()); - - for ( Map.Entry> entry : likelihoodReadMap.entrySet() ) { - // do not remove reduced reads! - if ( !entry.getKey().isReducedRead() ) { - final Allele bestAllele = getMostLikelyAllele(entry.getValue()); - if ( bestAllele != Allele.NO_CALL ) - alleleReadMap.get(bestAllele).add(entry.getKey()); - } - } - - // compute the reads to remove and actually remove them - final List readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log); - for ( final GATKSAMRecord read : readsToRemove ) - likelihoodReadMap.remove(read); - } - - public int size() { - return likelihoodReadMap.size(); - } - - public void add(PileupElement p, Allele a, Double likelihood) { - add(p.getRead(), a, likelihood); - } - - public boolean containsPileupElement(PileupElement p) { - return likelihoodReadMap.containsKey(p.getRead()); - } - - public boolean isEmpty() { - return likelihoodReadMap.isEmpty(); - } - - public Map> getLikelihoodReadMap() { - return likelihoodReadMap; - } - public void clear() { - alleles.clear(); - likelihoodReadMap.clear(); - } - - public Set getStoredElements() { - return likelihoodReadMap.keySet(); - } - - public Collection> getLikelihoodMapValues() { - return likelihoodReadMap.values(); - } - - public int getNumberOfStoredElements() { - return likelihoodReadMap.size(); - } - - public Map getLikelihoodsAssociatedWithPileupElement(PileupElement p) { - if (!likelihoodReadMap.containsKey(p.getRead())) - return null; - - return likelihoodReadMap.get(p.getRead()); - } - - public static Allele getMostLikelyAllele( final Map alleleMap ) { - double maxLike = Double.NEGATIVE_INFINITY; - double prevMaxLike = Double.NEGATIVE_INFINITY; - Allele mostLikelyAllele = Allele.NO_CALL; - - for (final Map.Entry el : alleleMap.entrySet()) { - if (el.getValue() > maxLike) { - prevMaxLike = maxLike; - maxLike = el.getValue(); - mostLikelyAllele = el.getKey(); - } else if( el.getValue() > prevMaxLike ) { - prevMaxLike = el.getValue(); - } - } - return (maxLike - prevMaxLike > INFORMATIVE_LIKELIHOOD_THRESHOLD ? mostLikelyAllele : Allele.NO_CALL ); - } -} diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java index f6e63deec..c85072fa2 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java @@ -67,7 +67,7 @@ public class BQSRReadTransformer extends ReadTransformer { this.enabled = engine.hasBQSRArgumentSet(); if ( enabled ) { final BQSRArgumentSet args = engine.getBQSRArgumentSet(); - this.bqsr = new BaseRecalibration(args.getRecalFile(), args.getQuantizationLevels(), args.shouldDisableIndelQuals(), args.getPreserveQscoresLessThan(), args.shouldEmitOriginalQuals()); + this.bqsr = new BaseRecalibration(args.getRecalFile(), args.getQuantizationLevels(), args.shouldDisableIndelQuals(), args.getPreserveQscoresLessThan(), args.shouldEmitOriginalQuals(), args.getGlobalQScorePrior()); } final BQSRMode mode = WalkerManager.getWalkerAnnotation(walker, BQSRMode.class); return mode.ApplicationTime(); diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java index 828f91c6f..bb62cd74d 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -46,6 +46,7 @@ package org.broadinstitute.sting.utils.recalibration; +import com.google.java.contract.Ensures; import net.sf.samtools.SAMTag; import net.sf.samtools.SAMUtils; import org.apache.log4j.Logger; @@ -57,6 +58,8 @@ import org.broadinstitute.sting.utils.recalibration.covariates.Covariate; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.io.File; +import java.util.ArrayList; +import java.util.List; /** * Utility methods to facilitate on-the-fly base quality score recalibration. @@ -75,21 +78,18 @@ public class BaseRecalibration { private final boolean disableIndelQuals; private final int preserveQLessThan; + private final double globalQScorePrior; private final boolean emitOriginalQuals; - private final NestedIntegerArray globalDeltaQs; - private final NestedIntegerArray deltaQReporteds; - - /** * Constructor using a GATK Report file - * + * * @param RECAL_FILE a GATK Report file containing the recalibration information * @param quantizationLevels number of bins to quantize the quality scores * @param disableIndelQuals if true, do not emit base indel qualities * @param preserveQLessThan preserve quality scores less than this value */ - public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean emitOriginalQuals) { + public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean emitOriginalQuals, final double globalQScorePrior) { RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE); recalibrationTables = recalibrationReport.getRecalibrationTables(); @@ -102,45 +102,8 @@ public class BaseRecalibration { this.disableIndelQuals = disableIndelQuals; this.preserveQLessThan = preserveQLessThan; + this.globalQScorePrior = globalQScorePrior; this.emitOriginalQuals = emitOriginalQuals; - - logger.info("Calculating cached tables..."); - - // - // Create a NestedIntegerArray that maps from rgKey x errorModel -> double, - // where the double is the result of this calculation. The entire calculation can - // be done upfront, on initialization of this BaseRecalibration structure - // - final NestedIntegerArray byReadGroupTable = recalibrationTables.getReadGroupTable(); - globalDeltaQs = new NestedIntegerArray( byReadGroupTable.getDimensions() ); - logger.info("Calculating global delta Q table..."); - for ( NestedIntegerArray.Leaf leaf : byReadGroupTable.getAllLeaves() ) { - final int rgKey = leaf.keys[0]; - final int eventIndex = leaf.keys[1]; - final double globalDeltaQ = calculateGlobalDeltaQ(rgKey, EventType.eventFrom(eventIndex)); - globalDeltaQs.put(globalDeltaQ, rgKey, eventIndex); - } - - - // The calculation of the deltaQ report is constant. key[0] and key[1] are the read group and qual, respectively - // and globalDeltaQ is a constant for the read group. So technically the delta Q reported is simply a lookup - // into a matrix indexed by rgGroup, qual, and event type. - // the code below actually creates this cache with a NestedIntegerArray calling into the actual - // calculateDeltaQReported code. - final NestedIntegerArray byQualTable = recalibrationTables.getQualityScoreTable(); - deltaQReporteds = new NestedIntegerArray( byQualTable.getDimensions() ); - logger.info("Calculating delta Q reported table..."); - for ( NestedIntegerArray.Leaf leaf : byQualTable.getAllLeaves() ) { - final int rgKey = leaf.keys[0]; - final int qual = leaf.keys[1]; - final int eventIndex = leaf.keys[2]; - final EventType event = EventType.eventFrom(eventIndex); - final double globalDeltaQ = getGlobalDeltaQ(rgKey, event); - final double deltaQReported = calculateDeltaQReported(rgKey, qual, event, globalDeltaQ, (byte)qual); - deltaQReporteds.put(deltaQReported, rgKey, qual, eventIndex); - } - - logger.info("done calculating cache"); } /** @@ -187,29 +150,37 @@ public class BaseRecalibration { // the rg key is constant over the whole read, the global deltaQ is too final int rgKey = fullReadKeySet[0][0]; + final RecalDatum empiricalQualRG = recalibrationTables.getReadGroupTable().get(rgKey, errorModel.ordinal()); - final double globalDeltaQ = getGlobalDeltaQ(rgKey, errorModel); + if( empiricalQualRG != null ) { + final double epsilon = ( globalQScorePrior > 0.0 && errorModel.equals(EventType.BASE_SUBSTITUTION) ? globalQScorePrior : empiricalQualRG.getEstimatedQReported() ); - for (int offset = 0; offset < readLength; offset++) { // recalibrate all bases in the read - final byte origQual = quals[offset]; + for (int offset = 0; offset < readLength; offset++) { // recalibrate all bases in the read + final byte origQual = quals[offset]; - // only recalibrate usable qualities (the original quality will come from the instrument -- reported quality) - if ( origQual >= preserveQLessThan ) { - // get the keyset for this base using the error model - final int[] keySet = fullReadKeySet[offset]; - final double deltaQReported = getDeltaQReported(keySet[0], keySet[1], errorModel, globalDeltaQ); - final double deltaQCovariates = calculateDeltaQCovariates(recalibrationTables, keySet, errorModel, globalDeltaQ, deltaQReported, origQual); + // only recalibrate usable qualities (the original quality will come from the instrument -- reported quality) + if ( origQual >= preserveQLessThan ) { + // get the keyset for this base using the error model + final int[] keySet = fullReadKeySet[offset]; + final RecalDatum empiricalQualQS = recalibrationTables.getQualityScoreTable().get(keySet[0], keySet[1], errorModel.ordinal()); + final List empiricalQualCovs = new ArrayList(); + for (int i = 2; i < requestedCovariates.length; i++) { + if (keySet[i] < 0) { + continue; + } + empiricalQualCovs.add(recalibrationTables.getTable(i).get(keySet[0], keySet[1], keySet[i], errorModel.ordinal())); + } - // calculate the recalibrated qual using the BQSR formula - double recalibratedQualDouble = origQual + globalDeltaQ + deltaQReported + deltaQCovariates; + double recalibratedQualDouble = hierarchicalBayesianQualityEstimate( epsilon, empiricalQualRG, empiricalQualQS, empiricalQualCovs ); - // recalibrated quality is bound between 1 and MAX_QUAL - final byte recalibratedQual = QualityUtils.boundQual(MathUtils.fastRound(recalibratedQualDouble), QualityUtils.MAX_RECALIBRATED_Q_SCORE); + // recalibrated quality is bound between 1 and MAX_QUAL + final byte recalibratedQual = QualityUtils.boundQual(MathUtils.fastRound(recalibratedQualDouble), QualityUtils.MAX_RECALIBRATED_Q_SCORE); - // return the quantized version of the recalibrated quality - final byte recalibratedQualityScore = quantizationInfo.getQuantizedQuals().get(recalibratedQual); + // return the quantized version of the recalibrated quality + final byte recalibratedQualityScore = quantizationInfo.getQuantizedQuals().get(recalibratedQual); - quals[offset] = recalibratedQualityScore; + quals[offset] = recalibratedQualityScore; + } } } @@ -218,102 +189,15 @@ public class BaseRecalibration { } } - private double getGlobalDeltaQ(final int rgKey, final EventType errorModel) { - final Double cached = globalDeltaQs.get(rgKey, errorModel.ordinal()); - - if ( TEST_CACHING ) { - final double calcd = calculateGlobalDeltaQ(rgKey, errorModel); - if ( calcd != cached ) - throw new IllegalStateException("calculated " + calcd + " and cached " + cached + " global delta q not equal at " + rgKey + " / " + errorModel); + @Ensures("result > 0.0") + protected static double hierarchicalBayesianQualityEstimate( final double epsilon, final RecalDatum empiricalQualRG, final RecalDatum empiricalQualQS, final List empiricalQualCovs ) { + final double globalDeltaQ = ( empiricalQualRG == null ? 0.0 : empiricalQualRG.getEmpiricalQuality(epsilon) - epsilon ); + final double deltaQReported = ( empiricalQualQS == null ? 0.0 : empiricalQualQS.getEmpiricalQuality(globalDeltaQ + epsilon) - (globalDeltaQ + epsilon) ); + double deltaQCovariates = 0.0; + for( final RecalDatum empiricalQualCov : empiricalQualCovs ) { + deltaQCovariates += ( empiricalQualCov == null ? 0.0 : empiricalQualCov.getEmpiricalQuality(deltaQReported + globalDeltaQ + epsilon) - (deltaQReported + globalDeltaQ + epsilon) ); } - return cachedWithDefault(cached); - } - - private double getDeltaQReported(final int rgKey, final int qualKey, final EventType errorModel, final double globalDeltaQ) { - final Double cached = deltaQReporteds.get(rgKey, qualKey, errorModel.ordinal()); - - if ( TEST_CACHING ) { - final double calcd = calculateDeltaQReported(rgKey, qualKey, errorModel, globalDeltaQ, (byte)qualKey); - if ( calcd != cached ) - throw new IllegalStateException("calculated " + calcd + " and cached " + cached + " global delta q not equal at " + rgKey + " / " + qualKey + " / " + errorModel); - } - - return cachedWithDefault(cached); - } - - /** - * @param d a Double (that may be null) that is the result of a delta Q calculation - * @return a double == d if d != null, or 0.0 if it is - */ - private double cachedWithDefault(final Double d) { - return d == null ? 0.0 : d; - } - - /** - * Note that this calculation is a constant for each rgKey and errorModel. We need only - * compute this value once for all data. - * - * @param rgKey read group key - * @param errorModel the event type - * @return global delta Q - */ - private double calculateGlobalDeltaQ(final int rgKey, final EventType errorModel) { - double result = 0.0; - - final RecalDatum empiricalQualRG = recalibrationTables.getReadGroupTable().get(rgKey, errorModel.ordinal()); - - if (empiricalQualRG != null) { - final double globalDeltaQEmpirical = empiricalQualRG.getEmpiricalQuality(); - final double aggregrateQReported = empiricalQualRG.getEstimatedQReported(); - result = globalDeltaQEmpirical - aggregrateQReported; - } - - return result; - } - - private double calculateDeltaQReported(final int rgKey, final int qualKey, final EventType errorModel, final double globalDeltaQ, final byte qualFromRead) { - double result = 0.0; - - final RecalDatum empiricalQualQS = recalibrationTables.getQualityScoreTable().get(rgKey, qualKey, errorModel.ordinal()); - if (empiricalQualQS != null) { - final double deltaQReportedEmpirical = empiricalQualQS.getEmpiricalQuality(); - result = deltaQReportedEmpirical - qualFromRead - globalDeltaQ; - } - - return result; - } - - private double calculateDeltaQCovariates(final RecalibrationTables recalibrationTables, final int[] key, final EventType errorModel, final double globalDeltaQ, final double deltaQReported, final byte qualFromRead) { - double result = 0.0; - - // for all optional covariates - for (int i = 2; i < requestedCovariates.length; i++) { - if (key[i] < 0) - continue; - - result += calculateDeltaQCovariate(recalibrationTables.getTable(i), - key[0], key[1], key[i], errorModel, - globalDeltaQ, deltaQReported, qualFromRead); - } - - return result; - } - - private double calculateDeltaQCovariate(final NestedIntegerArray table, - final int rgKey, - final int qualKey, - final int tableKey, - final EventType errorModel, - final double globalDeltaQ, - final double deltaQReported, - final byte qualFromRead) { - final RecalDatum empiricalQualCO = table.get(rgKey, qualKey, tableKey, errorModel.ordinal()); - if (empiricalQualCO != null) { - final double deltaQCovariateEmpirical = empiricalQualCO.getEmpiricalQuality(); - return deltaQCovariateEmpirical - qualFromRead - (globalDeltaQ + deltaQReported); - } else { - return 0.0; - } + return epsilon + globalDeltaQ + deltaQReported + deltaQCovariates; } } diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index 9430caaac..be537f294 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -77,6 +77,7 @@ import com.google.java.contract.Requires; import org.apache.commons.math.optimization.fitting.GaussianFunction; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** @@ -180,6 +181,7 @@ public class RecalDatum { if ( Double.isNaN(estimatedQReported) ) throw new IllegalArgumentException("estimatedQReported is NaN"); this.estimatedQReported = estimatedQReported; + empiricalQuality = UNINITIALIZED; } public final double getEstimatedQReported() { @@ -199,7 +201,7 @@ public class RecalDatum { * Returns the error rate (in real space) of this interval, or 0 if there are no observations * @return the empirical error rate ~= N errors / N obs */ - @Ensures("result >= 0.0") + @Ensures({"result >= 0.0"}) public double getEmpiricalErrorRate() { if ( numObservations == 0 ) return 0.0; @@ -221,8 +223,13 @@ public class RecalDatum { } public final double getEmpiricalQuality() { - if (empiricalQuality == UNINITIALIZED) - calcEmpiricalQuality(); + return getEmpiricalQuality(getEstimatedQReported()); + } + + public synchronized final double getEmpiricalQuality(final double conditionalPrior) { + if (empiricalQuality == UNINITIALIZED) { + calcEmpiricalQuality(conditionalPrior); + } return empiricalQuality; } @@ -319,13 +326,13 @@ public class RecalDatum { */ @Requires("empiricalQuality == UNINITIALIZED") @Ensures("empiricalQuality != UNINITIALIZED") - private synchronized void calcEmpiricalQuality() { + private synchronized void calcEmpiricalQuality(final double conditionalPrior) { // smoothing is one error and one non-error observation final long mismatches = (long)(getNumMismatches() + 0.5) + SMOOTHING_CONSTANT; final long observations = getNumObservations() + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT; - final double empiricalQual = RecalDatum.bayesianEstimateOfEmpiricalQuality(observations, mismatches, getEstimatedQReported()); + final double empiricalQual = RecalDatum.bayesianEstimateOfEmpiricalQuality(observations, mismatches, conditionalPrior); // This is the old and busted point estimate approach: //final double empiricalQual = -10 * Math.log10(getEmpiricalErrorRate()); diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java index 4cde2916d..f7c3440e4 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java @@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.recalibration.covariates.*; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.R.RScriptExecutor; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.classloader.PluginManager; @@ -310,7 +310,7 @@ public class RecalUtils { if(sortByCols) { reportTable = new GATKReportTable("RecalTable" + reportTableIndex++, "", columnNames.size(), GATKReportTable.TableSortingWay.SORT_BY_COLUMN); } else { - reportTable = new GATKReportTable("RecalTable" + reportTableIndex++, "", columnNames.size()); + reportTable = new GATKReportTable("RecalTable" + reportTableIndex++, "", columnNames.size(), GATKReportTable.TableSortingWay.DO_NOT_SORT); } for (final Pair columnName : columnNames) reportTable.addColumn(columnName.getFirst(), columnName.getSecond()); @@ -477,7 +477,7 @@ public class RecalUtils { } } - private static List generateValuesFromKeys(final List keys, final Covariate[] covariates, final Map covariateNameMap) { + protected static List generateValuesFromKeys(final List keys, final Covariate[] covariates, final Map covariateNameMap) { final List values = new ArrayList(4); values.add(covariates[RecalibrationTables.TableType.READ_GROUP_TABLE.ordinal()].formatKey((Integer)keys.get(0))); final int covariateIndex = (Integer)keys.get(1); diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java index 3ecc41109..f10c26ddc 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java @@ -131,7 +131,7 @@ public class RecalibrationReport { * Combines two recalibration reports by adding all observations and errors * * Note: This method DOES NOT recalculate the empirical qualities and quantized qualities. You have to recalculate - * them after combining. The reason for not calculating it is because this function is inteded for combining a + * them after combining. The reason for not calculating it is because this function is intended for combining a * series of recalibration reports, and it only makes sense to calculate the empirical qualities and quantized * qualities after all the recalibration reports have been combined. Having the user recalculate when appropriate, * makes this method faster @@ -246,7 +246,7 @@ public class RecalibrationReport { private RecalDatum getRecalDatum(final GATKReportTable reportTable, final int row, final boolean hasEstimatedQReportedColumn) { final long nObservations = asLong(reportTable.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME)); final double nErrors = asDouble(reportTable.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME)); - final double empiricalQuality = asDouble(reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME)); + //final double empiricalQuality = asDouble(reportTable.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME)); // the estimatedQreported column only exists in the ReadGroup table final double estimatedQReported = hasEstimatedQReportedColumn ? @@ -255,7 +255,7 @@ public class RecalibrationReport { final RecalDatum datum = new RecalDatum(nObservations, nErrors, (byte)1); datum.setEstimatedQReported(estimatedQReported); - datum.setEmpiricalQuality(empiricalQuality); + //datum.setEmpiricalQuality(empiricalQuality); // don't set the value here because we will want to recompute with a different conditional Q score prior value return datum; } diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java index 66c74d667..4fc9470f4 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java @@ -48,7 +48,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java index 0578ac60c..bccaea827 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java @@ -48,7 +48,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates; import org.broadinstitute.sting.utils.recalibration.ReadCovariates; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java new file mode 100644 index 000000000..9672bc5f3 --- /dev/null +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java @@ -0,0 +1,275 @@ +/* +* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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. 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LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012 Broad Institute, Inc. +* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 4. 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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. +* +* 6. 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. +* +* 7. MISCELLANEOUS +* 7.1 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. +* 7.2 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. +* 7.3 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. +* 7.4 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. +* 7.5 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. +* 7.6 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. +* 7.7 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.sting.utils.recalibration.covariates; + +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.ReadCovariates; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.collections.Pair; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.Map; +import java.util.Set; + +public abstract class RepeatCovariate implements ExperimentalCovariate { + protected int MAX_REPEAT_LENGTH; + protected int MAX_STR_UNIT_LENGTH; + private final HashMap repeatLookupTable = new HashMap(); + private final HashMap repeatReverseLookupTable = new HashMap(); + private int nextId = 0; + + // Initialize any member variables using the command-line arguments passed to the walkers + @Override + public void initialize(final RecalibrationArgumentCollection RAC) { + MAX_STR_UNIT_LENGTH = RAC.MAX_STR_UNIT_LENGTH; + MAX_REPEAT_LENGTH = RAC.MAX_REPEAT_LENGTH; + } + + @Override + public void recordValues(final GATKSAMRecord read, final ReadCovariates values) { + // store the original bases and then write Ns over low quality ones + final byte[] originalBases = read.getReadBases().clone(); + + final boolean negativeStrand = read.getReadNegativeStrandFlag(); + byte[] bases = read.getReadBases(); + if (negativeStrand) + bases = BaseUtils.simpleReverseComplement(bases); + + // don't record reads with N's + if (!BaseUtils.isAllRegularBases(bases)) + return; + + for (int i = 0; i < bases.length; i++) { + final Pair res = findTandemRepeatUnits(bases, i); + // to merge repeat unit and repeat length to get covariate value: + final String repeatID = getCovariateValueFromUnitAndLength(res.first, res.second); + final int key = keyForRepeat(repeatID); + + final int readOffset = (negativeStrand ? bases.length - i - 1 : i); + values.addCovariate(key, key, key, readOffset); + } + + // put the original bases back in + read.setReadBases(originalBases); + + } + + private Pair findTandemRepeatUnits(byte[] readBases, int offset) { + int maxBW = 0; + byte[] bestBWRepeatUnit = new byte[]{readBases[offset]}; + for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) { + // fix repeat unit length + //edge case: if candidate tandem repeat unit falls beyond edge of read, skip + if (offset+1-str < 0) + break; + + // get backward repeat unit and # repeats + byte[] backwardRepeatUnit = Arrays.copyOfRange(readBases, offset - str + 1, offset + 1); + maxBW = GATKVariantContextUtils.findNumberofRepetitions(backwardRepeatUnit, Arrays.copyOfRange(readBases, 0, offset + 1), false); + if (maxBW > 1) { + bestBWRepeatUnit = backwardRepeatUnit.clone(); + break; + } + } + byte[] bestRepeatUnit = bestBWRepeatUnit; + int maxRL = maxBW; + + if (offset < readBases.length-1) { + byte[] bestFWRepeatUnit = new byte[]{readBases[offset+1]}; + int maxFW = 0; + for (int str = 1; str <= MAX_STR_UNIT_LENGTH; str++) { + // fix repeat unit length + //edge case: if candidate tandem repeat unit falls beyond edge of read, skip + if (offset+str+1 > readBases.length) + break; + + // get forward repeat unit and # repeats + byte[] forwardRepeatUnit = Arrays.copyOfRange(readBases, offset +1, offset+str+1); + maxFW = GATKVariantContextUtils.findNumberofRepetitions(forwardRepeatUnit, Arrays.copyOfRange(readBases, offset + 1, readBases.length), true); + if (maxFW > 1) { + bestFWRepeatUnit = forwardRepeatUnit.clone(); + break; + } + } + // if FW repeat unit = BW repeat unit it means we're in the middle of a tandem repeat - add FW and BW components + if (Arrays.equals(bestFWRepeatUnit, bestBWRepeatUnit)) { + maxRL = maxBW + maxFW; + bestRepeatUnit = bestFWRepeatUnit; // arbitrary + } + else { + // tandem repeat starting forward from current offset. + // It could be the case that best BW unit was differnet from FW unit, but that BW still contains FW unit. + // For example, TTCTT(C) CCC - at (C) place, best BW unit is (TTC)2, best FW unit is (C)3. + // but correct representation at that place might be (C)4. + // Hence, if the FW and BW units don't match, check if BW unit can still be a part of FW unit and add + // representations to total + maxBW = GATKVariantContextUtils.findNumberofRepetitions(bestFWRepeatUnit, Arrays.copyOfRange(readBases, 0, offset + 1), false); + maxRL = maxFW + maxBW; + bestRepeatUnit = bestFWRepeatUnit; + + } + + } + + + + if(maxRL > MAX_REPEAT_LENGTH) { maxRL = MAX_REPEAT_LENGTH; } + return new Pair(bestRepeatUnit, maxRL); + + } + @Override + public final Object getValue(final String str) { + return str; + } + + @Override + public synchronized String formatKey(final int key) { + // This method is synchronized so that we don't attempt to do a get() + // from the reverse lookup table while that table is being updated + return repeatReverseLookupTable.get(key); + } + + @Requires({"repeatLength>=0", "repeatFromUnitAndLength != null"}) + @Ensures("result != null") + protected abstract String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength); + + + @Override + public int keyFromValue(final Object value) { + return keyForRepeat((String) value); + } + + /** + * Get the mapping from read group names to integer key values for all read groups in this covariate + * @return a set of mappings from read group names -> integer key values + */ + public Set> getKeyMap() { + return repeatLookupTable.entrySet(); + } + + private int keyForRepeat(final String repeatID) { + // Rather than synchronize this entire method (which would be VERY expensive for walkers like the BQSR), + // synchronize only the table updates. + + // Before entering the synchronized block, check to see if this read group is not in our tables. + // If it's not, either we will have to insert it, OR another thread will insert it first. + // This preliminary check avoids doing any synchronization most of the time. + if ( ! repeatLookupTable.containsKey(repeatID) ) { + + synchronized ( this ) { + + // Now we need to make sure the key is STILL not there, since another thread may have come along + // and inserted it while we were waiting to enter this synchronized block! + if ( ! repeatLookupTable.containsKey(repeatID) ) { + repeatLookupTable.put(repeatID, nextId); + repeatReverseLookupTable.put(nextId, repeatID); + nextId++; + } + } + } + + return repeatLookupTable.get(repeatID); + } + + + /** + * Splits repeat unit and num repetitions from covariate value. + * For example, if value if "ATG4" it returns (ATG,4) + * @param value Covariate value + * @return Split pair + */ + @Requires("value != null") + @Ensures({"result.first != null","result.second>=0"}) + public static Pair getRUandNRfromCovariate(final String value) { + + int k = 0; + for ( k=0; k < value.length(); k++ ) { + if (!BaseUtils.isRegularBase(value.getBytes()[k])) + break; + } + Integer nr = Integer.valueOf(value.substring(k,value.length())); // will throw NumberFormatException if format illegal + if (k == value.length() || nr <= 0) + throw new IllegalStateException("Covariate is not of form (Repeat Unit) + Integer"); + + return new Pair(value.substring(0,k), nr); + } + + /** + * Gets bases from tandem repeat representation (Repeat Unit),(Number of Repeats). + * For example, (AGC),3 returns AGCAGCAGC + * @param repeatUnit Tandem repeat unit + * @param numRepeats Number of repeats + * @return Expanded String + */ + @Requires({"numRepeats > 0","repeatUnit != null"}) + @Ensures("result != null") + public static String getBasesFromRUandNR(final String repeatUnit, final int numRepeats) { + final StringBuilder sb = new StringBuilder(); + + for (int i=0; i < numRepeats; i++) + sb.append(repeatUnit); + + return sb.toString(); + } + + // version given covariate key + public static String getBasesFromRUandNR(final String covariateValue) { + Pair pair = getRUandNRfromCovariate(covariateValue); + return getBasesFromRUandNR(pair.getFirst(), pair.getSecond()); + } + + @Override + public abstract int maximumKeyValue(); + + + +} diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java index 6586782b8..48f3d4b60 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java @@ -46,63 +46,24 @@ package org.broadinstitute.sting.utils.recalibration.covariates; -import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.recalibration.ReadCovariates; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; -import java.util.Arrays; +public class RepeatLengthCovariate extends RepeatCovariate { -/** - * Created with IntelliJ IDEA. - * User: rpoplin - * Date: 11/3/12 - */ - -public class RepeatLengthCovariate implements ExperimentalCovariate { - final int MAX_REPEAT_LENGTH = 20; - - // Initialize any member variables using the command-line arguments passed to the walkers - @Override - public void initialize(final RecalibrationArgumentCollection RAC) {} - - @Override - public void recordValues(final GATKSAMRecord read, final ReadCovariates values) { - byte[] readBytes = read.getReadBases(); - for (int i = 0; i < readBytes.length; i++) { - int maxRL = 0; - for (int str = 1; str <= 8; str++) { - if (i + str <= readBytes.length) { - maxRL = Math.max(maxRL, GATKVariantContextUtils.findNumberofRepetitions( - Arrays.copyOfRange(readBytes, i, i + str), - Arrays.copyOfRange(readBytes, i, readBytes.length) - )); - } - } - if(maxRL > MAX_REPEAT_LENGTH) { maxRL = MAX_REPEAT_LENGTH; } - values.addCovariate(maxRL, maxRL, maxRL, i); - } - } - - // Used to get the covariate's value from input csv file during on-the-fly recalibration - @Override - public final Object getValue(final String str) { - return Byte.parseByte(str); + @Requires({"repeatLength>=0", "repeatFromUnitAndLength != null"}) + @Ensures("result != null") + protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) { + return String.format("%d",repeatLength); } @Override - public String formatKey(final int key) { - return String.format("%d", key); - } - - @Override - public int keyFromValue(final Object value) { - return (value instanceof String) ? Integer.parseInt((String) value) : (Integer) value; - } - - @Override - public int maximumKeyValue() { - return MAX_REPEAT_LENGTH + 1; + public synchronized int maximumKeyValue() { + // Synchronized so that we don't query table size while the tables are being updated + //return repeatLookupTable.size() - 1; + // max possible values of covariate: for repeat unit, length is up to MAX_STR_UNIT_LENGTH, + // so we have 4^MAX_STR_UNIT_LENGTH * MAX_REPEAT_LENGTH possible values + return (1+MAX_REPEAT_LENGTH); } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java similarity index 89% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java index 0609260f0..c4fdaad8b 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java @@ -44,29 +44,27 @@ * 7.7 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.sting.gatk.walkers.varianteval.stratifications; +package org.broadinstitute.sting.utils.recalibration.covariates; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.variant.variantcontext.VariantContext; - -import java.util.Collections; -import java.util.List; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; -/** - * Required stratification grouping output by each comp ROD - */ -public class CompRod extends VariantStratifier implements RequiredStratification { +public class RepeatUnitAndLengthCovariate extends RepeatCovariate { + + @Requires({"repeatLength>=0", "repeatFromUnitAndLength != null"}) + @Ensures("result != null") + protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) { + return new String(repeatFromUnitAndLength) + String.format("%d",repeatLength); + } + @Override - public void initialize() { - for ( RodBinding rod : getVariantEvalWalker().getComps() ) { - states.add(rod.getName()); - } + public synchronized int maximumKeyValue() { + // Synchronized so that we don't query table size while the tables are being updated + //return repeatLookupTable.size() - 1; + // max possible values of covariate: for repeat unit, length is up to MAX_STR_UNIT_LENGTH, + // so we have 4^MAX_STR_UNIT_LENGTH * MAX_REPEAT_LENGTH possible values + return (1<<(2*MAX_STR_UNIT_LENGTH)) * MAX_REPEAT_LENGTH +1; } - public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { - return Collections.singletonList((Object)compName); - } } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java similarity index 91% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java index 74020ed18..ef0d3fc62 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java @@ -44,23 +44,30 @@ * 7.7 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.sting.gatk.walkers.varianteval.util; +package org.broadinstitute.sting.utils.recalibration.covariates; -import org.apache.commons.jexl2.Expression; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; +/** + * Created with IntelliJ IDEA. + * User: rpoplin + * Date: 11/3/12 + */ + +public class RepeatUnitCovariate extends RepeatCovariate { + + protected String getCovariateValueFromUnitAndLength(final byte[] repeatFromUnitAndLength, final int repeatLength) { + return new String(repeatFromUnitAndLength); -public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable { - /** - * Create a new matcher expression with name and JEXL expression exp - * - * @param name name - * @param exp expression - */ - public SortableJexlVCMatchExp(String name, Expression exp) { - super(name, exp); } - public int compareTo(SortableJexlVCMatchExp sortableJexlVCMatchExp) { - return this.name.compareTo(sortableJexlVCMatchExp.name); + + @Override + public synchronized int maximumKeyValue() { + // Synchronized so that we don't query table size while the tables are being updated + //return repeatLookupTable.size() - 1; + // max possible values of covariate: for repeat unit, length is up to MAX_STR_UNIT_LENGTH, + // so we have 4^MAX_STR_UNIT_LENGTH * MAX_REPEAT_LENGTH possible values + return (1<<(2*MAX_STR_UNIT_LENGTH)) +1; } + + } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java index 2815599d9..f82f24439 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java @@ -125,19 +125,19 @@ public class BQSRGathererUnitTest extends BaseTest { testTablesWithColumns(originalTable, calculatedTable, columnsToTest); // test the RecalTable0 table - columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); + columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.ESTIMATED_Q_REPORTED_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); originalTable = originalReport.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE); calculatedTable = calculatedReport.getTable(RecalUtils.READGROUP_REPORT_TABLE_TITLE); testTablesWithColumns(originalTable, calculatedTable, columnsToTest); // test the RecalTable1 table - columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.QUALITY_SCORE_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); + columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.QUALITY_SCORE_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); originalTable = originalReport.getTable(RecalUtils.QUALITY_SCORE_REPORT_TABLE_TITLE); calculatedTable = calculatedReport.getTable(RecalUtils.QUALITY_SCORE_REPORT_TABLE_TITLE); testTablesWithColumns(originalTable, calculatedTable, columnsToTest); // test the RecalTable2 table - columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.QUALITY_SCORE_COLUMN_NAME, RecalUtils.COVARIATE_VALUE_COLUMN_NAME, RecalUtils.COVARIATE_NAME_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); + columnsToTest = Arrays.asList(RecalUtils.READGROUP_COLUMN_NAME, RecalUtils.QUALITY_SCORE_COLUMN_NAME, RecalUtils.COVARIATE_VALUE_COLUMN_NAME, RecalUtils.COVARIATE_NAME_COLUMN_NAME, RecalUtils.EVENT_TYPE_COLUMN_NAME, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME, RecalUtils.NUMBER_ERRORS_COLUMN_NAME); originalTable = originalReport.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE); calculatedTable = calculatedReport.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE); testTablesWithColumns(originalTable, calculatedTable, columnsToTest); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java index b8a409d2f..f7907649d 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java @@ -188,12 +188,12 @@ public class BQSRIntegrationTest extends WalkerTest { public Object[][] createPRTestData() { List tests = new ArrayList(); - tests.add(new Object[]{1, new PRTest(" -qq -1", "5226c06237b213b9e9b25a32ed92d09a")}); - tests.add(new Object[]{1, new PRTest(" -qq 6", "b592a5c62b952a012e18adb898ea9c33")}); - tests.add(new Object[]{1, new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")}); + tests.add(new Object[]{1, new PRTest(" -qq -1", "fcc136b877fbde38791533b0f1ae39e4")}); + tests.add(new Object[]{1, new PRTest(" -qq 6", "f21b537c1689b8051b878ea5cc9b61a0")}); + tests.add(new Object[]{1, new PRTest(" -DIQ", "1d04a242bf825177d6a45eff9fbed647")}); for ( final int nct : Arrays.asList(1, 2, 4) ) { - tests.add(new Object[]{nct, new PRTest("", "ab2f209ab98ad3432e208cbd524a4c4a")}); + tests.add(new Object[]{nct, new PRTest("", "b6f343ac69c63cdb49205c13e67297fc")}); } return tests.toArray(new Object[][]{}); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElementUnitTest.java similarity index 68% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElementUnitTest.java index a3ebb132f..b6af954a0 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElementUnitTest.java @@ -46,74 +46,89 @@ package org.broadinstitute.sting.gatk.walkers.compression.reducereads; -import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.SortedSet; +import org.broadinstitute.sting.BaseTest; +import org.testng.Assert; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; -/** - * GenomeLocs are very useful objects to keep track of genomic locations and perform set operations - * with them. - * - * However, GenomeLocs are bound to strict validation through the GenomeLocParser and cannot - * be created easily for small tasks that do not require the rigors of the GenomeLocParser validation - * - * SimpleGenomeLoc is a simple utility to create GenomeLocs without going through the parser. Should - * only be used outside of the engine. - * - * User: carneiro - * Date: 10/16/12 - * Time: 2:07 PM - */ -public class SimpleGenomeLoc extends GenomeLoc { - private boolean finished; +import java.util.ArrayList; +import java.util.List; - public SimpleGenomeLoc(String contigName, int contigIndex, int start, int stop, boolean finished) { - super(contigName, contigIndex, start, stop); - this.finished = finished; +public class HeaderElementUnitTest extends BaseTest { + + private class HETest { + public byte base, baseQual, insQual, delQual; + public int MQ; + public boolean isClip; + + private HETest(final byte base, final byte baseQual, final byte insQual, final byte delQual, final int MQ, final boolean isClip) { + this.base = base; + this.baseQual = baseQual; + this.insQual = insQual; + this.delQual = delQual; + this.MQ = MQ; + this.isClip = isClip; + } } - public boolean isFinished() { - return finished; + private static final byte byteA = (byte)'A'; + private static final byte byte10 = (byte)10; + private static final byte byte20 = (byte)20; + private static final int minBaseQual = 20; + private static final int minMappingQual = 20; + + @DataProvider(name = "data") + public Object[][] createData() { + List tests = new ArrayList(); + + tests.add(new Object[]{new HETest(byteA, byte20, byte20, byte20, 20, false)}); + tests.add(new Object[]{new HETest(byteA, byte10, byte20, byte20, 20, false)}); + tests.add(new Object[]{new HETest(byteA, byte20, byte20, byte20, 10, false)}); + tests.add(new Object[]{new HETest(byteA, byte20, byte20, byte20, 20, true)}); + + return tests.toArray(new Object[][]{}); } - @Requires("a != null && b != null") - public static SimpleGenomeLoc merge(SimpleGenomeLoc a, SimpleGenomeLoc b) throws ReviewedStingException { - if(GenomeLoc.isUnmapped(a) || GenomeLoc.isUnmapped(b)) { - throw new ReviewedStingException("Tried to merge unmapped genome locs"); - } + @Test(dataProvider = "data", enabled = true) + public void testHE(HETest test) { - if (!(a.contiguousP(b))) { - throw new ReviewedStingException("The two genome locs need to be contiguous"); - } + HeaderElement headerElement = new HeaderElement(1000, 0); + // first test that if we add and then remove it, we have no data + headerElement.addBase(test.base, test.baseQual, test.insQual, test.delQual, test.MQ, minBaseQual, minMappingQual, test.isClip); + headerElement.addInsertionToTheRight(); + headerElement.removeBase(test.base, test.baseQual, test.insQual, test.delQual, test.MQ, minBaseQual, minMappingQual, test.isClip); + headerElement.removeInsertionToTheRight(); + testHeaderIsEmpty(headerElement); - return new SimpleGenomeLoc(a.getContig(), a.contigIndex, - Math.min(a.getStart(), b.getStart()), - Math.max(a.getStop(), b.getStop()), - a.isFinished()); + // now, test that the data was added as expected + for ( int i = 0; i < 10; i++ ) + headerElement.addBase(test.base, test.baseQual, test.insQual, test.delQual, test.MQ, minBaseQual, minMappingQual, test.isClip); + testHeaderData(headerElement, test); + + // test the insertion adding functionality + for ( int i = 0; i < 10; i++ ) + headerElement.addInsertionToTheRight(); + Assert.assertEquals(headerElement.numInsertionsToTheRight(), 10); } - /** - * Merges a list of *sorted* *contiguous* locs into one - * - * @param sortedLocs a sorted list of contiguous locs - * @return one merged loc - */ - public static SimpleGenomeLoc merge(SortedSet sortedLocs) { - SimpleGenomeLoc previousLoc = null; - for (SimpleGenomeLoc loc : sortedLocs) { - if (loc.isUnmapped()) { - throw new ReviewedStingException("Tried to merge unmapped genome locs"); - } - if (previousLoc != null && !previousLoc.contiguousP(loc)) { - throw new ReviewedStingException("The genome locs need to be contiguous"); - } - previousLoc = loc; - } - SimpleGenomeLoc firstLoc = sortedLocs.first(); - SimpleGenomeLoc lastLoc = sortedLocs.last(); - return merge(firstLoc, lastLoc); + private void testHeaderIsEmpty(final HeaderElement headerElement) { + Assert.assertFalse(headerElement.hasConsensusData()); + Assert.assertFalse(headerElement.hasFilteredData()); + Assert.assertFalse(headerElement.hasInsertionToTheRight()); + Assert.assertTrue(headerElement.isEmpty()); + Assert.assertEquals(headerElement.getRMS(), 0.0); + } + + private void testHeaderData(final HeaderElement headerElement, final HETest test) { + Assert.assertEquals(headerElement.getRMS(), (double)test.MQ); + Assert.assertEquals(headerElement.isVariantFromSoftClips(), test.isClip); + Assert.assertFalse(headerElement.isEmpty()); + Assert.assertFalse(headerElement.hasInsertionToTheRight()); + Assert.assertEquals(headerElement.hasConsensusData(), headerElement.basePassesFilters(test.baseQual, minBaseQual, test.MQ, minMappingQual)); + Assert.assertEquals(headerElement.hasFilteredData(), !headerElement.basePassesFilters(test.baseQual, minBaseQual, test.MQ, minMappingQual)); + Assert.assertFalse(headerElement.isVariantFromMismatches(0.05)); + Assert.assertEquals(headerElement.isVariant(0.05, 0.05), test.isClip); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java new file mode 100644 index 000000000..ea3544351 --- /dev/null +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java @@ -0,0 +1,439 @@ +/* +* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. +* 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. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012 Broad Institute, Inc. +* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 4. 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. +* +* 5. 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. +* +* 6. 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. +* +* 7. MISCELLANEOUS +* 7.1 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. +* 7.2 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. +* 7.3 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. +* 7.4 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. +* 7.5 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. +* 7.6 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. +* 7.7 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.sting.gatk.walkers.compression.reducereads; + +import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.samtools.SAMFileHeader; +import org.apache.commons.lang.ArrayUtils; +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Set; + +public class SlidingWindowUnitTest extends BaseTest { + + private static final int variantRegionLength = 1000; + private static final int globalStartPosition = 1000000; + + private static boolean[] createBitset(final List locs) { + final boolean[] variantRegionBitset = new boolean[variantRegionLength]; + for ( FinishedGenomeLoc loc : locs ) { + final int stop = loc.getStop() - globalStartPosition; + for ( int i = loc.getStart() - globalStartPosition; i <= stop; i++ ) + variantRegionBitset[i] = true; + } + return variantRegionBitset; + } + + ////////////////////////////////////////////////////////////////////////////////////// + //// This section tests the findVariantRegions() method and related functionality //// + ////////////////////////////////////////////////////////////////////////////////////// + + private static final FinishedGenomeLoc loc90to95 = new FinishedGenomeLoc("1", 0, 1000090, 1000095, false); + private static final FinishedGenomeLoc loc96to99 = new FinishedGenomeLoc("1", 0, 1000096, 1000099, false); + private static final FinishedGenomeLoc loc100to110 = new FinishedGenomeLoc("1", 0, 1000100, 1000110, false); + private static final FinishedGenomeLoc loc999 = new FinishedGenomeLoc("1", 0, 1000999, 1000999, false); + + private class FindVariantRegionsTest { + public List locs, expectedResult; + public boolean[] variantRegionBitset; + + private FindVariantRegionsTest(final List locs) { + this.locs = locs; + this.expectedResult = locs; + variantRegionBitset = createBitset(locs); + } + + private FindVariantRegionsTest(final List locs, final List expectedResult) { + this.locs = locs; + this.expectedResult = expectedResult; + variantRegionBitset = createBitset(locs); + } + } + + @DataProvider(name = "findVariantRegions") + public Object[][] createFindVariantRegionsData() { + List tests = new ArrayList(); + + tests.add(new Object[]{new FindVariantRegionsTest(Arrays.asList(loc90to95))}); + tests.add(new Object[]{new FindVariantRegionsTest(Arrays.asList(loc90to95, loc100to110))}); + tests.add(new Object[]{new FindVariantRegionsTest(Arrays.asList(loc90to95, loc96to99, loc100to110), Arrays.asList(new FinishedGenomeLoc("1", 0, 1000090, 1000110, false)))}); + tests.add(new Object[]{new FindVariantRegionsTest(Arrays.asList(loc90to95, loc999))}); + tests.add(new Object[]{new FindVariantRegionsTest(Arrays.asList(loc999))}); + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "findVariantRegions", enabled = true) + public void testFindVariantRegions(FindVariantRegionsTest test) { + final SlidingWindow slidingWindow = new SlidingWindow("1", 0, globalStartPosition); + final CompressionStash locs = slidingWindow.findVariantRegions(0, variantRegionLength, test.variantRegionBitset, true); + int index = 0; + for ( final FinishedGenomeLoc loc : locs ) { + Assert.assertTrue(loc.equals(test.expectedResult.get(index++))); + } + } + + @Test(enabled = true) + public void testNoClosingRegions() { + final SlidingWindow slidingWindow = new SlidingWindow("1", 0, globalStartPosition); + final CompressionStash locs = slidingWindow.findVariantRegions(0, variantRegionLength, createBitset(Arrays.asList(loc90to95, loc999)), false); + Assert.assertEquals(locs.size(), 1); + Assert.assertEquals(locs.iterator().next(), loc90to95); + } + + + ///////////////////////////////////////////////////////////////////////////// + //// This section tests the markSites() method and related functionality //// + ///////////////////////////////////////////////////////////////////////////// + + @Test(enabled = true) + public void testMarkedSitesClass() { + final SlidingWindow slidingWindow = new SlidingWindow("1", 0, globalStartPosition); + final SlidingWindow.MarkedSites markedSites = slidingWindow.new MarkedSites(); + + markedSites.updateRegion(100, 100); + Assert.assertEquals(markedSites.getStartLocation(), 100); + Assert.assertEquals(markedSites.getVariantSiteBitSet().length, 100); + + markedSites.updateRegion(300, 100); + Assert.assertEquals(markedSites.getStartLocation(), 300); + Assert.assertEquals(markedSites.getVariantSiteBitSet().length, 100); + + markedSites.getVariantSiteBitSet()[10] = true; + markedSites.updateRegion(290, 100); + Assert.assertEquals(markedSites.getStartLocation(), 290); + Assert.assertEquals(markedSites.getVariantSiteBitSet().length, 100); + Assert.assertFalse(markedSites.getVariantSiteBitSet()[10]); + + markedSites.getVariantSiteBitSet()[20] = true; + markedSites.updateRegion(290, 100); + Assert.assertEquals(markedSites.getStartLocation(), 290); + Assert.assertEquals(markedSites.getVariantSiteBitSet().length, 100); + Assert.assertTrue(markedSites.getVariantSiteBitSet()[20]); + + markedSites.updateRegion(300, 100); + Assert.assertEquals(markedSites.getStartLocation(), 300); + Assert.assertEquals(markedSites.getVariantSiteBitSet().length, 100); + + markedSites.getVariantSiteBitSet()[95] = true; + markedSites.updateRegion(390, 20); + Assert.assertEquals(markedSites.getStartLocation(), 390); + Assert.assertEquals(markedSites.getVariantSiteBitSet().length, 20); + Assert.assertTrue(markedSites.getVariantSiteBitSet()[5]); + + markedSites.updateRegion(340, 60); + Assert.assertEquals(markedSites.getStartLocation(), 340); + Assert.assertEquals(markedSites.getVariantSiteBitSet().length, 60); + + markedSites.getVariantSiteBitSet()[20] = true; + markedSites.updateRegion(350, 60); + Assert.assertEquals(markedSites.getStartLocation(), 350); + Assert.assertEquals(markedSites.getVariantSiteBitSet().length, 60); + Assert.assertTrue(markedSites.getVariantSiteBitSet()[10]); + } + + @Test(enabled = true) + public void testMarkVariantRegion() { + final SlidingWindow slidingWindow = new SlidingWindow("1", 0, globalStartPosition); + SlidingWindow.MarkedSites markedSites = slidingWindow.new MarkedSites(); + markedSites.updateRegion(100, 100); + + slidingWindow.markVariantRegion(markedSites, 40); + Assert.assertEquals(countTrueBits(markedSites.getVariantSiteBitSet()), 21); + + slidingWindow.markVariantRegion(markedSites, 5); + Assert.assertEquals(countTrueBits(markedSites.getVariantSiteBitSet()), 37); + + slidingWindow.markVariantRegion(markedSites, 95); + Assert.assertEquals(countTrueBits(markedSites.getVariantSiteBitSet()), 52); + } + + private static int countTrueBits(final boolean[] bitset) { + int count = 0; + for ( final boolean bit : bitset ) { + if ( bit ) + count++; + } + return count; + } + + + ///////////////////////////////////////////////////////////////// + //// This section tests the consensus creation functionality //// + ///////////////////////////////////////////////////////////////// + + private static final int readLength = 100; + private static final int testRegionSize = 1000; + private final List basicReads = new ArrayList(20); + private IndexedFastaSequenceFile seq; + private SAMFileHeader header; + + @BeforeClass + public void setup() throws FileNotFoundException { + seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); + + final int readFrequency = 20; + + basicReads.clear(); + for ( int i = 0; i < testRegionSize; i += readFrequency ) { + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead" + i, 0, globalStartPosition + i, readLength); + read.setReadBases(Utils.dupBytes((byte) 'A', readLength)); + read.setBaseQualities(Utils.dupBytes((byte)30, readLength)); + read.setMappingQuality(30); + basicReads.add(read); + } + } + + private class ConsensusCreationTest { + public final int expectedNumberOfReads; + public final List myReads = new ArrayList(20); + + private ConsensusCreationTest(final List locs, final boolean readsShouldBeLowQuality, final boolean variantBaseShouldBeLowQuality, final int expectedNumberOfReads) { + this.expectedNumberOfReads = expectedNumberOfReads; + + // first, add the basic reads to the collection + myReads.addAll(basicReads); + + // then add the permuted reads + for ( final GenomeLoc loc : locs ) + myReads.add(createVariantRead(loc, readsShouldBeLowQuality, variantBaseShouldBeLowQuality)); + } + + private GATKSAMRecord createVariantRead(final GenomeLoc loc, final boolean readShouldBeLowQuality, final boolean variantBaseShouldBeLowQuality) { + + final int startPos = loc.getStart() - 50; + + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead" + startPos, 0, startPos, readLength); + final byte[] bases = Utils.dupBytes((byte) 'A', readLength); + // create a mismatch + bases[50] = 'C'; + read.setReadBases(bases); + final byte[] baseQuals = Utils.dupBytes((byte) 30, readLength); + if ( variantBaseShouldBeLowQuality ) + baseQuals[50] = (byte)10; + read.setBaseQualities(baseQuals); + final byte mappingQual = readShouldBeLowQuality ? (byte)10 : (byte)30; + read.setMappingQuality(mappingQual); + return read; + } + } + + private static final GenomeLoc loc290 = new UnvalidatingGenomeLoc("1", 0, 1000290, 1000290); + private static final GenomeLoc loc295 = new UnvalidatingGenomeLoc("1", 0, 1000295, 1000295); + private static final GenomeLoc loc309 = new UnvalidatingGenomeLoc("1", 0, 1000309, 1000309); + private static final GenomeLoc loc310 = new UnvalidatingGenomeLoc("1", 0, 1000310, 1000310); + private static final GenomeLoc loc1100 = new UnvalidatingGenomeLoc("1", 0, 1001100, 1001100); + + @DataProvider(name = "ConsensusCreation") + public Object[][] createConsensusCreationTestData() { + List tests = new ArrayList(); + + // test high quality reads and bases + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(), false, false, 1)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290), false, false, 9)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290, loc295), false, false, 10)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290, loc309), false, false, 10)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290, loc310), false, false, 11)}); + + // test low quality reads + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(), true, false, 1)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290), true, false, 1)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290, loc295), true, false, 1)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290, loc309), true, false, 1)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290, loc310), true, false, 1)}); + + // test low quality bases + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(), false, true, 1)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290), false, true, 1)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290, loc295), false, true, 1)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290, loc309), false, true, 1)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc290, loc310), false, true, 1)}); + + // test mixture + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc1100), true, false, 2)}); + tests.add(new Object[]{new ConsensusCreationTest(Arrays.asList(loc1100), false, true, 3)}); + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "ConsensusCreation", enabled = true) + public void testConsensusCreationTest(ConsensusCreationTest test) { + final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 20, 20, 100, ReduceReads.DownsampleStrategy.Normal, false, 1, false); + for ( final GATKSAMRecord read : test.myReads ) + slidingWindow.addRead(read); + final Pair, CompressionStash> result = slidingWindow.close(); + + Assert.assertEquals(result.getFirst().size(), test.expectedNumberOfReads); + } + + + /////////////////////////////////////////////////////////// + //// This section tests the downsampling functionality //// + /////////////////////////////////////////////////////////// + + private class DSTest { + public final int dcov; + + private DSTest(final int dcov) { + this.dcov = dcov; + } + } + + @DataProvider(name = "Downsampling") + public Object[][] createDownsamplingTestData() { + List tests = new ArrayList(); + + for ( int i = 1; i < basicReads.size() + 10; i++ ) + tests.add(new Object[]{new DSTest(i)}); + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "Downsampling", enabled = true) + public void testDownsamplingTest(DSTest test) { + final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 20, 20, test.dcov, ReduceReads.DownsampleStrategy.Normal, false, 1, false); + final List result = slidingWindow.downsampleVariantRegion(basicReads); + + Assert.assertEquals(result.size(), Math.min(test.dcov, basicReads.size())); + } + + + ////////////////////////////////////////////////////////////// + //// This section tests the consensus base quals accuracy //// + ////////////////////////////////////////////////////////////// + + private class QualsTest { + public final List quals; + public final List myReads = new ArrayList(5); + + private QualsTest(final List quals) { + this.quals = quals; + for ( int i = 0; i < quals.size(); i++ ) { + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead" + i, 0, globalStartPosition, 1); + read.setReadBases(new byte[]{(byte)'A'}); + read.setBaseQualities(new byte[]{quals.get(i).byteValue()}); + read.setMappingQuality(30); + myReads.add(read); + } + } + } + + @DataProvider(name = "ConsensusQuals") + public Object[][] createConsensusQualsData() { + List tests = new ArrayList(); + + final int[] quals = new int[]{ 0, 5, 10, 15, 20, 30, 40, 50 }; + + for ( final int qual1 : quals ) { + for ( final int qual2 : quals ) { + for ( final int qual3 : quals ) { + tests.add(new Object[]{new QualsTest(Arrays.asList(qual1, qual2, qual3))}); + } + } + } + + return tests.toArray(new Object[][]{}); + } + + private static final byte minUsableConsensusQual = 10; + + @Test(dataProvider = "ConsensusQuals", enabled = true) + public void testConsensusQualsTest(QualsTest test) { + final SlidingWindow slidingWindow = new SlidingWindow("1", 0, 10, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, minUsableConsensusQual, 20, 100, ReduceReads.DownsampleStrategy.Normal, false, 1, false); + for ( final GATKSAMRecord read : test.myReads ) + slidingWindow.addRead(read); + final Pair, CompressionStash> result = slidingWindow.close(); + + Assert.assertEquals(result.getFirst().size(), 1); + final GATKSAMRecord read = result.getFirst().iterator().next(); + final int actualBaseQual = read.getReducedCount(0) * read.getBaseQualities()[0]; + final int expectedBaseQual = qualSum(test.quals); + Assert.assertEquals(actualBaseQual, expectedBaseQual); + } + + private static int qualSum(final List quals) { + int goodBases = 0; + int sum = 0; + for ( final int qual : quals ) { + if ( qual >= minUsableConsensusQual ) { + goodBases++; + sum += qual; + } + } + + // handle a low quality consensus + if ( sum == 0 ) { + for ( final int qual : quals ) { + goodBases++; + sum += qual; + } + } + + return sum - (sum % goodBases); + } + + + +} diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java index 047d69c5f..b5c8b3f99 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java index 14dedebc4..cc5576500 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java @@ -50,7 +50,7 @@ import net.sf.samtools.SAMUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index a84019988..45a42d018 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -108,7 +108,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -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("b41b95aaa2c453c9b75b3b29a9c2718e")); + Arrays.asList("35479a79e1ce7c15493bd77e58cadcaa")); executeTest("test Multiple SNP alleles", spec); } @@ -238,12 +238,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameterAllConfident() { - testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "9dbc9389db39cf9697e93e0bf529314f"); + testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "5649f72de04e1391e0f2bb86843d3d72"); } @Test public void testOutputParameterAllSites() { - testOutputParameters("--output_mode EMIT_ALL_SITES", "8b26088a035e579c4afd3b46737291e4"); + testOutputParameters("--output_mode EMIT_ALL_SITES", "cb151bb9e90680b12714d481091ed209"); } private void testOutputParameters(final String args, final String md5) { @@ -363,7 +363,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("39c7a813fd6ee82d3604f2a868b35b2a")); + Arrays.asList("8231ae37b52b927db9fc1e5c221b0ba0")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -391,13 +391,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSampleIndels1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, - Arrays.asList("3d3c5691973a223209a1341272d881be")); + Arrays.asList("a47810de2f6ef8087f4644064a0814bc")); List result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst(); 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 1:10450700-10551000", 1, - Arrays.asList("23b7a37a64065cee53a80495c8717eea")); + Arrays.asList("53b8d2b0fa63c5d1019855e8e0db28f0")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); } @@ -497,18 +497,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1, - Arrays.asList("092e42a712afb660ec79ff11c55933e2")); + Arrays.asList("8b9a9fc2e7150acbe2dac91b4620f304")); executeTest("test calling on a ReducedRead BAM", spec); } @Test public void testReducedBamSNPs() { - testReducedCalling("SNP", "c0de74ab8f4f14eb3a2c5d55c200ac5f"); + testReducedCalling("SNP", "b5991dddbfb59366614ff8819062649f"); } @Test public void testReducedBamINDELs() { - testReducedCalling("INDEL", "1c9aaf65ffaa12bb766855265a1c3f8e"); + testReducedCalling("INDEL", "a85c110fcac9574a54c7daccb1e2d5ae"); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java index f82c0a8ba..8b09e91ae 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java @@ -93,7 +93,7 @@ public class GenotypingEngineUnitTest extends BaseTest { haplotypeAlleles.add( Allele.create("AACA", false) ); haplotypeAlleles.add( Allele.create("CATA", false) ); haplotypeAlleles.add( Allele.create("CACA", false) ); - final ArrayList haplotypes = new ArrayList(); + final List haplotypes = new ArrayList(); haplotypes.add(new Haplotype("AATA".getBytes())); haplotypes.add(new Haplotype("AACA".getBytes())); haplotypes.add(new Haplotype("CATA".getBytes())); @@ -101,11 +101,11 @@ public class GenotypingEngineUnitTest extends BaseTest { final List haplotypeAllelesForSample = new ArrayList(); haplotypeAllelesForSample.add( Allele.create("CATA", false) ); haplotypeAllelesForSample.add( Allele.create("CACA", false) ); - final ArrayList> alleleMapper = new ArrayList>(); - ArrayList Aallele = new ArrayList(); + final List> alleleMapper = new ArrayList>(); + List Aallele = new ArrayList(); Aallele.add(haplotypes.get(0)); Aallele.add(haplotypes.get(1)); - ArrayList Callele = new ArrayList(); + List Callele = new ArrayList(); Callele.add(haplotypes.get(2)); Callele.add(haplotypes.get(3)); alleleMapper.add(Aallele); @@ -135,7 +135,7 @@ public class GenotypingEngineUnitTest extends BaseTest { haplotypeAlleles.add( Allele.create("TACA", false) ); haplotypeAlleles.add( Allele.create("TTCA", false) ); haplotypeAlleles.add( Allele.create("TTTA", false) ); - final ArrayList haplotypes = new ArrayList(); + final List haplotypes = new ArrayList(); haplotypes.add(new Haplotype("AATA".getBytes())); haplotypes.add(new Haplotype("AACA".getBytes())); haplotypes.add(new Haplotype("CATA".getBytes())); @@ -146,14 +146,14 @@ public class GenotypingEngineUnitTest extends BaseTest { final List haplotypeAllelesForSample = new ArrayList(); haplotypeAllelesForSample.add( Allele.create("TTTA", false) ); haplotypeAllelesForSample.add( Allele.create("AATA", true) ); - final ArrayList> alleleMapper = new ArrayList>(); - ArrayList Aallele = new ArrayList(); + final List> alleleMapper = new ArrayList>(); + List Aallele = new ArrayList(); Aallele.add(haplotypes.get(0)); Aallele.add(haplotypes.get(1)); - ArrayList Callele = new ArrayList(); + List Callele = new ArrayList(); Callele.add(haplotypes.get(2)); Callele.add(haplotypes.get(3)); - ArrayList Tallele = new ArrayList(); + List Tallele = new ArrayList(); Tallele.add(haplotypes.get(4)); Tallele.add(haplotypes.get(5)); Tallele.add(haplotypes.get(6)); @@ -187,16 +187,16 @@ public class GenotypingEngineUnitTest extends BaseTest { private class BasicGenotypingTestProvider extends TestDataProvider { byte[] ref; byte[] hap; - HashMap expected; + Map expected; - public BasicGenotypingTestProvider(String refString, String hapString, HashMap expected) { + public BasicGenotypingTestProvider(String refString, String hapString, Map expected) { super(BasicGenotypingTestProvider.class, String.format("Haplotype to VCF test: ref = %s, alignment = %s", refString,hapString)); ref = refString.getBytes(); hap = hapString.getBytes(); this.expected = expected; } - public HashMap calcAlignment() { + public Map calcAlignment() { final SWPairwiseAlignment alignment = new SWPairwiseAlignment(ref, hap); return GenotypingEngine.generateVCsFromAlignment( new Haplotype(hap), alignment.getAlignmentStart2wrt1(), alignment.getCigar(), ref, hap, genomeLocParser.createGenomeLoc("4",1,1+ref.length), "name"); } @@ -206,14 +206,14 @@ public class GenotypingEngineUnitTest extends BaseTest { public Object[][] makeBasicGenotypingTests() { for( int contextSize : new int[]{0,1,5,9,24,36} ) { - HashMap map = new HashMap(); + Map map = new HashMap(); map.put(1 + contextSize, (byte)'M'); final String context = Utils.dupString('G', contextSize); new BasicGenotypingTestProvider(context + "AGCTCGCATCGCGAGCATCGACTAGCCGATAG" + context, "CGCTCGCATCGCGAGCATCGACTAGCCGATAG", map); } for( int contextSize : new int[]{0,1,5,9,24,36} ) { - HashMap map = new HashMap(); + Map map = new HashMap(); map.put(2 + contextSize, (byte)'M'); map.put(21 + contextSize, (byte)'M'); final String context = Utils.dupString('G', contextSize); @@ -221,7 +221,7 @@ public class GenotypingEngineUnitTest extends BaseTest { } for( int contextSize : new int[]{0,1,5,9,24,36} ) { - HashMap map = new HashMap(); + Map map = new HashMap(); map.put(1 + contextSize, (byte)'M'); map.put(20 + contextSize, (byte)'I'); final String context = Utils.dupString('G', contextSize); @@ -229,7 +229,7 @@ public class GenotypingEngineUnitTest extends BaseTest { } for( int contextSize : new int[]{0,1,5,9,24,36} ) { - HashMap map = new HashMap(); + Map map = new HashMap(); map.put(1 + contextSize, (byte)'M'); map.put(20 + contextSize, (byte)'D'); final String context = Utils.dupString('G', contextSize); @@ -237,7 +237,7 @@ public class GenotypingEngineUnitTest extends BaseTest { } for( int contextSize : new int[]{1,5,9,24,36} ) { - HashMap map = new HashMap(); + Map map = new HashMap(); map.put(1, (byte)'M'); map.put(20, (byte)'D'); final String context = Utils.dupString('G', contextSize); @@ -245,7 +245,7 @@ public class GenotypingEngineUnitTest extends BaseTest { } for( int contextSize : new int[]{0,1,5,9,24,36} ) { - HashMap map = new HashMap(); + Map map = new HashMap(); map.put(2 + contextSize, (byte)'M'); map.put(20 + contextSize, (byte)'I'); map.put(30 + contextSize, (byte)'D'); @@ -254,7 +254,7 @@ public class GenotypingEngineUnitTest extends BaseTest { } for( int contextSize : new int[]{0,1,5,9,24,36} ) { - HashMap map = new HashMap(); + Map map = new HashMap(); map.put(1 + contextSize, (byte)'M'); map.put(20 + contextSize, (byte)'D'); map.put(28 + contextSize, (byte)'M'); @@ -267,8 +267,8 @@ public class GenotypingEngineUnitTest extends BaseTest { @Test(dataProvider = "BasicGenotypingTestProvider", enabled = true) public void testHaplotypeToVCF(BasicGenotypingTestProvider cfg) { - HashMap calculatedMap = cfg.calcAlignment(); - HashMap expectedMap = cfg.expected; + Map calculatedMap = cfg.calcAlignment(); + Map expectedMap = cfg.expected; logger.warn(String.format("Test: %s", cfg.toString())); if(!compareVCMaps(calculatedMap, expectedMap)) { logger.warn("calc map = " + calculatedMap); @@ -420,9 +420,9 @@ public class GenotypingEngineUnitTest extends BaseTest { } /** - * Private function to compare HashMap of VCs, it only checks the types and start locations of the VariantContext + * Private function to compare Map of VCs, it only checks the types and start locations of the VariantContext */ - private boolean compareVCMaps(HashMap calc, HashMap expected) { + private boolean compareVCMaps(Map calc, Map expected) { if( !calc.keySet().equals(expected.keySet()) ) { return false; } // sanity check for( Integer loc : expected.keySet() ) { Byte type = expected.get(loc); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 8f5e275e6..ad682734c 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -50,6 +50,7 @@ import org.broadinstitute.sting.WalkerTest; import org.testng.annotations.Test; import java.util.Arrays; +import java.util.Collections; public class HaplotypeCallerIntegrationTest extends WalkerTest { final static String REF = b37KGReference; @@ -67,18 +68,23 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "b8f7b741445ce6b6ea491c794ce75c17"); + HCTest(CEUTRIO_BAM, "", "72ce6a5e46644dfd73aeffba9d6131ea"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "a2c63f6e6e51a01019bdbd23125bdb15"); + HCTest(NA12878_BAM, "", "f9d696391f1f337092d70e3abcd32bfb"); + } + + @Test(enabled = false) + public void testHaplotypeCallerSingleSampleWithDbsnp() { + HCTest(NA12878_BAM, "-D " + b37dbSNP132, ""); } @Test public void testHaplotypeCallerMultiSampleGGA() { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", - "c679ae7f04bdfda896b5c046d35e043c"); + "4e8beb2cdc3d77427f14acf37cea2bd0"); } private void HCTestComplexGGA(String bam, String args, String md5) { @@ -90,13 +96,13 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "8730a9ebaeecae913dca2fb5a0d4e946"); + "75e1df0dcf3728fd2b6e4735c4cc88ce"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "1a034b7eb572e1b6f659d6e5d57b3e76"); + "1d244f2adbc72a0062eb673d56cbb5a8"); } private void HCTestComplexVariants(String bam, String args, String md5) { @@ -107,7 +113,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleComplex() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6c0c441b71848c2eea38ab5e2afe1120"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "a1bc844f62a9cb60dbb70d00ad36b85d"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -118,7 +124,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleSymbolic() { - HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "0761ff5cbf279be467833fa6708bf360"); + HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "23956e572f19ff26d25bbdfaa307675b"); } private void HCTestIndelQualityScores(String bam, String args, String md5) { @@ -129,7 +135,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "29f1125df5ab27cc937a144ae08ac735"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "1255f466aa2d288f015cd55d8fece1ac"); } // That problem bam came from a user on the forum and it spotted a problem where the ReadClipper @@ -140,17 +146,25 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void HCTestProblematicReadsModifiedInActiveRegions() { final String base = String.format("-T HaplotypeCaller -R %s -I %s", 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("8b1b8d1bd7feac1503fc4ffa6236cff7")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("103c91c4a78164949e166d3d27eb459b")); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); } @Test public void HCTestStructuralIndels() { final String base = String.format("-T HaplotypeCaller -R %s -I %s", 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("add0f4f51969b7caeea99005a7ba1aa4")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("87fe31a4bbd68a9eb5d5910db5011c82")); executeTest("HCTestStructuralIndels: ", spec); } + @Test + public void HCTestDoesNotFailOnBadRefBase() { + // don't care about the output - just want to make sure it doesn't fail + final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o /dev/null -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2 -stand_emit_conf 2"; + final WalkerTestSpec spec = new WalkerTestSpec(base, Collections.emptyList()); + executeTest("HCTestDoesNotFailOnBadRefBase: ", spec); + } + // -------------------------------------------------------------------------------------------------------------- // // testing reduced reads @@ -161,7 +175,15 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1, - Arrays.asList("8a400b0c46f41447fcc35a907e34f384")); + Arrays.asList("0fa19ec5cf737a3445544b59ecc995e9")); executeTest("HC calling on a ReducedRead BAM", spec); } + + @Test + public void testReducedBamWithReadsNotFullySpanningDeletion() { + WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( + "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1, + Arrays.asList("5f4cbdcc9bffee6bba258dfac89492ed")); + executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec); + } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPathsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPathsUnitTest.java new file mode 100644 index 000000000..a39ca23e3 --- /dev/null +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KBestPathsUnitTest.java @@ -0,0 +1,246 @@ +/* +* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. +* 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. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. +* Copyright 2012 Broad Institute, Inc. +* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. +* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. +* +* 4. 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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. +* +* 6. 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. +* +* 7. MISCELLANEOUS +* 7.1 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. +* 7.2 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. +* 7.3 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. +* 7.4 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. +* 7.5 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. +* 7.6 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. +* 7.7 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.sting.gatk.walkers.haplotypecaller; + +import net.sf.samtools.Cigar; +import net.sf.samtools.CigarElement; +import net.sf.samtools.CigarOperator; +import org.apache.commons.lang.ArrayUtils; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.sam.AlignmentUtils; +import org.jgrapht.graph.DefaultDirectedGraph; +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; + +/** + * Created with IntelliJ IDEA. + * User: rpoplin + * Date: 1/31/13 + */ + +public class KBestPathsUnitTest { + @DataProvider(name = "BasicBubbleDataProvider") + public Object[][] makeBasicBubbleDataProvider() { + List tests = new ArrayList(); + for ( final int refBubbleLength : Arrays.asList(1, 5, 10) ) { + for ( final int altBubbleLength : Arrays.asList(1, 5, 10) ) { + tests.add(new Object[]{refBubbleLength, altBubbleLength}); + } + } + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "BasicBubbleDataProvider") + public void testBasicBubbleData(final int refBubbleLength, final int altBubbleLength) { + // Construct the assembly graph + DefaultDirectedGraph graph = new DefaultDirectedGraph(DeBruijnEdge.class); + final int KMER_LENGTH = 3; + final String preRef = "ATGG"; + final String postRef = new String(Utils.dupBytes((byte) 'A', KMER_LENGTH-1)) + "GGGGC"; + + DeBruijnVertex v = new DeBruijnVertex(preRef.getBytes(), KMER_LENGTH); + DeBruijnVertex v2Ref = new DeBruijnVertex(Utils.dupBytes((byte) 'A', refBubbleLength+KMER_LENGTH-1), KMER_LENGTH); + DeBruijnVertex v2Alt = new DeBruijnVertex(ArrayUtils.addAll(Utils.dupBytes((byte) 'A', altBubbleLength + KMER_LENGTH - 1 - 1), Utils.dupBytes((byte) 'T',1)), KMER_LENGTH); + DeBruijnVertex v3 = new DeBruijnVertex(postRef.getBytes(), KMER_LENGTH); + + graph.addVertex(v); + graph.addVertex(v2Ref); + graph.addVertex(v2Alt); + graph.addVertex(v3); + graph.addEdge(v, v2Ref, new DeBruijnEdge(true, 10)); + graph.addEdge(v2Ref, v3, new DeBruijnEdge(true, 10)); + graph.addEdge(v, v2Alt, new DeBruijnEdge(false, 5)); + graph.addEdge(v2Alt, v3, new DeBruijnEdge(false, 5)); + + // Construct the test path + KBestPaths.Path path = new KBestPaths.Path(v, graph); + path = new KBestPaths.Path(path, graph.getEdge(v, v2Alt)); + path = new KBestPaths.Path(path, graph.getEdge(v2Alt, v3)); + + // Construct the actual cigar string implied by the test path + Cigar expectedCigar = new Cigar(); + expectedCigar.add(new CigarElement(preRef.length(), CigarOperator.M)); + if( refBubbleLength > altBubbleLength ) { + expectedCigar.add(new CigarElement(refBubbleLength - altBubbleLength, CigarOperator.D)); + expectedCigar.add(new CigarElement(altBubbleLength,CigarOperator.M)); + } else if ( refBubbleLength < altBubbleLength ) { + expectedCigar.add(new CigarElement(refBubbleLength,CigarOperator.M)); + expectedCigar.add(new CigarElement(altBubbleLength - refBubbleLength,CigarOperator.I)); + } else { + expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M)); + } + expectedCigar.add(new CigarElement(postRef.length() - (KMER_LENGTH - 1), CigarOperator.M)); + + Assert.assertEquals(path.calculateCigar().toString(), AlignmentUtils.consolidateCigar(expectedCigar).toString(), "Cigar string mismatch"); + } + + + @DataProvider(name = "TripleBubbleDataProvider") + public Object[][] makeTripleBubbleDataProvider() { + List tests = new ArrayList(); + for ( final int refBubbleLength : Arrays.asList(1, 5, 10) ) { + for ( final int altBubbleLength : Arrays.asList(1, 5, 10) ) { + for ( final boolean offRefBeginning : Arrays.asList(false) ) { + for ( final boolean offRefEnding : Arrays.asList(true, false) ) { + tests.add(new Object[]{refBubbleLength, altBubbleLength, offRefBeginning, offRefEnding}); + } + } + } + } + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "TripleBubbleDataProvider") + public void testTripleBubbleData(final int refBubbleLength, final int altBubbleLength, final boolean offRefBeginning, final boolean offRefEnding) { + // Construct the assembly graph + DefaultDirectedGraph graph = new DefaultDirectedGraph(DeBruijnEdge.class); + final int KMER_LENGTH = 3; + final String preAltOption = "ATCGATCGATCGATCGATCG"; + final String postAltOption = "CCCC"; + final String preRef = "ATGG"; + final String postRef = new String(Utils.dupBytes((byte) 'A', KMER_LENGTH-1)) + "GGCCG"; + final String midRef1 = new String(Utils.dupBytes((byte) 'A', KMER_LENGTH-1)) + "TTCCT"; + final String midRef2 = new String(Utils.dupBytes((byte) 'A', KMER_LENGTH-1)) + "CCCAAAAAAAAAAAA"; + + DeBruijnVertex preV = new DeBruijnVertex(preAltOption.getBytes(), KMER_LENGTH); + DeBruijnVertex v = new DeBruijnVertex(preRef.getBytes(), KMER_LENGTH); + DeBruijnVertex v2Ref = new DeBruijnVertex(Utils.dupBytes((byte) 'A', refBubbleLength+KMER_LENGTH-1), KMER_LENGTH); + DeBruijnVertex v2Alt = new DeBruijnVertex(ArrayUtils.addAll(Utils.dupBytes((byte) 'A', altBubbleLength + KMER_LENGTH - 1 - 1), Utils.dupBytes((byte) 'T',1)), KMER_LENGTH); + DeBruijnVertex v4Ref = new DeBruijnVertex(Utils.dupBytes((byte) 'C', refBubbleLength+KMER_LENGTH-1), KMER_LENGTH); + DeBruijnVertex v4Alt = new DeBruijnVertex(ArrayUtils.addAll(Utils.dupBytes((byte) 'C', altBubbleLength + KMER_LENGTH - 1 - 1), Utils.dupBytes((byte) 'T',1)), KMER_LENGTH); + DeBruijnVertex v6Ref = new DeBruijnVertex(Utils.dupBytes((byte) 'G', refBubbleLength+KMER_LENGTH-1), KMER_LENGTH); + DeBruijnVertex v6Alt = new DeBruijnVertex(ArrayUtils.addAll(Utils.dupBytes((byte) 'G', altBubbleLength + KMER_LENGTH - 1 - 1), Utils.dupBytes((byte) 'T',1)), KMER_LENGTH); + DeBruijnVertex v3 = new DeBruijnVertex(midRef1.getBytes(), KMER_LENGTH); + DeBruijnVertex v5 = new DeBruijnVertex(midRef2.getBytes(), KMER_LENGTH); + DeBruijnVertex v7 = new DeBruijnVertex(postRef.getBytes(), KMER_LENGTH); + DeBruijnVertex postV = new DeBruijnVertex(postAltOption.getBytes(), KMER_LENGTH); + + graph.addVertex(preV); + graph.addVertex(v); + graph.addVertex(v2Ref); + graph.addVertex(v2Alt); + graph.addVertex(v3); + graph.addVertex(v4Ref); + graph.addVertex(v4Alt); + graph.addVertex(v5); + graph.addVertex(v6Ref); + graph.addVertex(v6Alt); + graph.addVertex(v7); + graph.addVertex(postV); + graph.addEdge(preV, v, new DeBruijnEdge(false, 1)); + graph.addEdge(v, v2Ref, new DeBruijnEdge(true, 10)); + graph.addEdge(v2Ref, v3, new DeBruijnEdge(true, 10)); + graph.addEdge(v, v2Alt, new DeBruijnEdge(false, 5)); + graph.addEdge(v2Alt, v3, new DeBruijnEdge(false, 5)); + graph.addEdge(v3, v4Ref, new DeBruijnEdge(true, 10)); + graph.addEdge(v4Ref, v5, new DeBruijnEdge(true, 10)); + graph.addEdge(v3, v4Alt, new DeBruijnEdge(false, 5)); + graph.addEdge(v4Alt, v5, new DeBruijnEdge(false, 5)); + graph.addEdge(v5, v6Ref, new DeBruijnEdge(true, 11)); + graph.addEdge(v6Ref, v7, new DeBruijnEdge(true, 11)); + graph.addEdge(v5, v6Alt, new DeBruijnEdge(false, 55)); + graph.addEdge(v6Alt, v7, new DeBruijnEdge(false, 55)); + graph.addEdge(v7, postV, new DeBruijnEdge(false, 1)); + + // Construct the test path + KBestPaths.Path path = new KBestPaths.Path( (offRefBeginning ? preV : v), graph); + if( offRefBeginning ) { + path = new KBestPaths.Path(path, graph.getEdge(preV, v)); + } + path = new KBestPaths.Path(path, graph.getEdge(v, v2Alt)); + path = new KBestPaths.Path(path, graph.getEdge(v2Alt, v3)); + path = new KBestPaths.Path(path, graph.getEdge(v3, v4Ref)); + path = new KBestPaths.Path(path, graph.getEdge(v4Ref, v5)); + path = new KBestPaths.Path(path, graph.getEdge(v5, v6Alt)); + path = new KBestPaths.Path(path, graph.getEdge(v6Alt, v7)); + if( offRefEnding ) { + path = new KBestPaths.Path(path, graph.getEdge(v7,postV)); + } + + // Construct the actual cigar string implied by the test path + Cigar expectedCigar = new Cigar(); + if( offRefBeginning ) { + expectedCigar.add(new CigarElement(preAltOption.length(), CigarOperator.I)); + } + expectedCigar.add(new CigarElement(preRef.length() - ( offRefBeginning ? KMER_LENGTH - 1 : 0 ), CigarOperator.M)); + // first bubble + if( refBubbleLength > altBubbleLength ) { + expectedCigar.add(new CigarElement(refBubbleLength - altBubbleLength, CigarOperator.D)); + expectedCigar.add(new CigarElement(altBubbleLength,CigarOperator.M)); + } else if ( refBubbleLength < altBubbleLength ) { + expectedCigar.add(new CigarElement(refBubbleLength,CigarOperator.M)); + expectedCigar.add(new CigarElement(altBubbleLength - refBubbleLength,CigarOperator.I)); + } else { + expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M)); + } + expectedCigar.add(new CigarElement(midRef1.length() - (KMER_LENGTH - 1), CigarOperator.M)); + // second bubble is ref path + expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M)); + expectedCigar.add(new CigarElement(midRef2.length() - (KMER_LENGTH - 1), CigarOperator.M)); + // third bubble + if( refBubbleLength > altBubbleLength ) { + expectedCigar.add(new CigarElement(refBubbleLength - altBubbleLength, CigarOperator.D)); + expectedCigar.add(new CigarElement(altBubbleLength,CigarOperator.M)); + } else if ( refBubbleLength < altBubbleLength ) { + expectedCigar.add(new CigarElement(refBubbleLength,CigarOperator.M)); + expectedCigar.add(new CigarElement(altBubbleLength - refBubbleLength,CigarOperator.I)); + } else { + expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M)); + } + expectedCigar.add(new CigarElement(postRef.length() - (KMER_LENGTH - 1), CigarOperator.M)); + if( offRefEnding ) { + expectedCigar.add(new CigarElement(postAltOption.length() - (KMER_LENGTH - 1), CigarOperator.I)); + } + + Assert.assertEquals(path.calculateCigar().toString(), AlignmentUtils.consolidateCigar(expectedCigar).toString(), "Cigar string mismatch"); + } +} diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java index 5769a531e..24915d34b 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java @@ -78,7 +78,7 @@ public class SimpleDeBruijnAssemblerUnitTest extends BaseTest { } public DefaultDirectedGraph expectedGraph() { - DeBruijnVertex v = new DeBruijnVertex(sequence, 0); + DeBruijnVertex v = new DeBruijnVertex(sequence, KMER_LENGTH); DefaultDirectedGraph graph = new DefaultDirectedGraph(DeBruijnEdge.class); graph.addVertex(v); return graph; @@ -127,12 +127,12 @@ public class SimpleDeBruijnAssemblerUnitTest extends BaseTest { DefaultDirectedGraph graph = new DefaultDirectedGraph(DeBruijnEdge.class); DefaultDirectedGraph expectedGraph = new DefaultDirectedGraph(DeBruijnEdge.class); - DeBruijnVertex v = new DeBruijnVertex("ATGG".getBytes(), 0); - DeBruijnVertex v2 = new DeBruijnVertex("ATGGA".getBytes(), 0); - DeBruijnVertex v3 = new DeBruijnVertex("ATGGT".getBytes(), 0); - DeBruijnVertex v4 = new DeBruijnVertex("ATGGG".getBytes(), 0); - DeBruijnVertex v5 = new DeBruijnVertex("ATGGC".getBytes(), 0); - DeBruijnVertex v6 = new DeBruijnVertex("ATGGCCCCCC".getBytes(), 0); + DeBruijnVertex v = new DeBruijnVertex("ATGG".getBytes(), 1); + DeBruijnVertex v2 = new DeBruijnVertex("ATGGA".getBytes(), 1); + DeBruijnVertex v3 = new DeBruijnVertex("ATGGT".getBytes(), 1); + DeBruijnVertex v4 = new DeBruijnVertex("ATGGG".getBytes(), 1); + DeBruijnVertex v5 = new DeBruijnVertex("ATGGC".getBytes(), 1); + DeBruijnVertex v6 = new DeBruijnVertex("ATGGCCCCCC".getBytes(), 1); graph.addVertex(v); graph.addVertex(v2); @@ -192,12 +192,12 @@ public class SimpleDeBruijnAssemblerUnitTest extends BaseTest { DefaultDirectedGraph graph = new DefaultDirectedGraph(DeBruijnEdge.class); DefaultDirectedGraph expectedGraph = new DefaultDirectedGraph(DeBruijnEdge.class); - DeBruijnVertex v = new DeBruijnVertex("ATGG".getBytes(), 0); - DeBruijnVertex v2 = new DeBruijnVertex("ATGGA".getBytes(), 0); - DeBruijnVertex v3 = new DeBruijnVertex("ATGGT".getBytes(), 0); - DeBruijnVertex v4 = new DeBruijnVertex("ATGGG".getBytes(), 0); - DeBruijnVertex v5 = new DeBruijnVertex("ATGGC".getBytes(), 0); - DeBruijnVertex v6 = new DeBruijnVertex("ATGGCCCCCC".getBytes(), 0); + DeBruijnVertex v = new DeBruijnVertex("ATGG".getBytes(), 1); + DeBruijnVertex v2 = new DeBruijnVertex("ATGGA".getBytes(), 1); + DeBruijnVertex v3 = new DeBruijnVertex("ATGGT".getBytes(), 1); + DeBruijnVertex v4 = new DeBruijnVertex("ATGGG".getBytes(), 1); + DeBruijnVertex v5 = new DeBruijnVertex("ATGGC".getBytes(), 1); + DeBruijnVertex v6 = new DeBruijnVertex("ATGGCCCCCC".getBytes(), 1); graph.addVertex(v); graph.addVertex(v2); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index eba9c7780..275ababda 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -60,8 +60,8 @@ public class IndelRealignerIntegrationTest extends WalkerTest { 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 = "7574ab7d0b1ee5d44a0b3f85b6e944e6"; - private static final String base_md5_with_SW_or_VCF = "a918d69d26d3c87b29002ed31f428c48"; + private static final String base_md5 = "a102dd55451799e5f053c784b762087e"; + private static final String base_md5_with_SW_or_VCF = "06b8eefcbd785e929027feaa22bb060d"; @Test public void testDefaults() { @@ -84,7 +84,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec1 = new WalkerTestSpec( baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels, 1, - Arrays.asList("36718f10d523dfb0fa2a709480f24bd4")); + Arrays.asList("1b24b0f2a20aed1adc726d1b296a3192")); executeTest("realigner known indels only from VCF", spec1); } @@ -101,7 +101,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { public void testLods() { HashMap e = new HashMap(); e.put( "-LOD 60", base_md5 ); - e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "9a75a0f7ad0442c78d0f8df260e733a4" ); + e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "4bf28d3c0337682d439257874377a681" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -117,7 +117,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { 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("e98f51d71f0a82141b36a7e9f94db237")); + Arrays.asList("f4f6c3b2a2be0306a0ecd3def334bafe")); executeTest("realigner long run", spec); } @@ -126,7 +126,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW", 1, - Arrays.asList("58ac675d0699eb236d469b8e84513d11")); + Arrays.asList("71fb521f8febfe2dc683fc636e28ae7d")); executeTest("realigner no output tags", spec); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 748a16db9..d695f2d13 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -334,16 +334,6 @@ public class VariantEvalIntegrationTest extends WalkerTest { executeTestParallel("testSelect1", spec); } - @Test - public void testVEGenotypeConcordance() { - String vcfFile = "GenotypeConcordanceEval.vcf"; - - WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG --eval:VCF3 " + validationDataLocation + vcfFile + " --comp:VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", - 1, - Arrays.asList("810d55b67de592f6375d9dfb282145ef")); - executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); - } - @Test public void testVEMendelianViolationEvaluator() { String vcfFile = "/MendelianViolationEval.vcf"; @@ -355,12 +345,6 @@ public class VariantEvalIntegrationTest extends WalkerTest { executeTestParallel("testVEMendelianViolationEvaluator" + vcfFile, spec); } - @Test - public void testCompVsEvalAC() { - String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("659a15cc842f0310106fa595a26da71d")); - executeTestParallel("testCompVsEvalAC",spec); - } private static String withSelect(String cmd, String select, String name) { return String.format("%s -select '%s' -selectName %s", cmd, select, name); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java index 1fb056c78..31ed3dcc8 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java @@ -48,14 +48,14 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.PositionalBufferedStream; +import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.variant.vcf.*; import org.testng.Assert; import org.testng.annotations.Test; import java.io.StringBufferInputStream; -import java.util.ArrayList; -import java.util.Set; +import java.util.*; /** * test out pieces of the combine variants code @@ -76,6 +76,33 @@ public class CombineVariantsUnitTest { "##FORMAT=\n"+ "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"; + public static String VCF4headerStringsWithSamplesName = + "##fileformat=VCFv4.0\n" + + "##filedate=2010-06-21\n"+ + "##reference=NCBI36\n"+ + "##INFO=\n"+ + "##INFO=\n"+ + "##INFO=\n"+ + "##FILTER=\n"+ + "##FORMAT=\n"+ + "##FORMAT=\n"+ + "##FORMAT=\n"+ + "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA12878\tNA12891\n"; + + public static String VCF4headerStringsWithUniqueSamplesName = + "##fileformat=VCFv4.0\n" + + "##filedate=2010-06-21\n"+ + "##reference=NCBI36\n"+ + "##INFO=\n"+ + "##INFO=\n"+ + "##INFO=\n"+ + "##FILTER=\n"+ + "##FORMAT=\n"+ + "##FORMAT=\n"+ + "##FORMAT=\n"+ + "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA12892\n"; + + // altered info field public static String VCF4headerStringsBrokenInfo = "##fileformat=VCFv4.0\n"+ @@ -110,6 +137,26 @@ public class CombineVariantsUnitTest { return head; } + @Test + public void testHeadersWithSamplesNamesDuplicationThatIsNotAllowed() { + VCFHeader one = createHeader(VCF4headerStringsWithSamplesName); + VCFHeader two = createHeader(VCF4headerStringsWithSamplesName); + Map headers = new HashMap(); + headers.put("VCF4headerStringsWithSamplesName",one); + headers.put("VCF4headerStringsWithSamplesName2",two); + Assert.assertEquals(SampleUtils.verifyUniqueSamplesNames(headers),false); + } + + @Test + public void testHeadersWithoutSamplesNamesDuplication() { + VCFHeader one = createHeader(VCF4headerStringsWithSamplesName); + VCFHeader two = createHeader(VCF4headerStringsWithUniqueSamplesName); + Map headers = new HashMap(); + headers.put("VCF4headerStringsWithSamplesName",one); + headers.put("VCF4headerStringsWithSamplesName2",two); + Assert.assertEquals(SampleUtils.verifyUniqueSamplesNames(headers),true); + } + @Test public void testHeadersWhereOneIsAStrictSubsetOfTheOther() { VCFHeader one = createHeader(VCFHeaderUnitTest.VCF4headerStrings); @@ -117,7 +164,7 @@ public class CombineVariantsUnitTest { ArrayList headers = new ArrayList(); headers.add(one); headers.add(two); - Set lines = VCFUtils.smartMergeHeaders(headers, null); + Set lines = VCFUtils.smartMergeHeaders(headers, false); Assert.assertEquals(lines.size(), VCFHeaderUnitTest.VCF4headerStringCount); } @@ -128,7 +175,7 @@ public class CombineVariantsUnitTest { ArrayList headers = new ArrayList(); headers.add(one); headers.add(two); - Set lines = VCFUtils.smartMergeHeaders(headers, null); + Set lines = VCFUtils.smartMergeHeaders(headers, false); Assert.assertEquals(lines.size(), VCFHeaderUnitTest.VCF4headerStringCount); } @@ -139,7 +186,7 @@ public class CombineVariantsUnitTest { ArrayList headers = new ArrayList(); headers.add(one); headers.add(two); - Set lines = VCFUtils.smartMergeHeaders(headers, null); + Set lines = VCFUtils.smartMergeHeaders(headers, false); Assert.assertEquals(lines.size(), VCFHeaderUnitTest.VCF4headerStringCount); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java index 28f128dd3..2e31f6725 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java @@ -46,20 +46,16 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import com.sun.org.apache.xpath.internal.operations.Gt; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.walkers.variantutils.ConcordanceMetrics; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.variant.utils.BaseUtils; -import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.GenotypeBuilder; import org.broadinstitute.variant.variantcontext.GenotypeType; -import org.broadinstitute.variant.variantcontext.GenotypesContext; import org.broadinstitute.variant.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import org.broadinstitute.variant.vcf.VCFCodec; @@ -67,7 +63,6 @@ import org.broadinstitute.variant.vcf.VCFHeader; import org.testng.annotations.Test; import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.variant.vcf.*; import org.testng.Assert; import org.testng.annotations.BeforeClass; @@ -75,7 +70,6 @@ import java.io.File; import java.io.FileNotFoundException; import java.io.StringBufferInputStream; import java.util.ArrayList; -import java.util.Set; import java.util.Arrays; import java.util.List; import net.sf.picard.reference.ReferenceSequenceFile; @@ -111,8 +105,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest { private Pair getData1() { - Allele reference_A = Allele.create(BaseUtils.A,true); - Allele alt_C = Allele.create(BaseUtils.C); + Allele reference_A = Allele.create(BaseUtils.Base.A.base,true); + Allele alt_C = Allele.create(BaseUtils.Base.C.base); Genotype sam_1_1_eval = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_A,reference_A)); Genotype sam_1_2_eval = GenotypeBuilder.create("test1_sample2", Arrays.asList(reference_A,alt_C)); @@ -160,9 +154,9 @@ public class ConcordanceMetricsUnitTest extends BaseTest { private Pair getData2() { - Allele reference_A = Allele.create(BaseUtils.A,true); - Allele alt_C = Allele.create(BaseUtils.C); - Allele alt_T = Allele.create(BaseUtils.T); + Allele reference_A = Allele.create(BaseUtils.Base.A.base,true); + Allele alt_C = Allele.create(BaseUtils.Base.C.base); + Allele alt_T = Allele.create(BaseUtils.Base.T.base); Genotype sam_1_1_eval = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_A,reference_A)); Genotype sam_1_2_eval = GenotypeBuilder.create("test1_sample2", Arrays.asList(reference_A,alt_T)); @@ -190,7 +184,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest { } @Test(enabled=true) - public void testMismatchingAllele() { + public void testMismatchingAlleleInAlleleSubset() { Pair data = getData2(); VariantContext eval = data.getFirst(); VariantContext truth = data.getSecond(); @@ -213,10 +207,10 @@ public class ConcordanceMetricsUnitTest extends BaseTest { private Pair getData3() { - Allele reference_ACT = Allele.create(new byte[]{BaseUtils.A,BaseUtils.C,BaseUtils.T},true); - Allele alt_AC = Allele.create(new byte[]{BaseUtils.A,BaseUtils.C}); - Allele alt_A = Allele.create(BaseUtils.A); - Allele alt_ATT = Allele.create(new byte[]{BaseUtils.A,BaseUtils.T,BaseUtils.T}); + Allele reference_ACT = Allele.create(new byte[]{BaseUtils.Base.A.base,BaseUtils.Base.C.base,BaseUtils.Base.T.base},true); + Allele alt_AC = Allele.create(new byte[]{BaseUtils.Base.A.base,BaseUtils.Base.C.base}); + Allele alt_A = Allele.create(BaseUtils.Base.A.base); + Allele alt_ATT = Allele.create(new byte[]{BaseUtils.Base.A.base,BaseUtils.Base.T.base,BaseUtils.Base.T.base}); Genotype sam_1_1_eval = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_ACT,alt_ATT)); Genotype sam_1_2_eval = GenotypeBuilder.create("test1_sample2", Arrays.asList(alt_A,alt_A)); @@ -267,9 +261,9 @@ public class ConcordanceMetricsUnitTest extends BaseTest { private Pair getData4() { - Allele reference_A = Allele.create(BaseUtils.A,true); - Allele alt_C = Allele.create(BaseUtils.C); - Allele alt_T = Allele.create(BaseUtils.T); + Allele reference_A = Allele.create(BaseUtils.Base.A.base,true); + Allele alt_C = Allele.create(BaseUtils.Base.C.base); + Allele alt_T = Allele.create(BaseUtils.Base.T.base); Genotype sam_1_1_eval = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_A,reference_A)); Genotype sam_1_2_eval = GenotypeBuilder.create("test1_sample2", Arrays.asList(Allele.NO_CALL,Allele.NO_CALL)); @@ -316,9 +310,9 @@ public class ConcordanceMetricsUnitTest extends BaseTest { private Pair getData5() { - Allele reference_A = Allele.create(BaseUtils.A,true); - Allele alt_C = Allele.create(BaseUtils.C); - Allele alt_T = Allele.create(BaseUtils.T); + Allele reference_A = Allele.create(BaseUtils.Base.A.base,true); + Allele alt_C = Allele.create(BaseUtils.Base.C.base); + Allele alt_T = Allele.create(BaseUtils.Base.T.base); Genotype sam_1_1_eval = GenotypeBuilder.create("test1_sample1", Arrays.asList(reference_A,reference_A)); Genotype sam_1_2_eval = GenotypeBuilder.create("test1_sample2", new ArrayList(0)); @@ -368,8 +362,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest { private List> getData6() { - Allele reference_A = Allele.create(BaseUtils.A,true); - Allele alt_C = Allele.create(BaseUtils.C); + Allele reference_A = Allele.create(BaseUtils.Base.A.base,true); + Allele alt_C = Allele.create(BaseUtils.Base.C.base); // site 1 - @@ -396,8 +390,8 @@ public class ConcordanceMetricsUnitTest extends BaseTest { Pair testDataSite1 = new Pair(eval_1_builder.make(),truth_1_builder.make()); - reference_A = Allele.create(BaseUtils.A,true); - Allele alt_T = Allele.create(BaseUtils.T); + reference_A = Allele.create(BaseUtils.Base.A.base,true); + Allele alt_T = Allele.create(BaseUtils.Base.T.base); // site 2 - // sample 1: no-call/hom-ref @@ -421,7 +415,7 @@ public class ConcordanceMetricsUnitTest extends BaseTest { Pair testDataSite2 = new Pair(eval_1_builder.make(),truth_1_builder.make()); - Allele alt_G = Allele.create(BaseUtils.G); + Allele alt_G = Allele.create(BaseUtils.Base.G.base); // site 3 - // sample 1: alleles do not match @@ -605,10 +599,10 @@ public class ConcordanceMetricsUnitTest extends BaseTest { public List> getData7() { - Allele ref1 = Allele.create(BaseUtils.T,true); - Allele alt1 = Allele.create(BaseUtils.C); - Allele alt2 = Allele.create(BaseUtils.G); - Allele alt3 = Allele.create(BaseUtils.A); + Allele ref1 = Allele.create(BaseUtils.Base.T.base,true); + Allele alt1 = Allele.create(BaseUtils.Base.C.base); + Allele alt2 = Allele.create(BaseUtils.Base.G.base); + Allele alt3 = Allele.create(BaseUtils.Base.A.base); GenomeLoc loc1 = genomeLocParser.createGenomeLoc("chr1",1,1); VariantContextBuilder site1Eval = new VariantContextBuilder(); @@ -709,8 +703,13 @@ public class ConcordanceMetricsUnitTest extends BaseTest { List> data = getData7(); + int idx = 0; + int[] expecNotMatch = new int[]{0,0,0,0,0,1,1}; for ( Pair varPair : data ) { metrics.update(varPair.getFirst(),varPair.getSecond()); + Assert.assertEquals(metrics.getOverallSiteConcordance().get(ConcordanceMetrics.SiteConcordanceType.ALLELES_DO_NOT_MATCH),expecNotMatch[idx]); + logger.info(idx); + idx++; } Assert.assertEquals(metrics.getOverallSiteConcordance().get(ConcordanceMetrics.SiteConcordanceType.ALLELES_DO_NOT_MATCH),1); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java similarity index 71% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java index f824ea4d1..2ebb1d7d8 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java @@ -46,85 +46,94 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.commandline.ArgumentCollection; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.testng.annotations.Test; -import java.util.*; +import java.util.Arrays; -/** - * Filters a lifted-over VCF file for ref bases that have been changed. - */ -@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) -@Reference(window=@Window(start=0,stop=100)) -public class FilterLiftedVariants extends RodWalker { +public class GenotypeConcordanceIntegrationTest extends WalkerTest { - @ArgumentCollection - protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + protected static final String emptyMd5 = "d41d8cd98f00b204e9800998ecf8427e"; - private static final int MAX_VARIANT_SIZE = 100; - - @Output(doc="File to which variants should be written",required=true) - protected VariantContextWriter writer = null; - - private long failedLocs = 0, totalLocs = 0; - - 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 VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.emptySet(), samples); - writer.writeHeader(vcfHeader); + public static String baseTestString(String eval, String comp) { + return "-T GenotypeConcordance -R " + b37KGReference + " --eval " + validationDataLocation + eval + " --comp " + validationDataLocation + comp + " -o %s"; } - private void filterAndWrite(byte[] ref, VariantContext vc) { + @Test + public void testIndelConcordance() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("NA12878.Jan2013.haplotypeCaller.subset.indels.vcf", "NA12878.Jan2013.bestPractices.subset.indels.vcf"), + 0, + Arrays.asList("0f29a0c6dc44066228c8cb204fd53ec0") + ); - totalLocs++; + executeTest("test indel concordance", spec); + } + + @Test + public void testNonoverlapingSamples() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("GenotypeConcordanceNonOverlapTest_Eval.vcf", "GenotypeConcordanceNonOverlapTest_Comp.vcf"), + 0, + Arrays.asList("fc725022d47b4b5f8a6ef87f0f1ffe89") + ); - boolean failed = false; - byte[] recordRef = vc.getReference().getBases(); - for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) { - if ( recordRef[i] != ref[i] ) { - failed = true; - break; - } - } - - if ( failed ) - failedLocs++; - else - writer.add(vc); + executeTest("test non-overlapping samples", spec); } - public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( tracker == null ) - return 0; + @Test + public void testNonoverlappingSamplesMoltenized() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("GenotypeConcordanceNonOverlapTest_Eval.vcf", "GenotypeConcordanceNonOverlapTest_Comp.vcf") + " -moltenize", + 0, + Arrays.asList("370141088362d0ab7054be5249c49c11") + ); - Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation()); - for ( VariantContext vc : VCs ) - filterAndWrite(ref.getBases(), vc); - - return 0; + executeTest("Test moltenized output",spec); } - public Integer reduceInit() { return 0; } + @Test + public void testMultipleRecordsPerSite() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("GenotypeConcordance.multipleRecordsTest1.eval.vcf","GenotypeConcordance.multipleRecordsTest1.comp.vcf"), + 0, + Arrays.asList("352d59c4ac0cee5eb8ddbc9404b19ce9") + ); - public Integer reduce(Integer value, Integer sum) { return 0; } - - public void onTraversalDone(Integer result) { - System.out.println("Filtered " + failedLocs + " records out of " + totalLocs + " total records."); + executeTest("test multiple records per site",spec); } -} \ No newline at end of file + + @Test + public void testGQFilteringEval() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("genotypeConcordanceFilterTest.vcf","genotypeConcordanceFilterTest.vcf") + " -gfe 'GQ<30'", + 0, + Arrays.asList("b7b495ccfa6d50a6be3e095d3f6d3c52") + ); + + executeTest("Test filtering on the EVAL rod",spec); + } + + @Test + public void testFloatFilteringComp() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("genotypeConcordanceFilterTest.vcf","genotypeConcordanceFilterTest.vcf") + " -gfc 'LX<0.50'", + 0, + Arrays.asList("6406b16cde7960b8943edf594303afd6") + ); + + executeTest("Test filtering on the COMP rod", spec); + } + + @Test + public void testCombinedFilters() { + WalkerTestSpec spec = new WalkerTestSpec( + baseTestString("genotypeConcordanceFilterTest.vcf","genotypeConcordanceFilterTest.vcf") + " -gfc 'LX<0.52' -gfe 'DP<5' -gfe 'GQ<37'", + 0, + Arrays.asList("26ffd06215b6177acce0ea9f35d73d31") + ); + + executeTest("Test filtering on both rods",spec); + } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java similarity index 91% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java index faddf97da..2fe50ff68 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java @@ -44,25 +44,26 @@ * 7.7 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.sting.gatk.walkers.filters; +package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.sting.WalkerTest; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.testng.annotations.Test; +import java.util.Arrays; -public class FiltrationContext { +public class RegenotypeVariantsIntegrationTest extends WalkerTest { - private ReferenceContext ref; - private VariantContext vc; + @Test + public void testRegenotype() { + String testFile = privateTestDir + "combine.3.NA12892.vcf"; - public FiltrationContext(ReferenceContext ref, VariantContext vc) { - this.ref = ref; - this.vc = vc; + WalkerTestSpec spec = new WalkerTestSpec( + "-T RegenotypeVariants -R " + b36KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header", + 1, + Arrays.asList("46ff472fc7ef6734ad01170028d5924a") + ); + + executeTest("testRegenotype--" + testFile, spec); } - - public ReferenceContext getReferenceContext() { return ref; } - - public VariantContext getVariantContext() { return vc; } - - public void setVariantContext(VariantContext newVC) { vc = newVC; } -} \ No newline at end of file +} diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index aeb8d9318..c97f0bf02 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -229,19 +229,6 @@ public class SelectVariantsIntegrationTest extends WalkerTest { executeTest("testUsingDbsnpName--" + testFile, spec); } - @Test - public void testRegenotype() { - String testFile = privateTestDir + "combine.3.vcf"; - - WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", - 1, - Arrays.asList("46ff472fc7ef6734ad01170028d5924a") - ); - - executeTest("testRegenotype--" + testFile, spec); - } - @Test public void testRemoveMLE() { String testFile = privateTestDir + "vcfexample.withMLE.vcf"; @@ -255,19 +242,6 @@ public class SelectVariantsIntegrationTest extends WalkerTest { executeTest("testRemoveMLE--" + testFile, spec); } - @Test - public void testRemoveMLEAndRegenotype() { - String testFile = privateTestDir + "vcfexample.withMLE.vcf"; - - WalkerTestSpec spec = new WalkerTestSpec( - "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", - 1, - Arrays.asList("46ff472fc7ef6734ad01170028d5924a") - ); - - executeTest("testRemoveMLEAndRegenotype--" + testFile, spec); - } - @Test public void testMultipleRecordsAtOnePosition() { String testFile = privateTestDir + "selectVariants.onePosition.vcf"; diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java index 8f4876c6f..87e208af4 100644 --- a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java @@ -50,7 +50,7 @@ package org.broadinstitute.sting.utils.pairhmm; // the imports for unit testing. import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java index 8d94c4c4a..f20d6116b 100644 --- a/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java @@ -46,6 +46,7 @@ package org.broadinstitute.sting.utils.recalibration; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.recalibration.covariates.*; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; @@ -54,6 +55,8 @@ import org.broadinstitute.sting.utils.sam.ReadUtils; import org.testng.Assert; import org.testng.annotations.Test; +import java.util.Random; + /** * @author carneiro * @since 4/21/12 @@ -62,16 +65,8 @@ public class ReadCovariatesUnitTest { @Test(enabled = false) public void testCovariateGeneration() { + final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); final String RGID = "id"; - final int length = 10; - final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); - GATKSAMRecord read = ReadUtils.createRandomRead(length, false); - GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(RGID); - rg.setPlatform("illumina"); - read.setReadGroup(rg); - final byte[] mQuals = read.getBaseQualities(EventType.BASE_SUBSTITUTION); - final byte[] iQuals = read.getBaseQualities(EventType.BASE_INSERTION); - final byte[] dQuals = read.getBaseQualities(EventType.BASE_DELETION); ReadGroupCovariate rgCov = new ReadGroupCovariate(); QualityScoreCovariate qsCov = new QualityScoreCovariate(); @@ -89,33 +84,52 @@ public class ReadCovariatesUnitTest { requestedCovariates[2] = coCov; requestedCovariates[3] = cyCov; - ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates); + final int NUM_READS = 100; + final Random rnd = GenomeAnalysisEngine.getRandomGenerator(); - // check that the length is correct - Assert.assertEquals(rc.getMismatchesKeySet().length, length); - Assert.assertEquals(rc.getInsertionsKeySet().length, length); - Assert.assertEquals(rc.getDeletionsKeySet().length, length); + 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); - for (int i = 0; i < length; i++) { - // check that read group is always the same - Assert.assertEquals(rgCov.formatKey(rc.getMismatchesKeySet(i)[0]), RGID); - Assert.assertEquals(rgCov.formatKey(rc.getInsertionsKeySet(i)[0]), RGID); - Assert.assertEquals(rgCov.formatKey(rc.getDeletionsKeySet(i)[0]), RGID); + // check that the length is correct + Assert.assertEquals(rc.getMismatchesKeySet().length, length); + Assert.assertEquals(rc.getInsertionsKeySet().length, length); + Assert.assertEquals(rc.getDeletionsKeySet().length, length); - // 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]); + 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 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 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)); + } + + } - // 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/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java index 09f751fbc..da78932d1 100644 --- a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java @@ -50,6 +50,7 @@ package org.broadinstitute.sting.utils.recalibration; // the imports for unit testing. +import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; @@ -57,7 +58,9 @@ 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.Collections; public class RecalDatumUnitTest extends BaseTest { @@ -277,4 +280,31 @@ public class RecalDatumUnitTest extends BaseTest { Assert.assertFalse(Double.isInfinite(log10likelihood)); Assert.assertFalse(Double.isNaN(log10likelihood)); } + + @Test + public void basicHierarchicalBayesianQualityEstimateTest() { + + for( double epsilon = 15.0; epsilon <= 60.0; epsilon += 2.0 ) { + double RG_Q = 45.0; + RecalDatum RG = new RecalDatum( (long)100000000, (long) (100000000 * 1.0 / (Math.pow(10.0, RG_Q/10.0))), (byte)RG_Q); + double Q = 30.0; + RecalDatum QS = new RecalDatum( (long)100000000, (long) (100000000 * 1.0 / (Math.pow(10.0, Q/10.0))), (byte)Q); + RecalDatum COV = new RecalDatum( (long)15, (long) 1, (byte)45.0); // no data here so Bayesian prior has a huge effect on the empirical quality + + // initial epsilon condition shouldn't matter when there are a lot of observations + Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( epsilon, RG, QS, Collections.singletonList(COV)), Q, 1E-4 ); + } + + for( double epsilon = 15.0; epsilon <= 60.0; epsilon += 2.0 ) { + double RG_Q = 45.0; + RecalDatum RG = new RecalDatum( (long)10, (long) (10 * 1.0 / (Math.pow(10.0, RG_Q/10.0))), (byte)RG_Q); + double Q = 30.0; + RecalDatum QS = new RecalDatum( (long)10, (long) (10 * 1.0 / (Math.pow(10.0, Q/10.0))), (byte)Q); + RecalDatum COV = new RecalDatum( (long)15, (long) 1, (byte)45.0); // no data here so Bayesian prior has a huge effect on the empirical quality + + // initial epsilon condition dominates when there is no data + Assert.assertEquals(BaseRecalibration.hierarchicalBayesianQualityEstimate( epsilon, RG, QS, Collections.singletonList(COV)), epsilon, 1E-4 ); + } + + } } \ No newline at end of file diff --git a/protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java new file mode 100644 index 000000000..ea70deeea --- /dev/null +++ b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java @@ -0,0 +1,239 @@ +/* +* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). +* +* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. +* 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. OWNERSHIP OF INTELLECTUAL PROPERTY +* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. 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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. +* 7.3 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. +* 7.4 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. +* 7.5 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. +* 7.6 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. +* 7.7 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.sting.utils.recalibration; + +import com.google.java.contract.Requires; +import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; +import org.broadinstitute.sting.utils.recalibration.covariates.*; +import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.collections.Pair; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Random; + +public class RepeatCovariatesUnitTest { + + RepeatLengthCovariate rlCovariate; + RepeatUnitCovariate ruCovariate; + RepeatUnitAndLengthCovariate rurlCovariate; + RecalibrationArgumentCollection RAC; + + + + @BeforeClass + public void init() { + RAC = new RecalibrationArgumentCollection(); + rlCovariate = new RepeatLengthCovariate(); + ruCovariate = new RepeatUnitCovariate(); + rurlCovariate = new RepeatUnitAndLengthCovariate(); + rlCovariate.initialize(RAC); + ruCovariate.initialize(RAC); + rurlCovariate.initialize(RAC); + } + + + @Test(enabled = true) + public void testFindNumberOfRepetitions() { + // First, test logic to compute number of repetitions of a substring on a given string. + int result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(), "ACAC".getBytes(), true); + Assert.assertEquals(2,result); + result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(), "ACACACAC".getBytes(), true); + Assert.assertEquals(4,result); + result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(), "ACACACACGT".getBytes(), true); + Assert.assertEquals(4,result); + result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(), "GTACACACAC".getBytes(), true); + Assert.assertEquals(0,result); + result = GATKVariantContextUtils.findNumberofRepetitions("GCA".getBytes(), "GTAGGGT".getBytes(), true); + Assert.assertEquals(0,result); + result = GATKVariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(), "GCAGCAGTAGGGTGTACACACAC".getBytes(), true); + Assert.assertEquals(1,result); + result = GATKVariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(), "GTAGGGTGTACACACACGCAGCAT".getBytes(), true); + Assert.assertEquals(0,result); + result = GATKVariantContextUtils.findNumberofRepetitions("GCA".getBytes(), "GTAGGGTGTACACACACGCAGCAGCA".getBytes(), true); + Assert.assertEquals(0,result); + // Same tests but looking backward on string + result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(), "ACAC".getBytes(), false); + Assert.assertEquals(2,result); + result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(), "ACACACAC".getBytes(), false); + Assert.assertEquals(4,result); + result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(), "ACACACACGT".getBytes(), false); + Assert.assertEquals(0,result); + result = GATKVariantContextUtils.findNumberofRepetitions("AC".getBytes(), "GTACACACAC".getBytes(), false); + Assert.assertEquals(4,result); + result = GATKVariantContextUtils.findNumberofRepetitions("GCA".getBytes(), "GTAGGGT".getBytes(), false); + Assert.assertEquals(0,result); + result = GATKVariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(), "GCAGCAGTAGGGTGTACACACAC".getBytes(), false); + Assert.assertEquals(0,result); + result = GATKVariantContextUtils.findNumberofRepetitions("GCAGCA".getBytes(), "GTAGGGTGTACACACACGCAGCAT".getBytes(), false); + Assert.assertEquals(0,result); + result = GATKVariantContextUtils.findNumberofRepetitions("GCA".getBytes(), "GTAGGGTGTACACACACGCAGCAGCA".getBytes(), false); + Assert.assertEquals(3,result); + + // test logic to get repeat unit and number of repeats from covariate value + final String[] repUnits = new String[]{"AG","CCG","TCCA","T"}; + for (String ru : repUnits) { + for (int k=1; k < 10; k++) { + Pair pair = RepeatLengthCovariate.getRUandNRfromCovariate(String.format("%s%d",ru,k)); + Assert.assertEquals(pair.second.intValue(),k); + Assert.assertEquals(pair.first,ru); + } + } + + } + + /** + * Build synthetic reads with random content made up of tandem repeats, record computed Repeat Unit and # repeats and see if + * they match with read context + */ + @Test(enabled = true) + public void testManyObservations() { + final int NUM_UNITS = 10; + final int MAX_REPEAT_UNIT_LENGTH = RAC.MAX_STR_UNIT_LENGTH; + final int MAX_NUM_REPETITIONS = RAC.MAX_REPEAT_LENGTH; + final int NUM_TEST_CASES = 100; + + Random random = new Random(); + + for (int r = 0; r < NUM_TEST_CASES; r++) { + final StringBuilder sb = new StringBuilder(); + // for each unit, generate a repeat unit at random with given random length + final ArrayList repeatUnits = new ArrayList(); + final ArrayList numsRepetitions = new ArrayList(); + for (int n=0; n < NUM_UNITS; n++) { + final int repLength = 1+random.nextInt(MAX_REPEAT_UNIT_LENGTH); + final String repeatUnit = getRandomBases(repLength); + final int numRepetitions = 1+random.nextInt(MAX_NUM_REPETITIONS); + + // log for comparison with covariate + numsRepetitions.add(numRepetitions); + repeatUnits.add(repeatUnit); + + for (int k=0; k < numRepetitions; k++) + sb.append(repeatUnit); + + } + + final String readBases = sb.toString(); + System.out.println(readBases); + final int readLength = readBases.length(); + + final byte[] readQuals = new byte[readLength]; + Arrays.fill(readQuals,(byte)30); + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(readBases.getBytes(),readQuals,readLength+"M"); + + Covariate[] requestedCovariates = new Covariate[3]; + requestedCovariates[0] = rlCovariate; + requestedCovariates[1] = ruCovariate; + requestedCovariates[2] = rurlCovariate; + ReadCovariates rc = RecalUtils.computeCovariates(read, requestedCovariates); + + // check that the length is correct + Assert.assertEquals(rc.getMismatchesKeySet().length, readLength); + Assert.assertEquals(rc.getInsertionsKeySet().length, readLength); + Assert.assertEquals(rc.getDeletionsKeySet().length, readLength); + + for (int offset = 0; offset < readBases.length(); offset++) { // recalibrate all bases in the read + // check RepeatLength + final String rlValM = rlCovariate.formatKey(rc.getMismatchesKeySet(offset)[0]); + final String rlValI = rlCovariate.formatKey(rc.getInsertionsKeySet(offset)[0]); + final String rlValD = rlCovariate.formatKey(rc.getDeletionsKeySet(offset)[0]); + // check RepeatUnit + final String ruValM = ruCovariate.formatKey(rc.getMismatchesKeySet(offset)[1]); + final String ruValI = ruCovariate.formatKey(rc.getInsertionsKeySet(offset)[1]); + final String ruValD = ruCovariate.formatKey(rc.getDeletionsKeySet(offset)[1]); + // check RepeatUnitAndLength + final String rurlValM = rurlCovariate.formatKey(rc.getMismatchesKeySet(offset)[2]); + final String rurlValI = rurlCovariate.formatKey(rc.getInsertionsKeySet(offset)[2]); + final String rurlValD = rurlCovariate.formatKey(rc.getDeletionsKeySet(offset)[2]); + // check all 3 values are identical + Assert.assertEquals(rlValD,rlValI); + Assert.assertEquals(rlValM,rlValI); + Assert.assertEquals(ruValD,ruValI); + Assert.assertEquals(ruValM,ruValI); + Assert.assertEquals(rurlValD,rurlValI); + Assert.assertEquals(rurlValM,rurlValI); + + + int fw = GATKVariantContextUtils.findNumberofRepetitions(ruValM.getBytes(), readBases.substring(offset+1,readLength).getBytes(),true); + int bw = GATKVariantContextUtils.findNumberofRepetitions(ruValM.getBytes(), readBases.substring(0,offset+1).getBytes(),false); + Assert.assertEquals(Math.min(fw+bw,RAC.MAX_REPEAT_LENGTH),(int)Integer.valueOf(rlValM)); + } + + } + + + + + + + } + + /** + * Returns random bases of given length + * @param length required length + * @return given random string + */ + @Requires("length > 0") + String getRandomBases(final int length) { + byte[] bases = new byte[length]; + Random ran = new Random(); + for (int i=0; i < length; i++ ) { + int idx = ran.nextInt(4); + bases[i] = BaseUtils.baseIndexToSimpleBase(idx); + } + return new String(bases); + } + + +} diff --git a/public/java/src/org/broadinstitute/sting/alignment/Alignment.java b/public/java/src/org/broadinstitute/sting/alignment/Alignment.java index f979df39c..a4e04ab5d 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/Alignment.java +++ b/public/java/src/org/broadinstitute/sting/alignment/Alignment.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.alignment; import net.sf.samtools.*; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java index 2a560fb15..32126f0e3 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java +++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java index f467c403a..169ad7aa5 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java +++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java @@ -29,7 +29,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.*; import org.broadinstitute.sting.alignment.Aligner; import org.broadinstitute.sting.alignment.Alignment; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java index 5fc81cb9f..f60218fe9 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java +++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.bwa.BWAAligner; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.reference.bwt.*; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java b/public/java/src/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java new file mode 100644 index 000000000..b491c9f3d --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java @@ -0,0 +1,70 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.commandline; + +import org.broad.tribble.Feature; +import org.broadinstitute.sting.utils.interval.IntervalMergingRule; +import org.broadinstitute.sting.utils.interval.IntervalSetRule; + +import java.util.List; + +public class IntervalArgumentCollection { + /** + * Using this option one can instruct the GATK engine to traverse over only part of the genome. This argument can be specified multiple times. + * One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals). + * Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf). + * To specify the completely unmapped reads in the BAM file (i.e. those without a reference contig) use -L unmapped. + */ + @Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false) + public List> intervals = null; + + /** + * Using this option one can instruct the GATK engine NOT to traverse over certain parts of the genome. This argument can be specified multiple times. + * One may use samtools-style intervals either explicitly (e.g. -XL chr1 or -XL chr1:100-200) or listed in a file (e.g. -XL myFile.intervals). + * Additionally, one may specify a rod file to skip over the positions for which there is a record in the file (e.g. -XL file.vcf). + */ + @Input(fullName = "excludeIntervals", shortName = "XL", doc = "One or more genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file (including a rod file)", required = false) + public List> excludeIntervals = null; + + /** + * How should the intervals specified by multiple -L or -XL arguments be combined? Using this argument one can, for example, traverse over all of the positions + * for which there is a record in a VCF but just in chromosome 20 (-L chr20 -L file.vcf -isr INTERSECTION). + */ + @Argument(fullName = "interval_set_rule", shortName = "isr", doc = "Indicates the set merging approach the interval parser should use to combine the various -L or -XL inputs", required = false) + public IntervalSetRule intervalSetRule = IntervalSetRule.UNION; + + /** + * Should abutting (but not overlapping) intervals be treated as separate intervals? + */ + @Argument(fullName = "interval_merging", shortName = "im", doc = "Indicates the interval merging rule we should use for abutting intervals", required = false) + public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL; + + /** + * For example, '-L chr1:100' with a padding value of 20 would turn into '-L chr1:80-120'. + */ + @Argument(fullName = "interval_padding", shortName = "ip", doc = "Indicates how many basepairs of padding to include around each of the intervals specified with the -L/--intervals argument", required = false) + public int intervalPadding = 0; +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java index 1211d1982..111786e63 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java @@ -130,7 +130,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram { getArgumentCollection().phoneHomeType == GATKRunReport.PhoneHomeOption.STDOUT ) { if ( getArgumentCollection().gatkKeyFile == null ) { throw new UserException("Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. " + - "Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + + "Please see " + UserException.PHONE_HOME_DOCS_URL + " for more information and instructions on how to obtain a key."); } else { diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index a5926aeae..de5a96237 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -47,6 +47,7 @@ import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.gatk.io.stubs.Stub; import org.broadinstitute.sting.gatk.iterators.ReadTransformer; import org.broadinstitute.sting.gatk.iterators.ReadTransformersMode; +import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; @@ -55,7 +56,6 @@ import org.broadinstitute.sting.gatk.samples.SampleDBBuilder; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalUtils; @@ -223,6 +223,9 @@ public class GenomeAnalysisEngine { * @return the value of this traversal. */ public Object execute() { + // first thing is to make sure the AWS keys can be decrypted + GATKRunReport.checkAWSAreValid(); + //HeapSizeMonitor monitor = new HeapSizeMonitor(); //monitor.start(); setStartTime(new java.util.Date()); @@ -361,7 +364,6 @@ public class GenomeAnalysisEngine { * Returns a list of active, initialized read transformers * * @param walker the walker we need to apply read transformers too - * @return a non-null list of read transformers */ public void initializeReadTransformers(final Walker walker) { final List activeTransformers = new ArrayList(); @@ -436,12 +438,9 @@ public class GenomeAnalysisEngine { protected DownsamplingMethod getDownsamplingMethod() { GATKArgumentCollection argCollection = this.getArguments(); - // Legacy downsampler can only be selected via the command line, not via walker annotations - boolean useLegacyDownsampler = argCollection.useLegacyDownsampler; - DownsamplingMethod commandLineMethod = argCollection.getDownsamplingMethod(); - DownsamplingMethod walkerMethod = WalkerManager.getDownsamplingMethod(walker, useLegacyDownsampler); - DownsamplingMethod defaultMethod = DownsamplingMethod.getDefaultDownsamplingMethod(walker, useLegacyDownsampler); + DownsamplingMethod walkerMethod = WalkerManager.getDownsamplingMethod(walker); + DownsamplingMethod defaultMethod = DownsamplingMethod.getDefaultDownsamplingMethod(walker); DownsamplingMethod method = commandLineMethod != null ? commandLineMethod : (walkerMethod != null ? walkerMethod : defaultMethod); method.checkCompatibilityWithWalker(walker); @@ -574,15 +573,10 @@ public class GenomeAnalysisEngine { throw new UserException.CommandLineException("Pairs traversal cannot be used in conjunction with intervals."); } - // Use the legacy ReadShardBalancer if legacy downsampling is enabled - ShardBalancer readShardBalancer = downsamplingMethod != null && downsamplingMethod.useLegacyDownsampler ? - new LegacyReadShardBalancer() : - new ReadShardBalancer(); - if(intervals == null) - return readsDataSource.createShardIteratorOverAllReads(readShardBalancer); + return readsDataSource.createShardIteratorOverAllReads(new ReadShardBalancer()); else - return readsDataSource.createShardIteratorOverIntervals(intervals, readShardBalancer); + return readsDataSource.createShardIteratorOverIntervals(intervals, new ReadShardBalancer()); } else throw new ReviewedStingException("Unable to determine walker type for walker " + walker.getClass().getName()); @@ -672,41 +666,7 @@ public class GenomeAnalysisEngine { * Setup the intervals to be processed */ protected void initializeIntervals() { - // return if no interval arguments at all - if ( argCollection.intervals == null && argCollection.excludeIntervals == null ) - return; - - // Note that the use of '-L all' is no longer supported. - - // if include argument isn't given, create new set of all possible intervals - - final Pair includeExcludePair = IntervalUtils.parseIntervalBindingsPair( - this.referenceDataSource, - argCollection.intervals, - argCollection.intervalSetRule, argCollection.intervalMerging, argCollection.intervalPadding, - argCollection.excludeIntervals); - - final GenomeLocSortedSet includeSortedSet = includeExcludePair.getFirst(); - final GenomeLocSortedSet excludeSortedSet = includeExcludePair.getSecond(); - - // if no exclude arguments, can return parseIntervalArguments directly - if ( excludeSortedSet == null ) - intervals = includeSortedSet; - - // otherwise there are exclude arguments => must merge include and exclude GenomeLocSortedSets - else { - intervals = includeSortedSet.subtractRegions(excludeSortedSet); - - // logging messages only printed when exclude (-XL) arguments are given - final long toPruneSize = includeSortedSet.coveredSize(); - final long toExcludeSize = excludeSortedSet.coveredSize(); - final long intervalSize = intervals.coveredSize(); - logger.info(String.format("Initial include intervals span %d loci; exclude intervals span %d loci", toPruneSize, toExcludeSize)); - logger.info(String.format("Excluding %d loci from original intervals (%.2f%% reduction)", - toPruneSize - intervalSize, (toPruneSize - intervalSize) / (0.01 * toPruneSize))); - } - - logger.info(String.format("Processing %d bp from intervals", intervals.coveredSize())); + intervals = IntervalUtils.parseIntervalArguments(this.referenceDataSource, argCollection.intervalArguments); } /** @@ -829,7 +789,7 @@ public class GenomeAnalysisEngine { DownsamplingMethod downsamplingMethod = getDownsamplingMethod(); // Synchronize the method back into the collection so that it shows up when - // interrogating for the downsample method during command line recreation. + // interrogating for the downsampling method during command line recreation. setDownsamplingMethod(downsamplingMethod); logger.info(downsamplingMethod); @@ -842,7 +802,7 @@ public class GenomeAnalysisEngine { if (argCollection.keepProgramRecords) removeProgramRecords = false; - final boolean keepReadsInLIBS = walker instanceof ActiveRegionWalker && argCollection.newART; + final boolean keepReadsInLIBS = walker instanceof ActiveRegionWalker; return new SAMDataSource( samReaderIDs, diff --git a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java index 62c2cdd13..6dfb2c2a5 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java @@ -306,11 +306,10 @@ public class WalkerManager extends PluginManager { * downsampling method is specified on the command-line, the command-line version will * be used instead. * @param walker The walker to interrogate. - * @param useLegacyDownsampler If true, use the legacy downsampling implementation * @return The downsampling method, as specified by the walker. Null if none exists. */ - public static DownsamplingMethod getDownsamplingMethod(Walker walker, boolean useLegacyDownsampler) { - return getDownsamplingMethod(walker.getClass(), useLegacyDownsampler); + public static DownsamplingMethod getDownsamplingMethod( Walker walker ) { + return getDownsamplingMethod(walker.getClass()); } /** @@ -318,10 +317,9 @@ public class WalkerManager extends PluginManager { * downsampling method is specified on the command-line, the command-line version will * be used instead. * @param walkerClass The class of the walker to interrogate. - * @param useLegacyDownsampler If true, use the legacy downsampling implementation * @return The downsampling method, as specified by the walker. Null if none exists. */ - public static DownsamplingMethod getDownsamplingMethod(Class walkerClass, boolean useLegacyDownsampler) { + public static DownsamplingMethod getDownsamplingMethod( Class walkerClass ) { DownsamplingMethod downsamplingMethod = null; if( walkerClass.isAnnotationPresent(Downsample.class) ) { @@ -329,7 +327,7 @@ public class WalkerManager extends PluginManager { DownsampleType type = downsampleParameters.by(); Integer toCoverage = downsampleParameters.toCoverage() >= 0 ? downsampleParameters.toCoverage() : null; Double toFraction = downsampleParameters.toFraction() >= 0.0d ? downsampleParameters.toFraction() : null; - downsamplingMethod = new DownsamplingMethod(type,toCoverage,toFraction,useLegacyDownsampler); + downsamplingMethod = new DownsamplingMethod(type, toCoverage, toFraction); } return downsamplingMethod; diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index b6f0d5f90..bcf3e7044 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -26,11 +26,7 @@ package org.broadinstitute.sting.gatk.arguments; import net.sf.samtools.SAMFileReader; -import org.broad.tribble.Feature; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.IntervalBinding; +import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.downsampling.DownsampleType; import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod; @@ -38,8 +34,7 @@ import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.gatk.samples.PedigreeValidationType; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.utils.interval.IntervalSetRule; +import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; import java.util.ArrayList; @@ -74,10 +69,10 @@ public class GATKArgumentCollection { // // -------------------------------------------------------------------------------------------------------------- - @Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate? STANDARD is the default, can be NO_ET so nothing is posted to the run repository. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false) + @Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate? STANDARD is the default, can be NO_ET so nothing is posted to the run repository. Please see " + UserException.PHONE_HOME_DOCS_URL + " for details.", required = false) public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD; - @Argument(fullName = "gatk_key", shortName = "K", doc="GATK Key file. Required if running with -et NO_ET. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false) + @Argument(fullName = "gatk_key", shortName = "K", doc="GATK Key file. Required if running with -et NO_ET. Please see " + UserException.PHONE_HOME_DOCS_URL + " for details.", required = false) public File gatkKeyFile = null; /** @@ -100,41 +95,8 @@ public class GATKArgumentCollection { @Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false) public List readFilters = new ArrayList(); - /** - * Using this option one can instruct the GATK engine to traverse over only part of the genome. This argument can be specified multiple times. - * One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals). - * Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf). - * To specify the completely unmapped reads in the BAM file (i.e. those without a reference contig) use -L unmapped. - */ - @Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false) - public List> intervals = null; - - /** - * Using this option one can instruct the GATK engine NOT to traverse over certain parts of the genome. This argument can be specified multiple times. - * One may use samtools-style intervals either explicitly (e.g. -XL chr1 or -XL chr1:100-200) or listed in a file (e.g. -XL myFile.intervals). - * Additionally, one may specify a rod file to skip over the positions for which there is a record in the file (e.g. -XL file.vcf). - */ - @Input(fullName = "excludeIntervals", shortName = "XL", doc = "One or more genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file (including a rod file)", required = false) - public List> excludeIntervals = null; - - /** - * How should the intervals specified by multiple -L or -XL arguments be combined? Using this argument one can, for example, traverse over all of the positions - * for which there is a record in a VCF but just in chromosome 20 (-L chr20 -L file.vcf -isr INTERSECTION). - */ - @Argument(fullName = "interval_set_rule", shortName = "isr", doc = "Indicates the set merging approach the interval parser should use to combine the various -L or -XL inputs", required = false) - public IntervalSetRule intervalSetRule = IntervalSetRule.UNION; - - /** - * Should abutting (but not overlapping) intervals be treated as separate intervals? - */ - @Argument(fullName = "interval_merging", shortName = "im", doc = "Indicates the interval merging rule we should use for abutting intervals", required = false) - public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL; - - /** - * For example, '-L chr1:100' with a padding value of 20 would turn into '-L chr1:80-120'. - */ - @Argument(fullName = "interval_padding", shortName = "ip", doc = "Indicates how many basepairs of padding to include around each of the intervals specified with the -L/--intervals argument", required = false) - public int intervalPadding = 0; + @ArgumentCollection + public IntervalArgumentCollection intervalArguments = new IntervalArgumentCollection(); @Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false) public File referenceFile = null; @@ -165,9 +127,6 @@ public class GATKArgumentCollection { @Argument(fullName = "downsample_to_coverage", shortName = "dcov", doc = "Coverage [integer] to downsample to at any given locus; note that downsampled reads are randomly selected from all possible reads at a locus. For non-locus-based traversals (eg., ReadWalkers), this sets the maximum number of reads at each alignment start position.", required = false) public Integer downsampleCoverage = null; - @Argument(fullName = "use_legacy_downsampler", shortName = "use_legacy_downsampler", doc = "Use the legacy downsampling implementation instead of the newer, less-tested implementation", required = false) - public boolean useLegacyDownsampler = false; - /** * Gets the downsampling method explicitly specified by the user. If the user didn't specify * a default downsampling mechanism, return the default. @@ -177,7 +136,7 @@ public class GATKArgumentCollection { if ( downsamplingType == null && downsampleFraction == null && downsampleCoverage == null ) return null; - return new DownsamplingMethod(downsamplingType, downsampleCoverage, downsampleFraction, useLegacyDownsampler); + return new DownsamplingMethod(downsamplingType, downsampleCoverage, downsampleFraction); } /** @@ -191,7 +150,6 @@ public class GATKArgumentCollection { downsamplingType = method.type; downsampleCoverage = method.toCoverage; downsampleFraction = method.toFraction; - useLegacyDownsampler = method.useLegacyDownsampler; } // -------------------------------------------------------------------------------------------------------------- @@ -284,6 +242,9 @@ public class GATKArgumentCollection { @Argument(fullName = "preserve_qscores_less_than", shortName = "preserveQ", doc = "Bases with quality scores less than this threshold won't be recalibrated (with -BQSR)", required = false) public int PRESERVE_QSCORES_LESS_THAN = QualityUtils.MIN_USABLE_Q_SCORE; + @Argument(fullName = "globalQScorePrior", shortName = "globalQScorePrior", doc = "The global Qscore Bayesian prior to use in the BQSR. If specified, this value will be used as the prior for all mismatch quality scores instead of the actual reported quality score", required = false) + public double globalQScorePrior = -1.0; + // -------------------------------------------------------------------------------------------------------------- // // Other utility arguments @@ -448,10 +409,5 @@ public class GATKArgumentCollection { @Hidden public boolean generateShadowBCF = false; // TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed - - @Hidden - @Argument(fullName="newART", shortName = "newART", doc = "use the new ART traversal", required=false) - public boolean newART = false; - } diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java index 4f767f90b..90d6dda48 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.contexts; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java index f74724795..d5b7d0487 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java @@ -123,38 +123,10 @@ public class LocusReferenceView extends ReferenceView { if(bounds != null) { int expandedStart = getWindowStart( bounds ); int expandedStop = getWindowStop( bounds ); - initializeReferenceSequence(genomeLocParser.createGenomeLoc(bounds.getContig(), expandedStart, expandedStop)); + initializeReferenceSequence(genomeLocParser.createGenomeLoc(bounds.getContig(), bounds.getContigIndex(), expandedStart, expandedStop)); } } - /** Returns true if the specified location is fully within the bounds of the reference window loaded into - * this LocusReferenceView object. - */ - public boolean isLocationWithinBounds(GenomeLoc loc) { - return bounds.containsP(loc); - } - - /** Ensures that specified location is within the bounds of the reference window loaded into this - * LocusReferenceView object. If the location loc is within the current bounds (or if it is null), then nothing is done. - * Otherwise, the bounds are expanded on either side, as needed, to accomodate the location, and the reference seuqence for the - * new bounds is reloaded (can be costly!). If loc spans beyond the current contig, the expansion is performed - * to the start/stop of that contig only. - * @param loc - */ - public void expandBoundsToAccomodateLoc(GenomeLoc loc) { - if ( bounds==null || loc==null) return; // can bounds be null actually??? - if ( isLocationWithinBounds(loc) ) return; - if ( loc.getContigIndex() != bounds.getContigIndex() ) - throw new ReviewedStingException("Illegal attempt to expand reference view bounds to accommodate location on a different contig."); - - bounds = genomeLocParser.createGenomeLoc(bounds.getContig(), - Math.min(bounds.getStart(),loc.getStart()), - Math.max(bounds.getStop(),loc.getStop())); - int expandedStart = getWindowStart( bounds ); - int expandedStop = getWindowStop( bounds ); - initializeReferenceSequence(genomeLocParser.createGenomeLoc(bounds.getContig(), expandedStart, expandedStop)); - } - /** * Initialize the bounds of this shard, trimming the bounds so that they match the reference. * @param provider Provider covering the appropriate locus. @@ -210,7 +182,8 @@ public class LocusReferenceView extends ReferenceView { public ReferenceContext getReferenceContext( GenomeLoc genomeLoc ) { //validateLocation( genomeLoc ); - GenomeLoc window = genomeLocParser.createGenomeLoc( genomeLoc.getContig(), getWindowStart(genomeLoc), getWindowStop(genomeLoc) ); + GenomeLoc window = genomeLocParser.createGenomeLoc( genomeLoc.getContig(), bounds.getContigIndex(), + getWindowStart(genomeLoc), getWindowStop(genomeLoc) ); int refStart = -1; if (bounds != null) { @@ -237,16 +210,6 @@ public class LocusReferenceView extends ReferenceView { return super.getReferenceBases(genomeLoc); } - /** - * Validates that the genomeLoc is one base wide and is in the reference sequence. - * @param genomeLoc location to verify. - */ - private void validateLocation( GenomeLoc genomeLoc ) throws InvalidPositionException { - if( bounds != null && !bounds.containsP(genomeLoc) ) - throw new InvalidPositionException( - String.format("Requested position %s not within interval %s", genomeLoc, bounds)); - } - /** * Gets the start of the expanded window, bounded if necessary by the contig. * @param locus The locus to expand. diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java index f77819426..6b3661baa 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java @@ -162,14 +162,6 @@ public abstract class LocusView extends LocusIterator implements View { // Cache the current and apply filtering. AlignmentContext current = nextLocus; - // The old ALL_READS downsampling implementation -- use only if legacy downsampling was requested: - if ( sourceInfo.getDownsamplingMethod().useLegacyDownsampler && - sourceInfo.getDownsamplingMethod().type == DownsampleType.ALL_READS && - sourceInfo.getDownsamplingMethod().toCoverage != null ) { - - current.downsampleToCoverage(sourceInfo.getDownsamplingMethod().toCoverage); - } - // Indicate that the next operation will need to advance. nextLocus = null; @@ -214,7 +206,13 @@ public abstract class LocusView extends LocusIterator implements View { return locus.containsP(location); } - // TODO -- remove me + /** + * {@inheritDoc} + * + * Since this class has an actual LIBS, so this function will never throw an exception + * + * @return the LocusIteratorByState used by this view to get pileups + */ @Override public LocusIteratorByState getLIBS() { return loci.getLIBS(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java index 7d3cac33d..09b72f5eb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java @@ -77,13 +77,17 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView { * @return A tracker containing information about this locus. */ public RefMetaDataTracker getReferenceOrderedDataAtLocus( GenomeLoc loc, ReferenceContext referenceContext ) { - List bindings = states.isEmpty() ? Collections.emptyList() : new ArrayList(states.size()); + if ( states.isEmpty() ) + return RefMetaDataTracker.EMPTY_TRACKER; + else { + List bindings = new ArrayList(states.size()); - for ( ReferenceOrderedDataState state: states ) - // todo -- warning, I removed the reference to the name from states - bindings.add( state.iterator.seekForward(loc) ); + for ( ReferenceOrderedDataState state: states ) + // todo -- warning, I removed the reference to the name from states + bindings.add( state.iterator.seekForward(loc) ); - return new RefMetaDataTracker(bindings); + return new RefMetaDataTracker(bindings); + } } /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java index 0b41f15c0..8d7cfbaa7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java @@ -133,14 +133,7 @@ public class BAMScheduler implements Iterator { Map currentPosition; - // Only use the deprecated SAMDataSource.getCurrentPosition() if we're not using experimental downsampling - // TODO: clean this up once the experimental downsampling engine fork collapses - if ( dataSource.getReadsInfo().getDownsamplingMethod() != null && dataSource.getReadsInfo().getDownsamplingMethod().useLegacyDownsampler ) { - currentPosition = dataSource.getCurrentPosition(); - } - else { - currentPosition = dataSource.getInitialReaderPositions(); - } + currentPosition = dataSource.getInitialReaderPositions(); for(SAMReaderID reader: dataSource.getReaderIDs()) filePointer.addFileSpans(reader,createSpanToEndOfFile(currentPosition.get(reader).getGATKChunks().get(0).getChunkStart())); diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java index 428b7355c..72b778ec9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import org.broad.tribble.util.BlockCompressedStreamConstants; +import net.sf.samtools.util.BlockCompressedStreamConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.FileInputStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java index 9cf0a9493..aec41e340 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java @@ -25,17 +25,17 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import org.broad.tribble.util.SeekableBufferedStream; -import org.broad.tribble.util.SeekableFileStream; - import net.sf.samtools.*; - +import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import java.io.*; +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; import java.nio.ByteBuffer; import java.nio.ByteOrder; +import java.nio.channels.FileChannel; import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -70,9 +70,6 @@ public class GATKBAMIndex { private final File mFile; - //TODO: figure out a good value for this buffer size - private final int BUFFERED_STREAM_BUFFER_SIZE=8192; - /** * Number of sequences stored in this index. */ @@ -83,8 +80,8 @@ public class GATKBAMIndex { */ private final long[] sequenceStartCache; - private SeekableFileStream fileStream; - private SeekableBufferedStream bufferedStream; + private FileInputStream fileStream; + private FileChannel fileChannel; public GATKBAMIndex(final File file) { mFile = file; @@ -282,6 +279,7 @@ public class GATKBAMIndex { for (int i = sequenceIndex; i < referenceSequence; i++) { sequenceStartCache[i] = position(); + // System.out.println("# Sequence TID: " + i); final int nBins = readInteger(); // System.out.println("# nBins: " + nBins); @@ -294,18 +292,15 @@ public class GATKBAMIndex { final int nLinearBins = readInteger(); // System.out.println("# nLinearBins: " + nLinearBins); skipBytes(8 * nLinearBins); - } sequenceStartCache[referenceSequence] = position(); } - - private void openIndexFile() { try { - fileStream = new SeekableFileStream(mFile); - bufferedStream = new SeekableBufferedStream(fileStream,BUFFERED_STREAM_BUFFER_SIZE); + fileStream = new FileInputStream(mFile); + fileChannel = fileStream.getChannel(); } catch (IOException exc) { throw new ReviewedStingException("Unable to open index file (" + exc.getMessage() +")" + mFile, exc); @@ -314,7 +309,7 @@ public class GATKBAMIndex { private void closeIndexFile() { try { - bufferedStream.close(); + fileChannel.close(); fileStream.close(); } catch (IOException exc) { @@ -359,12 +354,7 @@ public class GATKBAMIndex { private void read(final ByteBuffer buffer) { try { int bytesExpected = buffer.limit(); - //BufferedInputStream cannot read directly into a byte buffer, so we read into an array - //and put the result into the bytebuffer after the if statement. - - //SeekableBufferedStream is evil, it will "read" beyond the end of the file if you let it! - final int bytesToRead = (int) Math.min(bufferedStream.length() - bufferedStream.position(), bytesExpected); //min of int and long will definitely be castable to an int. - int bytesRead = bufferedStream.read(byteArray,0,bytesToRead); + int bytesRead = fileChannel.read(buffer); // We have a rigid expectation here to read in exactly the number of bytes we've limited // our buffer to -- if we read in fewer bytes than this, or encounter EOF (-1), the index @@ -375,7 +365,6 @@ public class GATKBAMIndex { "Please try re-indexing the corresponding BAM file.", mFile)); } - buffer.put(byteArray,0,bytesRead); } catch(IOException ex) { throw new ReviewedStingException("Index: unable to read bytes from index file " + mFile); @@ -389,13 +378,10 @@ public class GATKBAMIndex { */ private ByteBuffer buffer = null; - //BufferedStream don't read into ByteBuffers, so we need this temporary array - private byte[] byteArray=null; private ByteBuffer getBuffer(final int size) { if(buffer == null || buffer.capacity() < size) { // Allocate a new byte buffer. For now, make it indirect to make sure it winds up on the heap for easier debugging. buffer = ByteBuffer.allocate(size); - byteArray = new byte[size]; buffer.order(ByteOrder.LITTLE_ENDIAN); } buffer.clear(); @@ -405,13 +391,7 @@ public class GATKBAMIndex { private void skipBytes(final int count) { try { - - //try to skip forward the requested amount. - long skipped = bufferedStream.skip(count); - - if( skipped != count ) { //if not managed to skip the requested amount - throw new ReviewedStingException("Index: unable to reposition file channel of index file " + mFile); - } + fileChannel.position(fileChannel.position() + count); } catch(IOException ex) { throw new ReviewedStingException("Index: unable to reposition file channel of index file " + mFile); @@ -420,8 +400,7 @@ public class GATKBAMIndex { private void seek(final long position) { try { - //to seek a new position, move the fileChannel, and reposition the bufferedStream - bufferedStream.seek(position); + fileChannel.position(position); } catch(IOException ex) { throw new ReviewedStingException("Index: unable to reposition of file channel of index file " + mFile); @@ -434,7 +413,7 @@ public class GATKBAMIndex { */ private long position() { try { - return bufferedStream.position(); + return fileChannel.position(); } catch (IOException exc) { throw new ReviewedStingException("Unable to read position from index file " + mFile, exc); diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LegacyReadShardBalancer.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LegacyReadShardBalancer.java deleted file mode 100644 index 510398157..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LegacyReadShardBalancer.java +++ /dev/null @@ -1,130 +0,0 @@ -/* -* Copyright (c) 2012 The Broad Institute -* -* 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.sting.gatk.datasources.reads; - -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.SAMFileSpan; - -import java.util.HashMap; -import java.util.Iterator; -import java.util.Map; -import java.util.NoSuchElementException; - -/** - * Divide up large file pointers containing reads into more manageable subcomponents. - * - * TODO: delete this class once the experimental downsampling engine fork collapses - */ -public class LegacyReadShardBalancer extends ShardBalancer { - /** - * Convert iterators of file pointers into balanced iterators of shards. - * @return An iterator over balanced shards. - */ - public Iterator iterator() { - return new Iterator() { - /** - * The cached shard to be returned next. Prefetched in the peekable iterator style. - */ - private Shard nextShard = null; - - /** - * The file pointer currently being processed. - */ - private FilePointer currentFilePointer; - - /** - * Ending position of the last shard in the file. - */ - private Map position = readsDataSource.getCurrentPosition(); - - { - if(filePointers.hasNext()) - currentFilePointer = filePointers.next(); - advance(); - } - - public boolean hasNext() { - return nextShard != null; - } - - public Shard next() { - if(!hasNext()) - throw new NoSuchElementException("No next read shard available"); - Shard currentShard = nextShard; - advance(); - return currentShard; - } - - public void remove() { - throw new UnsupportedOperationException("Unable to remove from shard balancing iterator"); - } - - private void advance() { - Map shardPosition; - nextShard = null; - - Map selectedReaders = new HashMap(); - while(selectedReaders.size() == 0 && currentFilePointer != null) { - shardPosition = currentFilePointer.fileSpans; - - for(SAMReaderID id: shardPosition.keySet()) { - SAMFileSpan fileSpan = new GATKBAMFileSpan(shardPosition.get(id).removeContentsBefore(position.get(id))); - selectedReaders.put(id,fileSpan); - } - - if(!isEmpty(selectedReaders)) { - Shard shard = new ReadShard(parser,readsDataSource,selectedReaders,currentFilePointer.locations,currentFilePointer.isRegionUnmapped); - readsDataSource.fillShard(shard); - - if(!shard.isBufferEmpty()) { - nextShard = shard; - break; - } - } - - selectedReaders.clear(); - currentFilePointer = filePointers.hasNext() ? filePointers.next() : null; - } - - position = readsDataSource.getCurrentPosition(); - } - - /** - * Detects whether the list of file spans contain any read data. - * @param selectedSpans Mapping of readers to file spans. - * @return True if file spans are completely empty; false otherwise. - */ - private boolean isEmpty(Map selectedSpans) { - for(SAMFileSpan fileSpan: selectedSpans.values()) { - if(!fileSpan.isEmpty()) - return false; - } - return true; - } - }; - } - -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index c9a3b0df0..d52e55d6d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -97,13 +97,6 @@ public class SAMDataSource { */ private final Map bamIndices = new HashMap(); - /** - * How far along is each reader? - * - * TODO: delete this once the experimental downsampling engine fork collapses - */ - private final Map readerPositions = new HashMap(); - /** * The merged header. */ @@ -298,8 +291,6 @@ public class SAMDataSource { this.sortOrder = sortOrder; } - initializeReaderPositions(readers); - mergedHeader = readers.getMergedHeader(); hasReadGroupCollisions = readers.hasReadGroupCollisions(); @@ -387,17 +378,6 @@ public class SAMDataSource { return resourcePool.getReaderID(read.getFileSource().getReader()); } - /** - * Retrieves the current position within the BAM file. - * @return A mapping of reader to current position. - * - * TODO: delete this once the experimental downsampling engine fork collapses - */ - @Deprecated - public Map getCurrentPosition() { - return readerPositions; - } - /** * Gets the merged header from the SAM file. * @return The merged header. @@ -475,67 +455,6 @@ public class SAMDataSource { } } - /** - * Legacy method to fill the given buffering shard with reads. - * - * Shard.fill() is used instead of this method unless legacy downsampling is enabled - * - * TODO: delete this method once the experimental downsampling engine fork collapses - * - * @param shard Shard to fill. - */ - @Deprecated - public void fillShard(Shard shard) { - if(!shard.buffersReads()) - throw new ReviewedStingException("Attempting to fill a non-buffering shard."); - - SAMReaders readers = resourcePool.getAvailableReaders(); - // Cache the most recently viewed read so that we can check whether we've reached the end of a pair. - SAMRecord read = null; - - Map positionUpdates = new IdentityHashMap(); - - CloseableIterator iterator = getIterator(readers,shard,sortOrder == SAMFileHeader.SortOrder.coordinate); - while(!shard.isBufferFull() && iterator.hasNext()) { - final SAMRecord nextRead = iterator.next(); - if ( read == null || (nextRead.getReferenceIndex().equals(read.getReferenceIndex())) ) { - // only add reads to the shard if they are on the same contig - read = nextRead; - shard.addRead(read); - noteFilePositionUpdate(positionUpdates,read); - } else { - break; - } - } - - // If the reads are sorted in queryname order, ensure that all reads - // having the same queryname become part of the same shard. - if(sortOrder == SAMFileHeader.SortOrder.queryname) { - while(iterator.hasNext()) { - SAMRecord nextRead = iterator.next(); - if(read == null || !read.getReadName().equals(nextRead.getReadName())) - break; - shard.addRead(nextRead); - noteFilePositionUpdate(positionUpdates,nextRead); - } - } - - iterator.close(); - - // Make the updates specified by the reader. - for(Map.Entry positionUpdate: positionUpdates.entrySet()) - readerPositions.put(readers.getReaderID(positionUpdate.getKey()),positionUpdate.getValue()); - } - - /* - * TODO: delete this method once the experimental downsampling engine fork collapses - */ - @Deprecated - private void noteFilePositionUpdate(Map positionMapping, SAMRecord read) { - GATKBAMFileSpan endChunk = new GATKBAMFileSpan(read.getFileSource().getFilePointer().getContentsFollowing()); - positionMapping.put(read.getFileSource().getReader(),endChunk); - } - public StingSAMIterator seek(Shard shard) { if(shard.buffersReads()) { return shard.iterator(); @@ -559,19 +478,6 @@ public class SAMDataSource { throw new ReviewedStingException("Unable to find id for reader associated with read " + read.getReadName()); } - /** - * Initialize the current reader positions - * - * TODO: delete this once the experimental downsampling engine fork collapses - * - * @param readers - */ - @Deprecated - private void initializeReaderPositions(SAMReaders readers) { - for(SAMReaderID id: getReaderIDs()) - readerPositions.put(id,new GATKBAMFileSpan(readers.getReader(id).getFilePointerSpanningReads())); - } - /** * Get the initial reader positions across all BAM files * @@ -646,7 +552,6 @@ public class SAMDataSource { enableVerification, readProperties.useOriginalBaseQualities(), new ReleasingIterator(readers,StingSAMIteratorAdapter.adapt(mergingIterator)), - readProperties.getDownsamplingMethod().toFraction, readProperties.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION), readProperties.getSupplementalFilters(), readProperties.getReadTransformers(), @@ -704,7 +609,6 @@ public class SAMDataSource { * @param enableVerification Verify the order of reads. * @param useOriginalBaseQualities True if original base qualities should be used. * @param wrappedIterator the raw data source. - * @param downsamplingFraction whether and how much to downsample the reads themselves (not at a locus). * @param noValidationOfReadOrder Another trigger for the verifying iterator? TODO: look into this. * @param supplementalFilters additional filters to apply to the reads. * @param defaultBaseQualities if the reads have incomplete quality scores, set them all to defaultBaseQuality. @@ -715,7 +619,6 @@ public class SAMDataSource { boolean enableVerification, boolean useOriginalBaseQualities, StingSAMIterator wrappedIterator, - Double downsamplingFraction, Boolean noValidationOfReadOrder, Collection supplementalFilters, List readTransformers, @@ -727,30 +630,25 @@ public class SAMDataSource { // * (otherwise we will process something that we may end up throwing away) * // // ************************************************************************************************ // + // Filters: wrappedIterator = StingSAMIteratorAdapter.adapt(new CountingFilteringIterator(readMetrics,wrappedIterator,supplementalFilters)); - // If we're using the new downsampling implementation, apply downsampling iterators at this - // point in the read stream for most (but not all) cases - if ( ! readProperties.getDownsamplingMethod().useLegacyDownsampler ) { + // Downsampling: - // For locus traversals where we're downsampling to coverage by sample, assume that the downsamplers - // will be invoked downstream from us in LocusIteratorByState. This improves performance by avoiding - // splitting/re-assembly of the read stream at this stage, and also allows for partial downsampling - // of individual reads. - boolean assumeDownstreamLIBSDownsampling = isLocusBasedTraversal && - readProperties.getDownsamplingMethod().type == DownsampleType.BY_SAMPLE && - readProperties.getDownsamplingMethod().toCoverage != null; + // For locus traversals where we're downsampling to coverage by sample, assume that the downsamplers + // will be invoked downstream from us in LocusIteratorByState. This improves performance by avoiding + // splitting/re-assembly of the read stream at this stage, and also allows for partial downsampling + // of individual reads. + boolean assumeDownstreamLIBSDownsampling = isLocusBasedTraversal && + readProperties.getDownsamplingMethod().type == DownsampleType.BY_SAMPLE && + readProperties.getDownsamplingMethod().toCoverage != null; - if ( ! assumeDownstreamLIBSDownsampling ) { - wrappedIterator = applyDownsamplingIterator(wrappedIterator); - } + // Apply downsampling iterators here only in cases where we know that LocusIteratorByState won't be + // doing any downsampling downstream of us + if ( ! assumeDownstreamLIBSDownsampling ) { + wrappedIterator = applyDownsamplingIterator(wrappedIterator); } - // Use the old fractional downsampler only if we're using legacy downsampling: - // TODO: remove this statement (and associated classes) once the downsampling engine fork collapses - if ( readProperties.getDownsamplingMethod().useLegacyDownsampler && downsamplingFraction != null ) - wrappedIterator = new LegacyDownsampleIterator(wrappedIterator, downsamplingFraction); - // unless they've said not to validate read ordering (!noValidationOfReadOrder) and we've enabled verification, // verify the read ordering by applying a sort order iterator if (!noValidationOfReadOrder && enableVerification) diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java index 2c03363ba..5b4c2afda 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java @@ -95,7 +95,10 @@ public abstract class Shard implements HasGenomeLocation { */ private final Map fileSpans; - + /** + * Lazy-calculated span of all of the genome locs in this shard + */ + private GenomeLoc spanningLocation = null; /** * Statistics about which reads in this shards were used and which were filtered away. @@ -148,27 +151,34 @@ public abstract class Shard implements HasGenomeLocation { /** * Returns the span of the genomeLocs comprising this shard - * @param - * @return + * @return a GenomeLoc that starts as the first position in getGenomeLocs() and stops at the stop of the last + * position in getGenomeLocs() */ public GenomeLoc getLocation() { - if ( getGenomeLocs() == null ) - return GenomeLoc.WHOLE_GENOME; + if ( spanningLocation == null ) { + if ( getGenomeLocs() == null ) + spanningLocation = GenomeLoc.WHOLE_GENOME; + else if ( getGenomeLocs().size() == 0 ) { + spanningLocation = getGenomeLocs().get(0); + } else { + int start = Integer.MAX_VALUE; + int stop = Integer.MIN_VALUE; + String contig = null; - int start = Integer.MAX_VALUE; - int stop = Integer.MIN_VALUE; - String contig = null; + for ( GenomeLoc loc : getGenomeLocs() ) { + if ( GenomeLoc.isUnmapped(loc) ) + // special case the unmapped region marker, just abort out + return loc; + contig = loc.getContig(); + if ( loc.getStart() < start ) start = loc.getStart(); + if ( loc.getStop() > stop ) stop = loc.getStop(); + } - for ( GenomeLoc loc : getGenomeLocs() ) { - if ( GenomeLoc.isUnmapped(loc) ) - // special case the unmapped region marker, just abort out - return loc; - contig = loc.getContig(); - if ( loc.getStart() < start ) start = loc.getStart(); - if ( loc.getStop() > stop ) stop = loc.getStop(); + spanningLocation = parser.createGenomeLoc(contig, start, stop); + } } - return parser.createGenomeLoc(contig, start, stop); + return spanningLocation; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/public/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java new file mode 100644 index 000000000..6bfa56828 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java @@ -0,0 +1,260 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.downsampling; + +import net.sf.samtools.SAMReadGroupRecord; +import org.broadinstitute.sting.utils.*; +import org.broadinstitute.sting.utils.pileup.*; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.variantcontext.Allele; + +import java.io.PrintStream; +import java.util.*; + +public class AlleleBiasedDownsamplingUtils { + + /** + * Computes an allele biased version of the given pileup + * + * @param pileup the original pileup + * @param downsamplingFraction the fraction of total reads to remove per allele + * @param log logging output + * @return allele biased pileup + */ + public static ReadBackedPileup createAlleleBiasedBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { + // special case removal of all or no reads + if ( downsamplingFraction <= 0.0 ) + return pileup; + if ( downsamplingFraction >= 1.0 ) + return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList()); + + final ArrayList[] alleleStratifiedElements = new ArrayList[4]; + for ( int i = 0; i < 4; i++ ) + alleleStratifiedElements[i] = new ArrayList(); + + // start by stratifying the reads by the alleles they represent at this position + for ( final PileupElement pe : pileup ) { + // we do not want to remove a reduced read + if ( !pe.getRead().isReducedRead() ) { + final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase()); + if ( baseIndex != -1 ) + alleleStratifiedElements[baseIndex].add(pe); + } + } + + // make a listing of allele counts + final int[] alleleCounts = new int[4]; + for ( int i = 0; i < 4; i++ ) + alleleCounts[i] = alleleStratifiedElements[i].size(); + + // do smart down-sampling + int numReadsToRemove = (int)(pileup.getNumberOfElements() * downsamplingFraction); // floor + final int[] targetAlleleCounts = runSmartDownsampling(alleleCounts, numReadsToRemove); + + final HashSet readsToRemove = new HashSet(numReadsToRemove); + for ( int i = 0; i < 4; i++ ) { + final ArrayList alleleList = alleleStratifiedElements[i]; + // if we don't need to remove any reads, then don't + if ( alleleList.size() > targetAlleleCounts[i] ) + readsToRemove.addAll(downsampleElements(alleleList, alleleList.size() - targetAlleleCounts[i], log)); + } + + // clean up pointers so memory can be garbage collected if needed + for ( int i = 0; i < 4; i++ ) + alleleStratifiedElements[i].clear(); + + // we need to keep the reads sorted because the FragmentUtils code will expect them in coordinate order and will fail otherwise + final List readsToKeep = new ArrayList(pileup.getNumberOfElements() - numReadsToRemove); + for ( final PileupElement pe : pileup ) { + if ( !readsToRemove.contains(pe) ) { + readsToKeep.add(pe); + } + } + + return new ReadBackedPileupImpl(pileup.getLocation(), new ArrayList(readsToKeep)); + } + + private static int scoreAlleleCounts(final int[] alleleCounts) { + if ( alleleCounts.length < 2 ) + return 0; + + // sort the counts (in ascending order) + final int[] alleleCountsCopy = alleleCounts.clone(); + Arrays.sort(alleleCountsCopy); + + final int maxCount = alleleCountsCopy[alleleCounts.length - 1]; + final int nextBestCount = alleleCountsCopy[alleleCounts.length - 2]; + + int remainderCount = 0; + for ( int i = 0; i < alleleCounts.length - 2; i++ ) + remainderCount += alleleCountsCopy[i]; + + // try to get the best score: + // - in the het case the counts should be equal with nothing else + // - in the hom case the non-max should be zero + return Math.min(maxCount - nextBestCount + remainderCount, Math.abs(nextBestCount + remainderCount)); + } + + /** + * Computes an allele biased version of the given pileup + * + * @param alleleCounts the original pileup + * @param numReadsToRemove fraction of total reads to remove per allele + * @return allele biased pileup + */ + protected static int[] runSmartDownsampling(final int[] alleleCounts, final int numReadsToRemove) { + final int numAlleles = alleleCounts.length; + + int maxScore = scoreAlleleCounts(alleleCounts); + int[] alleleCountsOfMax = alleleCounts; + + final int numReadsToRemovePerAllele = numReadsToRemove / 2; + + for ( int i = 0; i < numAlleles; i++ ) { + for ( int j = i; j < numAlleles; j++ ) { + final int[] newCounts = alleleCounts.clone(); + + // split these cases so we don't lose on the floor (since we divided by 2) + if ( i == j ) { + newCounts[i] = Math.max(0, newCounts[i] - numReadsToRemove); + } else { + newCounts[i] = Math.max(0, newCounts[i] - numReadsToRemovePerAllele); + newCounts[j] = Math.max(0, newCounts[j] - numReadsToRemovePerAllele); + } + + final int score = scoreAlleleCounts(newCounts); + + if ( score < maxScore ) { + maxScore = score; + alleleCountsOfMax = newCounts; + } + } + } + + return alleleCountsOfMax; + } + + /** + * Performs allele biased down-sampling on a pileup and computes the list of elements to remove + * + * @param elements original list of records + * @param numElementsToRemove the number of records to remove + * @param log logging output + * @return the list of pileup elements TO REMOVE + */ + private static List downsampleElements(final List elements, final int numElementsToRemove, final PrintStream log) { + ArrayList elementsToRemove = new ArrayList(numElementsToRemove); + + // are there no elements to remove? + if ( numElementsToRemove == 0 ) + return elementsToRemove; + + // should we remove all of the elements? + final int pileupSize = elements.size(); + if ( numElementsToRemove == pileupSize ) { + logAllElements(elements, log); + elementsToRemove.addAll(elements); + return elementsToRemove; + } + + // create a bitset describing which elements to remove + final BitSet itemsToRemove = new BitSet(pileupSize); + for ( Integer selectedIndex : MathUtils.sampleIndicesWithoutReplacement(pileupSize, numElementsToRemove) ) { + itemsToRemove.set(selectedIndex); + } + + for ( int i = 0; i < pileupSize; i++ ) { + if ( itemsToRemove.get(i) ) { + final T element = elements.get(i); + logElement(element, log); + elementsToRemove.add(element); + } + } + + return elementsToRemove; + } + + /** + * Computes reads to remove based on an allele biased down-sampling + * + * @param alleleReadMap original list of records per allele + * @param downsamplingFraction the fraction of total reads to remove per allele + * @param log logging output + * @return list of reads TO REMOVE from allele biased down-sampling + */ + public static List selectAlleleBiasedReads(final Map> alleleReadMap, final double downsamplingFraction, final PrintStream log) { + int totalReads = 0; + for ( final List reads : alleleReadMap.values() ) + totalReads += reads.size(); + + int numReadsToRemove = (int)(totalReads * downsamplingFraction); + + // make a listing of allele counts + final List alleles = new ArrayList(alleleReadMap.keySet()); + alleles.remove(Allele.NO_CALL); // ignore the no-call bin + final int numAlleles = alleles.size(); + final int[] alleleCounts = new int[numAlleles]; + for ( int i = 0; i < numAlleles; i++ ) + alleleCounts[i] = alleleReadMap.get(alleles.get(i)).size(); + + // do smart down-sampling + final int[] targetAlleleCounts = runSmartDownsampling(alleleCounts, numReadsToRemove); + + final List readsToRemove = new ArrayList(numReadsToRemove); + for ( int i = 0; i < numAlleles; i++ ) { + final List alleleBin = alleleReadMap.get(alleles.get(i)); + + if ( alleleBin.size() > targetAlleleCounts[i] ) { + readsToRemove.addAll(downsampleElements(alleleBin, alleleBin.size() - targetAlleleCounts[i], log)); + } + } + + return readsToRemove; + } + + private static void logAllElements(final List elements, final PrintStream log) { + if ( log != null ) { + for ( final T obj : elements ) { + logElement(obj, log); + } + } + } + + private static void logElement(final T obj, final PrintStream log) { + if ( log != null ) { + + final GATKSAMRecord read; + if ( obj instanceof PileupElement ) + read = ((PileupElement)obj).getRead(); + else + read = (GATKSAMRecord)obj; + + final SAMReadGroupRecord readGroup = read.getReadGroup(); + log.println(String.format("%s\t%s\t%s\t%s", read.getReadName(), readGroup.getSample(), readGroup.getLibrary(), readGroup.getPlatformUnit())); + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/DownsamplingMethod.java b/public/java/src/org/broadinstitute/sting/gatk/downsampling/DownsamplingMethod.java index bc32f9188..5aa27608d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/downsampling/DownsamplingMethod.java +++ b/public/java/src/org/broadinstitute/sting/gatk/downsampling/DownsamplingMethod.java @@ -50,35 +50,43 @@ public class DownsamplingMethod { */ public final Double toFraction; - /** - * Use the legacy downsampling implementation instead of the newer implementation? - */ - public final boolean useLegacyDownsampler; - /** * Expresses no downsampling applied at all. */ - public static final DownsamplingMethod NONE = new DownsamplingMethod(DownsampleType.NONE,null,null,false); + public static final DownsamplingMethod NONE = new DownsamplingMethod(DownsampleType.NONE, null, null); /** * Default type to use if no type is specified */ - public static DownsampleType DEFAULT_DOWNSAMPLING_TYPE = DownsampleType.BY_SAMPLE; + public static final DownsampleType DEFAULT_DOWNSAMPLING_TYPE = DownsampleType.BY_SAMPLE; /** * Default target coverage for locus-based traversals */ - public static int DEFAULT_LOCUS_BASED_TRAVERSAL_DOWNSAMPLING_COVERAGE = 1000; + public static final int DEFAULT_LOCUS_TRAVERSAL_DOWNSAMPLING_COVERAGE = 1000; - public DownsamplingMethod( DownsampleType type, Integer toCoverage, Double toFraction, boolean useLegacyDownsampler ) { + /** + * Default downsampling method for locus-based traversals + */ + public static final DownsamplingMethod DEFAULT_LOCUS_TRAVERSAL_DOWNSAMPLING_METHOD = + new DownsamplingMethod(DEFAULT_DOWNSAMPLING_TYPE, DEFAULT_LOCUS_TRAVERSAL_DOWNSAMPLING_COVERAGE, null); + + /** + * Default downsampling method for read-based traversals + */ + public static final DownsamplingMethod DEFAULT_READ_TRAVERSAL_DOWNSAMPLING_METHOD = NONE; + + + public DownsamplingMethod( DownsampleType type, Integer toCoverage, Double toFraction ) { this.type = type != null ? type : DEFAULT_DOWNSAMPLING_TYPE; - this.toCoverage = toCoverage; - this.toFraction = toFraction; - this.useLegacyDownsampler = useLegacyDownsampler; if ( type == DownsampleType.NONE ) { - toCoverage = null; - toFraction = null; + this.toCoverage = null; + this.toFraction = null; + } + else { + this.toCoverage = toCoverage; + this.toFraction = toFraction; } validate(); @@ -87,34 +95,28 @@ public class DownsamplingMethod { private void validate() { // Can't leave toFraction and toCoverage null unless type is NONE if ( type != DownsampleType.NONE && toFraction == null && toCoverage == null ) - throw new UserException.CommandLineException("Must specify either toFraction or toCoverage when downsampling."); + throw new UserException("Must specify either toFraction or toCoverage when downsampling."); // Fraction and coverage cannot both be specified. if ( toFraction != null && toCoverage != null ) - throw new UserException.CommandLineException("Downsampling coverage and fraction are both specified. Please choose only one."); + throw new UserException("Downsampling coverage and fraction are both specified. Please choose only one."); // toCoverage must be > 0 when specified if ( toCoverage != null && toCoverage <= 0 ) { - throw new UserException.CommandLineException("toCoverage must be > 0 when downsampling to coverage"); + throw new UserException("toCoverage must be > 0 when downsampling to coverage"); } // toFraction must be >= 0.0 and <= 1.0 when specified if ( toFraction != null && (toFraction < 0.0 || toFraction > 1.0) ) { - throw new UserException.CommandLineException("toFraction must be >= 0.0 and <= 1.0 when downsampling to a fraction of reads"); + throw new UserException("toFraction must be >= 0.0 and <= 1.0 when downsampling to a fraction of reads"); } } public void checkCompatibilityWithWalker( Walker walker ) { boolean isLocusTraversal = walker instanceof LocusWalker || walker instanceof ActiveRegionWalker; - if ( ! isLocusTraversal && useLegacyDownsampler && toCoverage != null ) { - throw new UserException.CommandLineException("Downsampling to coverage for read-based traversals (eg., ReadWalkers) is not supported in the legacy downsampling implementation. " + - "The newer downsampling implementation does not have this limitation."); - } - - if ( isLocusTraversal && ! useLegacyDownsampler && type == DownsampleType.ALL_READS && toCoverage != null ) { - throw new UserException.CommandLineException("Downsampling to coverage with the ALL_READS method for locus-based traversals (eg., LocusWalkers) is not yet supported in the new downsampling implementation (though it is supported for ReadWalkers). " + - "You can run with --use_legacy_downsampler for a broken and poorly-maintained implementation of ALL_READS to-coverage downsampling, but this is not recommended."); + if ( isLocusTraversal && type == DownsampleType.ALL_READS && toCoverage != null ) { + throw new UserException("Downsampling to coverage with the ALL_READS method for locus-based traversals (eg., LocusWalkers) is not currently supported (though it is supported for ReadWalkers)."); } } @@ -128,31 +130,22 @@ public class DownsamplingMethod { builder.append(String.format("Method: %s, ", type)); if ( toCoverage != null ) { - builder.append(String.format("Target Coverage: %d, ", toCoverage)); + builder.append(String.format("Target Coverage: %d", toCoverage)); } else { - builder.append(String.format("Target Fraction: %.2f, ", toFraction)); - } - - if ( useLegacyDownsampler ) { - builder.append("Using the legacy downsampling implementation"); - } - else { - builder.append("Using the new downsampling implementation"); + builder.append(String.format("Target Fraction: %.2f", toFraction)); } } return builder.toString(); } - public static DownsamplingMethod getDefaultDownsamplingMethod( Walker walker, boolean useLegacyDownsampler ) { + public static DownsamplingMethod getDefaultDownsamplingMethod( Walker walker ) { if ( walker instanceof LocusWalker || walker instanceof ActiveRegionWalker ) { - return new DownsamplingMethod(DEFAULT_DOWNSAMPLING_TYPE, DEFAULT_LOCUS_BASED_TRAVERSAL_DOWNSAMPLING_COVERAGE, - null, useLegacyDownsampler); + return DEFAULT_LOCUS_TRAVERSAL_DOWNSAMPLING_METHOD; } else { - // Downsampling is off by default for non-locus-based traversals - return new DownsamplingMethod(DownsampleType.NONE, null, null, useLegacyDownsampler); + return DEFAULT_READ_TRAVERSAL_DOWNSAMPLING_METHOD; } } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java b/public/java/src/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java index 600834012..b06d5f5b4 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java @@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.downsampling; import net.sf.samtools.SAMRecord; -import java.util.ArrayList; import java.util.Collection; +import java.util.LinkedList; import java.util.List; /** @@ -41,7 +41,7 @@ import java.util.List; */ public class PassThroughDownsampler implements ReadsDownsampler { - private ArrayList selectedReads; + private LinkedList selectedReads; public PassThroughDownsampler() { clear(); @@ -59,9 +59,13 @@ public class PassThroughDownsampler implements ReadsDownsam } public boolean hasFinalizedItems() { - return selectedReads.size() > 0; + return ! selectedReads.isEmpty(); } + /** + * Note that this list is a linked list and so doesn't support fast random access + * @return + */ public List consumeFinalizedItems() { // pass by reference rather than make a copy, for speed List downsampledItems = selectedReads; @@ -74,7 +78,7 @@ public class PassThroughDownsampler implements ReadsDownsam } public T peekFinalized() { - return selectedReads.isEmpty() ? null : selectedReads.get(0); + return selectedReads.isEmpty() ? null : selectedReads.getFirst(); } public T peekPending() { @@ -90,7 +94,7 @@ public class PassThroughDownsampler implements ReadsDownsam } public void clear() { - selectedReads = new ArrayList(); + selectedReads = new LinkedList(); } public void reset() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java b/public/java/src/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java index 0d7a0dd14..4331fd723 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java @@ -29,9 +29,7 @@ import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import java.util.ArrayList; -import java.util.Collection; -import java.util.List; +import java.util.*; /** * Reservoir Downsampler: Selects n reads out of a stream whose size is not known in advance, with @@ -42,10 +40,25 @@ import java.util.List; * @author David Roazen */ public class ReservoirDownsampler implements ReadsDownsampler { + private final int targetSampleSize; - private ArrayList reservoir; + /** + * if true, this downsampler will be optimized for the case + * where most of the time we won't fill up anything like the + * targetSampleSize elements. If this is false, we will allocate + * internal buffers to targetSampleSize initially, which minimizes + * the cost of allocation if we often use targetSampleSize or more + * elements. + */ + private final boolean expectFewOverflows; - private int targetSampleSize; + /** + * At times this can be a linked list or an array list, depending on how we're accessing the + * data and whether or not we're expecting few overflows + */ + private List reservoir; + + private boolean isLinkedList; private int totalReadsSeen; @@ -56,17 +69,35 @@ public class ReservoirDownsampler implements ReadsDownsampl * * @param targetSampleSize Size of the reservoir used by this downsampler. Number of items retained * after downsampling will be min(totalReads, targetSampleSize) + * @param expectFewOverflows if true, this downsampler will be optimized for the case + * where most of the time we won't fill up anything like the + * targetSampleSize elements. If this is false, we will allocate + * internal buffers to targetSampleSize initially, which minimizes + * the cost of allocation if we often use targetSampleSize or more + * elements. */ - public ReservoirDownsampler ( int targetSampleSize ) { + public ReservoirDownsampler ( final int targetSampleSize, final boolean expectFewOverflows) { if ( targetSampleSize <= 0 ) { throw new ReviewedStingException("Cannot do reservoir downsampling with a sample size <= 0"); } this.targetSampleSize = targetSampleSize; + this.expectFewOverflows = expectFewOverflows; clear(); reset(); } + /** + * Construct a ReservoirDownsampler + * + * @param targetSampleSize Size of the reservoir used by this downsampler. Number of items retained + * after downsampling will be min(totalReads, targetSampleSize) + */ + public ReservoirDownsampler ( int targetSampleSize ) { + this(targetSampleSize, false); + } + + public void submit ( T newRead ) { totalReadsSeen++; @@ -74,7 +105,12 @@ public class ReservoirDownsampler implements ReadsDownsampl reservoir.add(newRead); } else { - int randomSlot = GenomeAnalysisEngine.getRandomGenerator().nextInt(totalReadsSeen); + if ( isLinkedList ) { + reservoir = new ArrayList(reservoir); + isLinkedList = false; + } + + final int randomSlot = GenomeAnalysisEngine.getRandomGenerator().nextInt(totalReadsSeen); if ( randomSlot < targetSampleSize ) { reservoir.set(randomSlot, newRead); } @@ -93,10 +129,15 @@ public class ReservoirDownsampler implements ReadsDownsampl } public List consumeFinalizedItems() { - // pass by reference rather than make a copy, for speed - List downsampledItems = reservoir; - clear(); - return downsampledItems; + if ( reservoir.isEmpty() ) { + // if there's nothing here, don't both allocating a new list completely + return Collections.emptyList(); + } else { + // pass by reference rather than make a copy, for speed + List downsampledItems = reservoir; + clear(); + return downsampledItems; + } } public boolean hasPendingItems() { @@ -119,9 +160,18 @@ public class ReservoirDownsampler implements ReadsDownsampl // NO-OP } + /** + * Clear the data structures used to hold information + */ public void clear() { - reservoir = new ArrayList(targetSampleSize); - totalReadsSeen = 0; // an internal stat used by the downsampling process, so not cleared by reset() below + // if we aren't expecting many overflows, allocate a linked list not an arraylist + reservoir = expectFewOverflows ? new LinkedList() : new ArrayList(targetSampleSize); + + // it's a linked list if we allocate one + isLinkedList = expectFewOverflows; + + // an internal stat used by the downsampling process, so not cleared by reset() below + totalReadsSeen = 0; } public void reset() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index c127899f6..371cce778 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java @@ -245,12 +245,7 @@ public abstract class MicroScheduler implements MicroSchedulerMBean { } else if (walker instanceof ReadPairWalker) { return new TraverseReadPairs(); } else if (walker instanceof ActiveRegionWalker) { - if ( engine.getArguments().newART ) { - // todo -- create optimized traversal - return new TraverseActiveRegionsOptimized(); - } else { - return new TraverseActiveRegionsOriginal(); - } + return new TraverseActiveRegions(); } else { throw new UnsupportedOperationException("Unable to determine traversal type, the walker is an unknown type."); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java index f587442d7..e9a2b56c2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java @@ -111,9 +111,6 @@ public class WindowMaker implements Iterable, I this.sourceInfo = shard.getReadProperties(); this.readIterator = new GATKSAMIterator(iterator); - // Use the legacy version of LocusIteratorByState if legacy downsampling was requested: - if ( sourceInfo.getDownsamplingMethod().useLegacyDownsampler ) - throw new IllegalArgumentException("legacy downsampler no longer supported in the window maker"); this.libs = new LocusIteratorByState(readIterator,sourceInfo,genomeLocParser,sampleNames); this.sourceIterator = new PeekableIterator(libs); diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/FastqFileWriter.java b/public/java/src/org/broadinstitute/sting/gatk/io/FastqFileWriter.java new file mode 100644 index 000000000..acef3e500 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/io/FastqFileWriter.java @@ -0,0 +1,77 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.io; + +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.sam.ReadUtils; + +import java.io.FileNotFoundException; +import java.io.PrintStream; + +/** + * User: carneiro + * Date: 1/27/13 + * Time: 12:54 AM + */ +public class FastqFileWriter { + private PrintStream output; + + public FastqFileWriter(String filename) { + try { + this.output = new PrintStream(filename); + } catch (FileNotFoundException e) { + throw new ReviewedStingException("Can't open file " + filename); + } + } + + public void addAlignment(GATKSAMRecord read) { + output.println("@" + read.getReadName()); + + if (read.getReadNegativeStrandFlag()) { + output.println(ReadUtils.getBasesReverseComplement(read)); + output.println("+"); + output.println(ReadUtils.convertReadQualToString(invertQuals(read.getBaseQualities()))); + } else { + output.println(ReadUtils.convertReadBasesToString(read)); + output.println("+"); + output.println(ReadUtils.convertReadQualToString(read)); + } + } + + public void close() { + this.output.close(); + } + + private byte[] invertQuals (byte[] quals) { + final int l = quals.length; + byte[] invertedQuals = new byte[l]; + for (int i=0; iafter the run finishes and the GATKRunReport will collect all of the report information * into this object. Call postReport to write out the report, as an XML document, to either STDOUT, * a file (in which case the output is gzipped), or with no arguments the report will be posted to the * GATK run report database. + * + * @author depristo + * @since 2010 */ public class GATKRunReport { + protected static final String REPORT_BUCKET_NAME = "GATK_Run_Reports"; + protected static final String TEST_REPORT_BUCKET_NAME = "GATK_Run_Reports_Test"; + protected final static String AWS_ACCESS_KEY_MD5 = "43433e5488d60788042ed5de3dcf9b0a"; + protected final static String AWS_SECRET_KEY_MD5 = "0aa28b227ecacbdc9d2d5e8d82b10d32"; + + private static final DateFormat DATE_FORMAT = new SimpleDateFormat("yyyy/MM/dd HH.mm.ss"); + + /** + * number of milliseconds before the S3 put operation is timed-out: + */ + private static final long S3_PUT_TIME_OUT = 10 * 1000; + /** * The root file system directory where we keep common report data */ - private static File REPORT_DIR = new File("/humgen/gsa-hpprojects/GATK/reports"); + private final static File REPORT_DIR = new File("/humgen/gsa-hpprojects/GATK/reports"); - private static final String REPORT_BUCKET_NAME = "GATK_Run_Reports"; /** * The full path to the direct where submitted (and uncharacterized) report files are written */ - private static File REPORT_SUBMIT_DIR = new File(REPORT_DIR.getAbsolutePath() + "/submitted"); + private final static File REPORT_SUBMIT_DIR = new File(REPORT_DIR.getAbsolutePath() + "/submitted"); /** * Full path to the sentinel file that controls whether reports are written out. If this file doesn't * exist, no long will be written */ - private static File REPORT_SENTINEL = new File(REPORT_DIR.getAbsolutePath() + "/ENABLE"); - - // number of milliseconds before the S3 put operation is timed-out: - private static final long S3PutTimeOut = 10 * 1000; - - 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"; + private final static File REPORT_SENTINEL = new File(REPORT_DIR.getAbsolutePath() + "/ENABLE"); /** * our log */ protected static final Logger logger = Logger.getLogger(GATKRunReport.class); + // ----------------------------------------------------------------- + // elements captured for the report + // ----------------------------------------------------------------- @Element(required = false, name = "id") - private final String id; + private String id; @Element(required = false, name = "exception") - private final ExceptionToXML mException; + private GATKRunReportException mException; - @Element(required = true, name = "start_time") + @Element(required = true, name = "start-time") private String startTime = "ND"; - @Element(required = true, name = "end_time") + @Element(required = true, name = "end-time") private String endTime; - @Element(required = true, name = "run_time") + @Element(required = true, name = "run-time") private long runTime = 0; - @Element(required = true, name = "walker_name") + @Element(required = true, name = "walker-name") private String walkerName; - @Element(required = true, name = "svn_version") + @Element(required = true, name = "svn-version") private String svnVersion; - @Element(required = true, name = "total_memory") + @Element(required = true, name = "total-memory") private long totalMemory; - @Element(required = true, name = "max_memory") + @Element(required = true, name = "max-memory") private long maxMemory; - @Element(required = true, name = "user_name") + @Element(required = true, name = "user-name") private String userName; - @Element(required = true, name = "host_name") + @Element(required = true, name = "host-name") private String hostName; @Element(required = true, name = "java") @@ -143,31 +154,80 @@ public class GATKRunReport { @Element(required = true, name = "tag") private String tag; - // ----------------------------------------------------------------- - // elements related to multi-threading and efficiency - // ----------------------------------------------------------------- - - @Element(required = true, name = "numThreads") + @Element(required = true, name = "num-threads") private int numThreads; - @Element(required = true, name = "percent_time_running") + @Element(required = true, name = "percent-time-running") private String percentTimeRunning; - @Element(required = true, name = "percent_time_waiting") + @Element(required = true, name = "percent-time-waiting") private String percentTimeWaiting; - @Element(required = true, name = "percent_time_blocking") + @Element(required = true, name = "percent-time-blocking") private String percentTimeBlocking; - @Element(required = true, name = "percent_time_waiting_for_io") + @Element(required = true, name = "percent-time-waiting-for-io") private String percentTimeWaitingForIO; + /** The error message, if one occurred, or null if none did */ + public String errorMessage = null; + /** The error that occurred, if one did, or null if none did */ + public Throwable errorThrown = null; + + /** + * How should the GATK report its usage? + */ public enum PhoneHomeOption { /** Disable phone home */ NO_ET, /** Standard option. Writes to local repository if it can be found, or S3 otherwise */ STANDARD, + /** Forces the report to go to S3 */ + AWS, /** Force output to STDOUT. For debugging only */ STDOUT } - private static final DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH.mm.ss"); + /** + * To allow us to deserial reports from XML + */ + private GATKRunReport() { } + + /** + * Read a GATKRunReport from the serialized XML representation in String reportAsXML + * @param stream an input stream containing a serialized XML report + * @return a reconstituted GATKRunReport from reportAsXML + * @throws Exception if parsing fails for any reason + */ + @Ensures("result != null") + protected static GATKRunReport deserializeReport(final InputStream stream) throws Exception { + final Serializer serializer = new Persister(); + return serializer.read(GATKRunReport.class, stream); + } + + /** + * Create a new GATKRunReport from a report on S3 + * + * Assumes that s3Object has already been written to S3, and this function merely + * fetches it from S3 and deserializes it. The access keys must have permission to + * GetObject from S3. + * + * @param downloaderAccessKey AWS access key with permission to GetObject from bucketName + * @param downloaderSecretKey AWS secret key with permission to GetObject from bucketName + * @param bucketName the name of the bucket holding the report + * @param s3Object the s3Object we wrote to S3 in bucketName that we want to get back and decode + * @return a deserialized report derived from s3://bucketName/s3Object.getName() + * @throws Exception + */ + @Ensures("result != null") + protected static GATKRunReport deserializeReport(final String downloaderAccessKey, + final String downloaderSecretKey, + final String bucketName, + final S3Object s3Object) throws Exception { + final S3Service s3Service = initializeAWSService(downloaderAccessKey, downloaderSecretKey); + + // Retrieve the whole data object we created previously + final S3Object objectComplete = s3Service.getObject(bucketName, s3Object.getName()); + + // Read the data from the object's DataInputStream using a loop, and print it out. + return deserializeReport(new GZIPInputStream(objectComplete.getDataInputStream())); + } /** * Create a new RunReport and population all of the fields with values from the walker and engine @@ -189,9 +249,9 @@ public class GATKRunReport { // runtime performance metrics Date end = new java.util.Date(); - endTime = dateFormat.format(end); + endTime = DATE_FORMAT.format(end); if ( engine.getStartTime() != null ) { // made it this far during initialization - startTime = dateFormat.format(engine.getStartTime()); + startTime = DATE_FORMAT.format(engine.getStartTime()); runTime = (end.getTime() - engine.getStartTime().getTime()) / 1000L; // difference in seconds } @@ -217,7 +277,7 @@ public class GATKRunReport { machine = Utils.join("-", Arrays.asList(System.getProperty("os.name"), System.getProperty("os.arch"))); // if there was an exception, capture it - this.mException = e == null ? null : new ExceptionToXML(e); + this.mException = e == null ? null : new GATKRunReportException(e); numThreads = engine.getTotalNumberOfThreads(); percentTimeRunning = getThreadEfficiencyPercent(engine, ThreadEfficiencyMonitor.State.USER_CPU); @@ -226,6 +286,11 @@ public class GATKRunReport { percentTimeWaitingForIO = getThreadEfficiencyPercent(engine, ThreadEfficiencyMonitor.State.WAITING_FOR_IO); } + /** + * Get the random alpha-numeric ID of this GATKRunReport + * @return a non-null string ID + */ + @Ensures("result != null") public String getID() { return id; } @@ -237,62 +302,113 @@ public class GATKRunReport { * @param state the state whose occupancy we wish to know * @return a string representation of the percent occupancy of state, or NA is not possible */ + @Requires({"engine != null", "state != null"}) + @Ensures("result != null") private String getThreadEfficiencyPercent(final GenomeAnalysisEngine engine, final ThreadEfficiencyMonitor.State state) { final ThreadEfficiencyMonitor tem = engine.getThreadEfficiencyMonitor(); return tem == null ? "NA" : String.format("%.2f", tem.getStatePercent(state)); } + /** + * Get a filename (no path) appropriate for this report + * + * @return a non-null string filename + */ + @Ensures("result != null") + protected String getReportFileName() { + return getID() + ".report.xml.gz"; + } + + // --------------------------------------------------------------------------- + // + // Main public interface method for posting reports + // + // --------------------------------------------------------------------------- + + /** + * Post this GATK report to the destination implied by the PhoneHomeOption type + * + * Guaranteed to never throw an exception (exception noted below) and to return + * with a reasonable (~10 seconds) time regardless of successful writing of the report. + * + * @throws IllegalArgumentException if type == null + * @param type the type of phoning home we want to do + * @return true if a report was successfully written, false otherwise + */ + public boolean postReport(final PhoneHomeOption type) { + if ( type == null ) throw new IllegalArgumentException("type cannot be null"); - public void postReport(PhoneHomeOption type) { logger.debug("Posting report of type " + type); switch (type) { case NO_ET: // don't do anything - break; + return false; case STANDARD: - if ( repositoryIsOnline() ) { - postReportToLocalDisk(REPORT_SUBMIT_DIR); + case AWS: + if ( type == PhoneHomeOption.STANDARD && repositoryIsOnline() ) { + return postReportToLocalDisk(getLocalReportFullPath()) != null; } else { - postReportToAWSS3(); + wentToAWS = true; + return postReportToAWSS3() != null; } - break; case STDOUT: - postReportToStream(System.out); - break; + return postReportToStream(System.out); default: exceptDuringRunReport("BUG: unexpected PhoneHomeOption "); - break; + return false; } } + // --------------------------------------------------------------------------- + // + // Code for sending reports to local files + // + // --------------------------------------------------------------------------- + /** * Write an XML representation of this report to the stream, throwing a StingException if the marshalling * fails for any reason. * - * @param stream + * @param stream an output stream to write the report to */ - private void postReportToStream(OutputStream stream) { - Serializer serializer = new Persister(new Format(new HyphenStyle())); + @Requires("stream != null") + protected boolean postReportToStream(final OutputStream stream) { + final Serializer serializer = new Persister(); try { serializer.write(this, stream); - //throw new StingException("test"); + return true; } catch (Exception e) { - throw new ReviewedStingException("Failed to marshal the data to the file " + stream, e); + return false; } } - private final String getKey() { - return getID() + ".report.xml.gz"; + /** + * Get the full path as a file where we'll write this report to local disl + * @return a non-null File + */ + @Ensures("result != null") + protected File getLocalReportFullPath() { + return new File(REPORT_SUBMIT_DIR, getReportFileName()); } + /** + * Is the local GATKRunReport repository available for writing reports? + * + * @return true if and only if the common run report repository is available and online to receive reports + */ + private boolean repositoryIsOnline() { + return REPORT_SENTINEL.exists(); + } + + /** * Main entry point to writing reports to disk. Posts the XML report to the common GATK run report repository. * If this process fails for any reason, all exceptions are handled and this routine merely prints a warning. * That is, postReport() is guarenteed not to fail for any reason. + * + * @return the path where the file was written, or null if any failure occurred */ - private File postReportToLocalDisk(File rootDir) { - final String filename = getKey(); - final File destination = new File(rootDir, filename); - + @Requires("destination != null") + private File postReportToLocalDisk(final File destination) { try { final BufferedOutputStream out = new BufferedOutputStream( new GZIPOutputStream( @@ -309,63 +425,187 @@ public class GATKRunReport { } } + // --------------------------------------------------------------------------- + // + // Code for sending reports to s3 + // + // --------------------------------------------------------------------------- + + /** + * Get the name of the S3 bucket where we should upload this report + * + * @return the string name of the s3 bucket + */ + @Ensures("result != null") + protected String getS3ReportBucket() { + return s3ReportBucket; + } + + /** + * Decrypts encrypted AWS key from encryptedKeySource + * @param encryptedKeySource a file containing an encrypted AWS key + * @return a decrypted AWS key as a String + */ + @Ensures("result != null") + public static String decryptAWSKey(final File encryptedKeySource) throws FileNotFoundException { + if ( encryptedKeySource == null ) throw new IllegalArgumentException("encryptedKeySource cannot be null"); + return decryptAWSKey(new FileInputStream(encryptedKeySource)); + } + + /** + * @see #decryptAWSKey(java.io.File) but with input from an inputstream + */ + @Requires("encryptedKeySource != null") + @Ensures("result != null") + private static String decryptAWSKey(final InputStream encryptedKeySource) { + final PublicKey key = CryptUtils.loadGATKDistributedPublicKey(); + final byte[] fromDisk = IOUtils.readStreamIntoByteArray(encryptedKeySource); + final byte[] decrypted = CryptUtils.decryptData(fromDisk, key); + return new String(decrypted); + } + + /** + * Get the decrypted AWS key sorted in the resource directories of name + * @param name the name of the file containing the needed AWS key + * @return a non-null GATK + */ + @Requires("name != null") + @Ensures("result != null") + private static String getAWSKey(final String name) { + final Resource resource = new Resource(name, GATKRunReport.class); + return decryptAWSKey(resource.getResourceContentsAsStream()); + } + + /** + * Get the AWS access key for the GATK user + * @return a non-null AWS access key for the GATK user + */ + @Ensures("result != null") + protected static String getAWSUploadAccessKey() { + return getAWSKey("resources/GATK_AWS_access.key"); + } + + /** + * Get the AWS secret key for the GATK user + * @return a non-null AWS secret key for the GATK user + */ + @Ensures("result != null") + protected static String getAWSUploadSecretKey() { + return getAWSKey("resources/GATK_AWS_secret.key"); + } + + /** + * Check that the AWS keys can be decrypted and are what we expect them to be + * + * @throws ReviewedStingException if anything goes wrong + */ + public static void checkAWSAreValid() { + try { + final String accessKeyMD5 = Utils.calcMD5(getAWSUploadAccessKey()); + final String secretKeyMD5 = Utils.calcMD5(getAWSUploadSecretKey()); + + if ( ! AWS_ACCESS_KEY_MD5.equals(accessKeyMD5) ) { + throw new ReviewedStingException("Invalid AWS access key found, expected MD5 " + AWS_ACCESS_KEY_MD5 + " but got " + accessKeyMD5); + } + if ( ! AWS_SECRET_KEY_MD5.equals(secretKeyMD5) ) { + throw new ReviewedStingException("Invalid AWS secret key found, expected MD5 " + AWS_SECRET_KEY_MD5 + " but got " + secretKeyMD5); + } + + } catch ( Exception e ) { + throw new ReviewedStingException("Couldn't decrypt AWS keys, something is wrong with the GATK distribution"); + } + } + + /** + * Get an initialized S3Service for use in communicating with AWS/s3 + * + * @param awsAccessKey our AWS access key to use + * @param awsSecretKey our AWS secret key to use + * @return an initialized S3Service object that can be immediately used to interact with S3 + * @throws S3ServiceException + */ + @Requires({"awsAccessKey != null", "awsSecretKey != null"}) + @Ensures("result != null") + protected static S3Service initializeAWSService(final String awsAccessKey, final String awsSecretKey) throws S3ServiceException { + // To communicate with S3, create a class that implements an S3Service. We will use the REST/HTTP + // implementation based on HttpClient, as this is the most robust implementation provided with JetS3t. + final AWSCredentials awsCredentials = new AWSCredentials(awsAccessKey, awsSecretKey); + return new RestS3Service(awsCredentials); + } + + /** + * A runnable that pushes this GATKReport up to s3. + * + * Should be run in a separate thread so we can time it out if something is taking too long + */ private class S3PutRunnable implements Runnable { + /** Was the upload operation successful? */ + public final AtomicBoolean isSuccess; + /** The name of this report */ + private final String filename; + /** The contents of this report */ + private final byte[] contents; - public AtomicBoolean isSuccess; - private final String key; - private final byte[] report; + /** The s3Object that we created to upload, or null if it failed */ + public S3Object s3Object = null; - public S3Object s3Object; - public String errorMsg; - public Throwable errorThrow; - - public S3PutRunnable(String key, byte[] report){ - isSuccess = new AtomicBoolean(); - this.key = key; - this.report = report; + @Requires({"filename != null", "contents != null"}) + public S3PutRunnable(final String filename, final byte[] contents){ + this.isSuccess = new AtomicBoolean(); + this.filename = filename; + this.contents = contents; } public void run() { try { - // Your Amazon Web Services (AWS) login credentials are required to manage S3 accounts. These credentials - // are stored in an AWSCredentials object: + switch ( awsMode ) { + case FAIL_WITH_EXCEPTION: + throw new IllegalStateException("We are throwing an exception for testing purposes"); + case TIMEOUT: + try { + Thread.sleep(S3_PUT_TIME_OUT * 100); + } catch ( InterruptedException e ) { + // supposed to be empty + } + break; + case NORMAL: + // IAM GATK user credentials -- only right is to PutObject into GATK_Run_Report bucket + final S3Service s3Service = initializeAWSService(getAWSUploadAccessKey(), getAWSUploadSecretKey()); - // IAM GATK user credentials -- only right is to PutObject into GATK_Run_Report bucket - String awsAccessKey = "AKIAJXU7VIHBPDW4TDSQ"; // GATK AWS user - String awsSecretKey = "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"; // GATK AWS user - AWSCredentials awsCredentials = new AWSCredentials(awsAccessKey, awsSecretKey); - - // To communicate with S3, create a class that implements an S3Service. We will use the REST/HTTP - // implementation based on HttpClient, as this is the most robust implementation provided with JetS3t. - S3Service s3Service = new RestS3Service(awsCredentials); - - // Create an S3Object based on a file, with Content-Length set automatically and - // Content-Type set based on the file's extension (using the Mimetypes utility class) - S3Object fileObject = new S3Object(key, report); - //logger.info("Created S3Object" + fileObject); - //logger.info("Uploading " + localFile + " to AWS bucket"); - s3Object = s3Service.putObject(REPORT_BUCKET_NAME, fileObject); - isSuccess.set(true); + // Create an S3Object based on a file, with Content-Length set automatically and + // Content-Type set based on the file's extension (using the Mimetypes utility class) + final S3Object fileObject = new S3Object(filename, contents); + //logger.info("Created S3Object" + fileObject); + //logger.info("Uploading " + localFile + " to AWS bucket"); + s3Object = s3Service.putObject(getS3ReportBucket(), fileObject); + isSuccess.set(true); + break; + default: + throw new IllegalStateException("Unexpected AWS exception"); + } } catch ( S3ServiceException e ) { - setException("S3 exception occurred", e); + exceptDuringRunReport("S3 exception occurred", e); } catch ( NoSuchAlgorithmException e ) { - setException("Couldn't calculate MD5", e); + exceptDuringRunReport("Couldn't calculate MD5", e); } catch ( IOException e ) { - setException("Couldn't read report file", e); + exceptDuringRunReport("Couldn't read report file", e); + } catch ( Exception e ) { + exceptDuringRunReport("An unexpected exception occurred during posting", e); } } - - private void setException(String msg, Throwable e){ - errorMsg=msg; - errorThrow=e; - } } - private void postReportToAWSS3() { + /** + * Post this GATK report to the AWS s3 GATK_Run_Report log + * + * @return the s3Object pointing to our pushed report, or null if we failed to push + */ + protected S3Object postReportToAWSS3() { // modifying example code from http://jets3t.s3.amazonaws.com/toolkit/code-samples.html this.hostName = Utils.resolveHostname(); // we want to fill in the host name - final String key = getKey(); + final String key = getReportFileName(); logger.debug("Generating GATK report to AWS S3 with key " + key); + try { // create an byte output stream so we can capture the output as a byte[] final ByteArrayOutputStream byteStream = new ByteArrayOutputStream(8096); @@ -375,17 +615,17 @@ public class GATKRunReport { final byte[] report = byteStream.toByteArray(); // stop us from printing the annoying, and meaningless, mime types warning - Logger mimeTypeLogger = Logger.getLogger(org.jets3t.service.utils.Mimetypes.class); + final Logger mimeTypeLogger = Logger.getLogger(org.jets3t.service.utils.Mimetypes.class); mimeTypeLogger.setLevel(Level.FATAL); // Set the S3 upload on its own thread with timeout: - S3PutRunnable s3run = new S3PutRunnable(key,report); - Thread s3thread = new Thread(s3run); + final S3PutRunnable s3run = new S3PutRunnable(key,report); + final Thread s3thread = new Thread(s3run); s3thread.setDaemon(true); s3thread.setName("S3Put-Thread"); s3thread.start(); - s3thread.join(S3PutTimeOut); + s3thread.join(S3_PUT_TIME_OUT); if(s3thread.isAlive()){ s3thread.interrupt(); @@ -393,69 +633,198 @@ public class GATKRunReport { } else if(s3run.isSuccess.get()) { logger.info("Uploaded run statistics report to AWS S3"); logger.debug("Uploaded to AWS: " + s3run.s3Object); + return s3run.s3Object; } else { - if((s3run.errorMsg != null) && (s3run.errorThrow != null)){ - exceptDuringRunReport(s3run.errorMsg,s3run.errorThrow); - } else { - exceptDuringRunReport("Run statistics report upload to AWS S3 failed"); - } + // an exception occurred, the thread should have already invoked the exceptDuringRunReport function } } catch ( IOException e ) { exceptDuringRunReport("Couldn't read report file", e); } catch ( InterruptedException e) { exceptDuringRunReport("Run statistics report upload interrupted", e); } + + return null; } - private void exceptDuringRunReport(String msg, Throwable e) { + // --------------------------------------------------------------------------- + // + // Error handling code + // + // --------------------------------------------------------------------------- + + /** + * Note that an exception occurred during creating or writing this report + * @param msg the message to print + * @param e the exception that occurred + */ + @Ensures("exceptionOccurredDuringPost()") + private void exceptDuringRunReport(final String msg, final Throwable e) { + this.errorMessage = msg; + this.errorThrown = e; logger.debug("A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***]. Message is: " + msg + ". Error message is: " + e.getMessage()); - //e.printStackTrace(); } - private void exceptDuringRunReport(String msg) { + /** + * Note that an exception occurred during creating or writing this report + * @param msg the message to print + */ + @Ensures("exceptionOccurredDuringPost()") + private void exceptDuringRunReport(final String msg) { + this.errorMessage = msg; logger.debug("A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***]. Message is " + msg); } - /** - * Returns true if and only if the common run report repository is available and online to receive reports - * - * @return + * Did an error occur during the posting of this run report? + * @return true if so, false if not */ - private boolean repositoryIsOnline() { - return REPORT_SENTINEL.exists(); + public boolean exceptionOccurredDuringPost() { + return getErrorMessage() != null; } /** - * A helper class for formatting in XML the throwable chain starting at e. + * If an error occurred during posting of this report, retrieve the message of the error that occurred, or null if + * no error occurred + * @return a string describing the error that occurred, or null if none did */ - private class ExceptionToXML { - @Element(required = false, name = "message") - String message = null; + public String getErrorMessage() { + return errorMessage; + } - @ElementList(required = false, name = "stacktrace") - final List stackTrace = new ArrayList(); + /** + * Get the throwable that caused the exception during posting of this message, or null if none was available + * + * Note that getting a null valuable from this function doesn't not imply that no error occurred. Some + * errors that occurred many not have generated a throwable. + * + * @return the Throwable that caused the error, or null if no error occurred or was not caused by a throwable + */ + public Throwable getErrorThrown() { + return errorThrown; + } - @Element(required = false, name = "cause") - ExceptionToXML cause = null; + /** + * Helper method to format the exception that occurred during posting, or a string saying none occurred + * @return a non-null string + */ + @Ensures("result != null") + protected String formatError() { + return exceptionOccurredDuringPost() + ? String.format("Exception message=%s with cause=%s", getErrorMessage(), getErrorThrown()) + : "No exception occurred"; + } - @Element(required = false, name = "is-user-exception") - Boolean isUserException; + // --------------------------------------------------------------------------- + // + // Equals and hashcode -- purely for comparing reports for testing + // + // --------------------------------------------------------------------------- - @Element(required = false, name = "exception-class") - Class exceptionClass; + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; - public ExceptionToXML(Throwable e) { - message = e.getMessage(); - exceptionClass = e.getClass(); - isUserException = e instanceof UserException; - for (StackTraceElement element : e.getStackTrace()) { - stackTrace.add(element.toString()); - } + GATKRunReport that = (GATKRunReport) o; - if ( e.getCause() != null ) { - cause = new ExceptionToXML(e.getCause()); - } - } + if (maxMemory != that.maxMemory) return false; + if (nIterations != that.nIterations) return false; + if (numThreads != that.numThreads) return false; + if (runTime != that.runTime) return false; + if (totalMemory != that.totalMemory) return false; + if (endTime != null ? !endTime.equals(that.endTime) : that.endTime != null) return false; + if (hostName != null ? !hostName.equals(that.hostName) : that.hostName != null) return false; + if (id != null ? !id.equals(that.id) : that.id != null) return false; + if (javaVersion != null ? !javaVersion.equals(that.javaVersion) : that.javaVersion != null) return false; + if (mException != null ? !mException.equals(that.mException) : that.mException != null) return false; + if (machine != null ? !machine.equals(that.machine) : that.machine != null) return false; + if (percentTimeBlocking != null ? !percentTimeBlocking.equals(that.percentTimeBlocking) : that.percentTimeBlocking != null) + return false; + if (percentTimeRunning != null ? !percentTimeRunning.equals(that.percentTimeRunning) : that.percentTimeRunning != null) + return false; + if (percentTimeWaiting != null ? !percentTimeWaiting.equals(that.percentTimeWaiting) : that.percentTimeWaiting != null) + return false; + if (percentTimeWaitingForIO != null ? !percentTimeWaitingForIO.equals(that.percentTimeWaitingForIO) : that.percentTimeWaitingForIO != null) + return false; + if (startTime != null ? !startTime.equals(that.startTime) : that.startTime != null) return false; + if (svnVersion != null ? !svnVersion.equals(that.svnVersion) : that.svnVersion != null) return false; + if (tag != null ? !tag.equals(that.tag) : that.tag != null) return false; + if (userName != null ? !userName.equals(that.userName) : that.userName != null) return false; + if (walkerName != null ? !walkerName.equals(that.walkerName) : that.walkerName != null) return false; + + return true; + } + + @Override + public int hashCode() { + int result = id != null ? id.hashCode() : 0; + result = 31 * result + (mException != null ? mException.hashCode() : 0); + result = 31 * result + (startTime != null ? startTime.hashCode() : 0); + result = 31 * result + (endTime != null ? endTime.hashCode() : 0); + result = 31 * result + (int) (runTime ^ (runTime >>> 32)); + result = 31 * result + (walkerName != null ? walkerName.hashCode() : 0); + result = 31 * result + (svnVersion != null ? svnVersion.hashCode() : 0); + result = 31 * result + (int) (totalMemory ^ (totalMemory >>> 32)); + result = 31 * result + (int) (maxMemory ^ (maxMemory >>> 32)); + result = 31 * result + (userName != null ? userName.hashCode() : 0); + result = 31 * result + (hostName != null ? hostName.hashCode() : 0); + result = 31 * result + (javaVersion != null ? javaVersion.hashCode() : 0); + result = 31 * result + (machine != null ? machine.hashCode() : 0); + result = 31 * result + (int) (nIterations ^ (nIterations >>> 32)); + result = 31 * result + (tag != null ? tag.hashCode() : 0); + result = 31 * result + numThreads; + result = 31 * result + (percentTimeRunning != null ? percentTimeRunning.hashCode() : 0); + result = 31 * result + (percentTimeWaiting != null ? percentTimeWaiting.hashCode() : 0); + result = 31 * result + (percentTimeBlocking != null ? percentTimeBlocking.hashCode() : 0); + result = 31 * result + (percentTimeWaitingForIO != null ? percentTimeWaitingForIO.hashCode() : 0); + return result; + } + + // --------------------------------------------------------------------------- + // + // Code specifically for testing the GATKRunReport + // + // --------------------------------------------------------------------------- + + /** + * Enum specifying how the S3 uploader should behave. Must be normal by default. Purely for testing purposes + */ + protected enum AWSMode { + NORMAL, // write normally to AWS + FAIL_WITH_EXCEPTION, // artificially fail during writing + TIMEOUT // sleep, so we time out + } + /** Our AWS mode */ + private AWSMode awsMode = AWSMode.NORMAL; + /** The bucket were we send the GATK report on AWS/s3 */ + private String s3ReportBucket = REPORT_BUCKET_NAME; + /** Did we send the report to AWS? */ + private boolean wentToAWS = false; + + /** + * Send the report to the AWS test bucket -- for testing only + */ + protected void sendAWSToTestBucket() { + s3ReportBucket = TEST_REPORT_BUCKET_NAME; + } + + /** + * Has the report been written to AWS? + * + * Does not imply anything about the success of the send, just that it was attempted + * + * @return true if the report has been sent to AWS, false otherwise + */ + protected boolean wentToAWS() { + return wentToAWS; + } + + /** + * Purely for testing purposes. Tells the AWS uploader whether to actually upload or simulate errors + * @param mode what we want to do + */ + @Requires("mode != null") + protected void setAwsMode(final AWSMode mode) { + this.awsMode = mode; } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReportException.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReportException.java new file mode 100644 index 000000000..431d99867 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReportException.java @@ -0,0 +1,99 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.phonehome; + +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.simpleframework.xml.Element; +import org.simpleframework.xml.ElementList; + +import java.util.ArrayList; +import java.util.List; + +/** + * A helper class for formatting in XML the throwable chain starting at e. + */ +class GATKRunReportException { + @Element(required = false, name = "message") + String message = null; + + @ElementList(required = false, name = "stacktrace") + final List stackTrace = new ArrayList(); + + @Element(required = false, name = "cause") + GATKRunReportException cause = null; + + @Element(required = false, name = "is-user-exception") + Boolean isUserException; + + @Element(required = false, name = "exception-class") + Class exceptionClass; + + /** + * Allow us to deserialize from XML + */ + public GATKRunReportException() { } + + public GATKRunReportException(Throwable e) { + message = e.getMessage(); + exceptionClass = e.getClass(); + isUserException = e instanceof UserException; + for (StackTraceElement element : e.getStackTrace()) { + stackTrace.add(element.toString()); + } + + if ( e.getCause() != null ) { + cause = new GATKRunReportException(e.getCause()); + } + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + + GATKRunReportException that = (GATKRunReportException) o; + + if (cause != null ? !cause.equals(that.cause) : that.cause != null) return false; + if (exceptionClass != null ? !exceptionClass.equals(that.exceptionClass) : that.exceptionClass != null) + return false; + if (isUserException != null ? !isUserException.equals(that.isUserException) : that.isUserException != null) + return false; + if (message != null ? !message.equals(that.message) : that.message != null) return false; + if (stackTrace != null ? !stackTrace.equals(that.stackTrace) : that.stackTrace != null) return false; + + return true; + } + + @Override + public int hashCode() { + int result = message != null ? message.hashCode() : 0; + result = 31 * result + (stackTrace != null ? stackTrace.hashCode() : 0); + result = 31 * result + (cause != null ? cause.hashCode() : 0); + result = 31 * result + (isUserException != null ? isUserException.hashCode() : 0); + result = 31 * result + (exceptionClass != null ? exceptionClass.hashCode() : 0); + return result; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key b/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key new file mode 100644 index 000000000..5b3e0c2ec Binary files /dev/null and b/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key differ diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key b/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key new file mode 100644 index 000000000..9f1224a54 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key @@ -0,0 +1 @@ +,¼«œ ºñ©£HQÏPˆÀÖç¢á{-LùC1bE͈ti·wád£^¥éye'±¾ñÛ%èðÜ°ŒR5dÇgYè4ÕP$0qÔé2Gã v$©²Ê¡lXºóÊPµË?a€Ñú¹] —g³®ß¦JWø-…ëU"©u>ózht)ÖÓ-̧[ò0Ë!ïº#‰ÕÞ)ÒâfÜÊÓ*ñ3ìÞÄÞz2ÁA1û`ê¼hid (âõ¬‹;•ôµÀr]‹ãºÛÔÖ¥Ž@®(µ|¤` \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java index 9cb38b840..5a1b015fe 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java @@ -61,6 +61,7 @@ public class RefMetaDataTracker { final Map bindings; final protected static Logger logger = Logger.getLogger(RefMetaDataTracker.class); + public final static RefMetaDataTracker EMPTY_TRACKER = new RefMetaDataTracker(); // ------------------------------------------------------------------------------------------ // diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index c7edebd81..09f053187 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.variantcontext.*; import java.util.*; @@ -194,17 +195,18 @@ public class VariantContextAdaptors { return null; // we weren't given enough reference context to create the VariantContext final byte refBaseForIndel = ref.getBases()[index]; + final boolean refBaseIsDash = dbsnp.getNCBIRefBase().equals("-"); boolean addPaddingBase; if ( isSNP(dbsnp) || isMNP(dbsnp) ) addPaddingBase = false; else if ( isIndel(dbsnp) || dbsnp.getVariantType().contains("mixed") ) - addPaddingBase = VariantContextUtils.requiresPaddingBase(stripNullDashes(getAlleleList(dbsnp))); + addPaddingBase = refBaseIsDash || GATKVariantContextUtils.requiresPaddingBase(stripNullDashes(getAlleleList(dbsnp))); else return null; // can't handle anything else Allele refAllele; - if ( dbsnp.getNCBIRefBase().equals("-") ) + if ( refBaseIsDash ) refAllele = Allele.create(refBaseForIndel, true); else if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java index 45dbb6dc8..5d2aa6be3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java @@ -25,6 +25,8 @@ package org.broadinstitute.sting.gatk.traversals; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.WalkerManager; @@ -32,47 +34,95 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.providers.*; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension; +import org.broadinstitute.sting.gatk.walkers.ActiveRegionTraversalParameters; import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.activeregion.ActivityProfile; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.activeregion.*; import org.broadinstitute.sting.utils.progressmeter.ProgressMeter; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import java.util.LinkedList; -import java.util.List; +import java.io.PrintStream; +import java.util.*; /** - * Created with IntelliJ IDEA. + * Implement active region traversal + * * User: depristo * Date: 1/9/13 * Time: 4:45 PM - * To change this template use File | Settings | File Templates. + * + * Live region: + * + * The ART tracks a thing called the live region. The live region is a position on a specific contig + * of the alignment start of the last read we processed during this traversal. Because the + * read stream is sorted, future reads must occurs in the the live region. Therefore the the dead region + * (everything to the left of the live boundary) cannot have any more read data. The live / dead + * regions are used to decide when we can safely call map on active regions, as only active regions + * contained completely within the dead region (including extensions) have a complete set of read data + * in the collected read list. All of the data related to the live region is captured by the local + * variable spanOfLastReadSeen + * */ -public abstract class TraverseActiveRegions extends TraversalEngine,LocusShardDataProvider> { - protected final static boolean DEBUG = false; +public class TraverseActiveRegions extends TraversalEngine,LocusShardDataProvider> { + protected final static Logger logger = Logger.getLogger(TraversalEngine.class); + protected final static boolean LOG_READ_CARRYING = false; // set by the tranversal + private boolean walkerHasPresetRegions = false; private int activeRegionExtension = -1; private int maxRegionSize = -1; + private int minRegionSize = -1; + + private final LinkedList workQueue = new LinkedList(); + + private LinkedList myReads = new LinkedList(); + private GenomeLoc spanOfLastReadSeen = null; + private ActivityProfile activityProfile = null; + int maxReadsInMemory = 0; + ActiveRegionWalker walker; /** - * our log, which we want to capture anything from this class + * Have the debugging output streams been initialized already? + * + * We have to do lazy initialization because when the initialize() function is called + * the streams aren't yet initialized in the GATK walker. */ - protected final static Logger logger = Logger.getLogger(TraversalEngine.class); - protected final LinkedList workQueue = new LinkedList(); + private boolean streamsInitialized = false; - abstract protected T processActiveRegion(final ActiveRegion activeRegion, final T sum, final ActiveRegionWalker walker); + @Override + public void initialize(GenomeAnalysisEngine engine, Walker walker, ProgressMeter progressMeter) { + super.initialize(engine, walker, progressMeter); - /** - * Special function called in LinearMicroScheduler to empty out the work queue. - * Ugly for now but will be cleaned up when we push this functionality more into the engine - */ - public abstract T endTraversal(final Walker walker, T sum); + this.walker = (ActiveRegionWalker)walker; + if ( this.walker.wantsExtendedReads() && ! this.walker.wantsNonPrimaryReads() ) { + throw new IllegalArgumentException("Active region walker " + this.walker + " requested extended events but not " + + "non-primary reads, an inconsistent state. Please modify the walker"); + } + + ActiveRegionTraversalParameters annotation = walker.getClass().getAnnotation(ActiveRegionTraversalParameters.class); + this.activeRegionExtension = this.walker.activeRegionExtension == null ? annotation.extension() : this.walker.activeRegionExtension; + this.maxRegionSize = this.walker.activeRegionMaxSize == null ? annotation.maxRegion() : this.walker.activeRegionMaxSize; + this.minRegionSize = annotation.minRegion(); + final double bandPassSigma = this.walker.bandPassSigma == null ? annotation.bandPassSigma() : this.walker.bandPassSigma; + walkerHasPresetRegions = this.walker.hasPresetActiveRegions(); + + activityProfile = new BandPassActivityProfile(engine.getGenomeLocParser(), BandPassActivityProfile.MAX_FILTER_SIZE, bandPassSigma); + if ( walkerHasPresetRegions ) { + // we load all of the preset locations into the + for ( final GenomeLoc loc : this.walker.getPresetActiveRegions()) { + workQueue.add(new ActiveRegion(loc, null, true, engine.getGenomeLocParser(), getActiveRegionExtension())); + } + } + } + + // ------------------------------------------------------------------------------------- + // + // Utility functions + // + // ------------------------------------------------------------------------------------- protected int getActiveRegionExtension() { return activeRegionExtension; @@ -82,22 +132,18 @@ public abstract class TraverseActiveRegions extends TraversalEngine extends TraversalEngine activeRegions) { - if ( profile.isEmpty() ) - throw new IllegalStateException("trying to incorporate an empty active profile " + profile); - - final ActivityProfile bandPassFiltered = profile.bandPassFilter(); - activeRegions.addAll(bandPassFiltered.createActiveRegions( getActiveRegionExtension(), getMaxRegionSize() )); - return new ActivityProfile( engine.getGenomeLocParser(), profile.hasPresetRegions() ); - } - - protected final ActivityProfileResult walkerActiveProb(final ActiveRegionWalker walker, - final RefMetaDataTracker tracker, final ReferenceContext refContext, - final AlignmentContext locus, final GenomeLoc location) { - if ( walker.hasPresetActiveRegions() ) { - return new ActivityProfileResult(location, walker.presetActiveRegions.overlaps(location) ? 1.0 : 0.0); - } else { - return walker.isActive( tracker, refContext, locus ); - } - } - protected ReferenceOrderedView getReferenceOrderedView(final ActiveRegionWalker walker, final LocusShardDataProvider dataProvider, final LocusView locusView) { @@ -147,17 +164,391 @@ public abstract class TraverseActiveRegions extends TraversalEngine walker ) { - // Just want to output the active regions to a file, not actually process them - for( final ActiveRegion activeRegion : workQueue ) { - if( activeRegion.isActive ) { - walker.activeRegionOutStream.println( activeRegion.getLocation() ); + private boolean appearedInLastShard(final GenomeLoc locOfLastReadAtTraversalStart, final GATKSAMRecord read) { + if ( locOfLastReadAtTraversalStart == null ) + // we're in the first shard, so obviously the answer is no + return false; + else { + // otherwise check to see if the alignment occurred in the previous shard + return read.getAlignmentStart() <= locOfLastReadAtTraversalStart.getStart() + // we're on the same contig + && read.getReferenceIndex() == locOfLastReadAtTraversalStart.getContigIndex(); + } + + } + + @Override + public T traverse( final ActiveRegionWalker walker, + final LocusShardDataProvider dataProvider, + T sum) { + if ( LOG_READ_CARRYING || logger.isDebugEnabled() ) + logger.info(String.format("TraverseActiveRegions.traverse: Shard is %s", dataProvider)); + + final LocusView locusView = new AllLocusView(dataProvider); + final LocusReferenceView referenceView = new LocusReferenceView( walker, dataProvider ); + final ReferenceOrderedView referenceOrderedDataView = getReferenceOrderedView(walker, dataProvider, locusView); + + // We keep processing while the next reference location is within the interval + final GenomeLoc locOfLastReadAtTraversalStart = spanOfLastSeenRead(); + + while( locusView.hasNext() ) { + final AlignmentContext locus = locusView.next(); + final GenomeLoc location = locus.getLocation(); + + rememberLastLocusLocation(location); + + // get all of the new reads that appear in the current pileup, and them to our list of reads + // provided we haven't seen them before + final Collection reads = locusView.getLIBS().transferReadsFromAllPreviousPileups(); + for( final GATKSAMRecord read : reads ) { + if ( ! appearedInLastShard(locOfLastReadAtTraversalStart, read) ) { + rememberLastReadLocation(read); + myReads.add(read); + } + } + + // skip this location -- it's not part of our engine intervals + if ( outsideEngineIntervals(location) ) + continue; + + // we've move across some interval boundary, restart profile + final boolean flushProfile = ! activityProfile.isEmpty() + && ( activityProfile.getContigIndex() != location.getContigIndex() + || location.getStart() != activityProfile.getStop() + 1); + sum = processActiveRegions(walker, sum, flushProfile, false); + + dataProvider.getShard().getReadMetrics().incrementNumIterations(); + + // create reference context. Note that if we have a pileup of "extended events", the context will + // hold the (longest) stretch of deleted reference bases (if deletions are present in the pileup). + final ReferenceContext refContext = referenceView.getReferenceContext(location); + + // Iterate forward to get all reference ordered data covering this location + final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation(), refContext); + + // Call the walkers isActive function for this locus and add them to the list to be integrated later + addIsActiveResult(walker, tracker, refContext, locus); + + maxReadsInMemory = Math.max(myReads.size(), maxReadsInMemory); + printProgress(locus.getLocation()); + } + + updateCumulativeMetrics(dataProvider.getShard()); + + return sum; + } + + /** + * Special function called in LinearMicroScheduler to empty out the work queue. + * Ugly for now but will be cleaned up when we push this functionality more into the engine + */ + public T endTraversal(final Walker walker, T sum) { + return processActiveRegions((ActiveRegionWalker)walker, sum, true, true); + } + + // ------------------------------------------------------------------------------------- + // + // Functions to manage and interact with the live / dead zone + // + // ------------------------------------------------------------------------------------- + + /** + * Update the live region to reflect that the last read we've seen in the traversal is read + * + * Requires that sequential calls always be provided reads in coordinate sorted order + * + * @param read the last read we've seen during the traversal + */ + protected void rememberLastReadLocation(final GATKSAMRecord read) { + final GenomeLoc currentLocation = engine.getGenomeLocParser().createGenomeLoc(read); + if ( spanOfLastReadSeen == null ) + spanOfLastReadSeen = currentLocation; + else { + if ( currentLocation.isBefore(spanOfLastReadSeen) ) + throw new IllegalStateException("Updating last read seen in the traversal with read " + read + " with span " + currentLocation + " but this occurs before the previously seen read " + spanOfLastReadSeen); + spanOfLastReadSeen = currentLocation; + } + } + + /** + * Update the live region to reflect that we've reached locus + * + * This function is complementary to #rememberLastReadLocation, but if we don't have any reads for a long + * time (e.g., there's no coverage) we will keep active regions around far longer than necessary. + * + * Only updates the span if it's beyond the last seen + * + * @param currentLocation the current location we've processed on the genome + */ + protected void rememberLastLocusLocation(final GenomeLoc currentLocation) { + if ( spanOfLastReadSeen == null ) + spanOfLastReadSeen = currentLocation; + else { + if ( currentLocation.isPast(spanOfLastReadSeen) ) + spanOfLastReadSeen = currentLocation; + } + } + + + /** + * Get a GenomeLoc indicating the start (heading to the right) of the live ART region. + * @return the left-most position of the live region on the genome + */ + protected GenomeLoc spanOfLastSeenRead() { + return spanOfLastReadSeen; + } + + /** + * Is the active region completely within the traversal's dead zone? + * + * @param region the region we want to test + * @return true if the extended location of region is completely within the current dead zone, false otherwise + */ + protected boolean regionCompletelyWithinDeadZone(final ActiveRegion region) { + if ( spanOfLastSeenRead() == null ) + return false; + + final int contigCmp = region.getExtendedLoc().compareContigs(spanOfLastSeenRead()); + if ( contigCmp > 0 ) + throw new IllegalStateException("Active region " + region + " on a contig after last seen read " + spanOfLastSeenRead()); + else { + return contigCmp < 0 || region.getExtendedLoc().getStop() < spanOfLastSeenRead().getStart(); + } + } + + /** + * Is the read dead? That is, can it no longer be in any future active region, and therefore can be discarded? + * + * read: start |--------> stop ------ stop + extension + * region: start |-----------------| end + * + * Since the regions are coming in order, read could potentially be contained in a future interval if + * stop + activeRegionExtension >= end. If, on the other hand, stop + extension is < the end + * of this region, then we can discard it, since any future region could only include reads + * up to end + 1 - extension. + * + * Note that this function doesn't care about the dead zone. We're assuming that by + * actually calling this function with an active region that region is already in the dead zone, + * so checking that the read is in the dead zone doesn't make sense. + * + * @param read the read we're testing + * @param activeRegion the current active region + * @return true if the read is dead, false other + */ + @Requires({"read != null", "activeRegion != null"}) + private boolean readCannotOccurInAnyMoreActiveRegions(final GATKSAMRecord read, final ActiveRegion activeRegion) { + return read.getReferenceIndex() < activeRegion.getLocation().getContigIndex() || + ( read.getReferenceIndex() == activeRegion.getLocation().getContigIndex() + && read.getAlignmentEnd() + getActiveRegionExtension() < activeRegion.getLocation().getStop() ); + } + + // ------------------------------------------------------------------------------------- + // + // Functions to write out activity profiles and active regions + // + // ------------------------------------------------------------------------------------- + + /** + * Initialize the debugging output streams (activity profile and active regions), if not done so already + */ + @Ensures("streamsInitialized == true") + private void initializeOutputStreamsIfNecessary() { + if ( ! streamsInitialized ) { + streamsInitialized = true; + if ( walker.activityProfileOutStream != null ) { + printIGVFormatHeader(walker.activityProfileOutStream, "line", "ActivityProfile"); + } + + if ( walker.activeRegionOutStream != null ) { + printIGVFormatHeader(walker.activeRegionOutStream, "line", "ActiveRegions"); } } } + + /** + * Helper function to write out a IGV formatted line to out, at loc, with values + * + * http://www.broadinstitute.org/software/igv/IGV + * + * @param out a non-null PrintStream where we'll write our line + * @param graphType the type of graph to show in IGV for this track + * @param columns the column names for this IGV track + */ + @Requires({ + "out != null", + "graphType != null", + "columns.length > 0" + }) + private void printIGVFormatHeader(final PrintStream out, final String graphType, final String ... columns ) { + out.printf("#track graphType=%s%n", graphType); + out.printf("Chromosome\tStart\tEnd\tFeature\t%s%n", Utils.join("\t", columns)); + + } + + /** + * Helper function to write out a IGV formatted line to out, at loc, with values + * + * http://www.broadinstitute.org/software/igv/IGV + * + * @param out a non-null PrintStream where we'll write our line + * @param loc the location of values + * @param featureName string name of this feature (see IGV format) + * @param values the floating point values to associate with loc and feature name in out + */ + @Requires({ + "out != null", + "loc != null", + "values.length > 0" + }) + private void printIGVFormatRow(final PrintStream out, final GenomeLoc loc, final String featureName, final double ... values) { + // note that start and stop are 0 based, but the stop is exclusive so we don't subtract 1 + out.printf("%s\t%d\t%d\t%s", loc.getContig(), loc.getStart() - 1, loc.getStop(), featureName); + for ( final double value : values ) + out.print(String.format("\t%.3f", value)); + out.println(); + } + + /** + * Write out activity profile information, if requested by the walker + * + * @param states the states in the current activity profile + */ + @Requires("states != null") + private void writeActivityProfile(final List states) { + if ( walker.activityProfileOutStream != null ) { + initializeOutputStreamsIfNecessary(); + for ( final ActivityProfileState state : states ) { + printIGVFormatRow(walker.activityProfileOutStream, state.getLoc(), "state", Math.min(state.isActiveProb, 1.0)); + } + } + } + + /** + * Write out each active region to the walker activeRegionOutStream + * + * @param region the region we're currently operating on + */ + @Requires("region != null") + private void writeActiveRegion(final ActiveRegion region) { + if( walker.activeRegionOutStream != null ) { + initializeOutputStreamsIfNecessary(); + printIGVFormatRow(walker.activeRegionOutStream, region.getLocation().getStartLocation(), + "end-marker", 0.0); + printIGVFormatRow(walker.activeRegionOutStream, region.getLocation(), + "size=" + region.getLocation().size(), region.isActive() ? 1.0 : -1.0); + } + } + + + // ------------------------------------------------------------------------------------- + // + // Functions to process active regions that are ready for map / reduce calls + // + // ------------------------------------------------------------------------------------- + + /** + * Invoke the walker isActive function, and incorporate its result into the activity profile + * + * @param walker the walker we're running + * @param tracker the ref meta data tracker to pass on to the isActive function of walker + * @param refContext the refContext to pass on to the isActive function of walker + * @param locus the AlignmentContext to pass on to the isActive function of walker + */ + private void addIsActiveResult(final ActiveRegionWalker walker, + final RefMetaDataTracker tracker, final ReferenceContext refContext, + final AlignmentContext locus) { + // must be called, even if we won't use the result, to satisfy walker contract + final ActivityProfileState state = walker.isActive( tracker, refContext, locus ); + if ( ! walkerHasPresetRegions ) { + activityProfile.add(state); + } + } + + /** + * Take the individual isActive calls and integrate them into contiguous active regions and + * add these blocks of work to the work queue + * band-pass filter the list of isActive probabilities and turn into active regions + */ + private T processActiveRegions(final ActiveRegionWalker walker, T sum, final boolean flushActivityProfile, final boolean forceAllRegionsToBeActive) { + if ( ! walkerHasPresetRegions ) { + // We don't have preset regions, so we get our regions from the activity profile + final Collection activeRegions = activityProfile.popReadyActiveRegions(getActiveRegionExtension(), getMinRegionSize(), getMaxRegionSize(), flushActivityProfile); + workQueue.addAll(activeRegions); + if ( ! activeRegions.isEmpty() && logger.isDebugEnabled() ) logger.debug("Integrated " + activityProfile.size() + " isActive calls into " + activeRegions.size() + " regions." ); + } + + // Since we've traversed sufficiently past this point (or this contig!) in the workQueue we can unload those regions and process them + while( workQueue.peek() != null ) { + final ActiveRegion activeRegion = workQueue.peek(); + if ( forceAllRegionsToBeActive || regionCompletelyWithinDeadZone(activeRegion) ) { + writeActivityProfile(activeRegion.getSupportingStates()); + writeActiveRegion(activeRegion); + sum = processActiveRegion( workQueue.remove(), sum, walker ); + } else { + break; + } + } + + return sum; + } + + private T processActiveRegion(final ActiveRegion activeRegion, final T sum, final ActiveRegionWalker walker) { + final Iterator liveReads = myReads.iterator(); + while ( liveReads.hasNext() ) { + boolean killed = false; + final GATKSAMRecord read = liveReads.next(); + final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read ); + + if( activeRegion.getLocation().overlapsP( readLoc ) ) { + activeRegion.add(read); + + if ( ! walker.wantsNonPrimaryReads() ) { + liveReads.remove(); + killed = true; + } + } else if( walker.wantsExtendedReads() && activeRegion.getExtendedLoc().overlapsP( readLoc )) { + activeRegion.add( read ); + } + + if ( ! killed && readCannotOccurInAnyMoreActiveRegions(read, activeRegion) ) { + liveReads.remove(); + } + } + + if ( logger.isDebugEnabled() ) { + logger.debug(">> Map call with " + activeRegion.getReads().size() + " " + (activeRegion.isActive() ? "active" : "inactive") + " reads @ " + activeRegion.getLocation() + " with full extent: " + activeRegion.getReadSpanLoc()); + } + + if ( LOG_READ_CARRYING ) + logger.info(String.format("Processing region %20s span=%3d active?=%5b with %4d reads. Overall max reads carried is %s", + activeRegion.getLocation(), activeRegion.getLocation().size(), activeRegion.isActive(), activeRegion.size(), maxReadsInMemory)); + + final M x = walker.map(activeRegion, null); + return walker.reduce( x, sum ); + } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOptimized.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOptimized.java deleted file mode 100644 index 809c7ea6a..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOptimized.java +++ /dev/null @@ -1,253 +0,0 @@ -/* - * Copyright (c) 2012 The Broad Institute - * - * 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.sting.gatk.traversals; - -import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.providers.*; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.activeregion.ActivityProfile; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; - -import java.util.*; - -/** - * Created by IntelliJ IDEA. - * User: rpoplin - * Date: 12/9/11 - */ - -public class TraverseActiveRegionsOptimized extends TraverseActiveRegions { - private LinkedList myReads = new LinkedList(); - private Shard lastShard = null; - - @Override - public T traverse( final ActiveRegionWalker walker, - final LocusShardDataProvider dataProvider, - T sum) { - if ( DEBUG ) logger.warn(String.format("TraverseActiveRegions.traverse: Shard is %s", dataProvider)); - - final HashSet maybeDuplicatedReads = new HashSet(); - // TODO -- there's got to be a better way to know this - if ( lastShard != dataProvider.getShard() ) { - maybeDuplicatedReads.addAll(myReads); - logger.info("Crossing shard boundary requires us to check for duplicates against " + maybeDuplicatedReads.size() + " reads"); - if ( DEBUG ) logger.warn("Clearing myReads"); - } - lastShard = dataProvider.getShard(); - - final LocusView locusView = new AllLocusView(dataProvider); - - final LocusReferenceView referenceView = new LocusReferenceView( walker, dataProvider ); - - final List activeRegions = new LinkedList(); - ActivityProfile profile = new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions() ); - - ReferenceOrderedView referenceOrderedDataView = getReferenceOrderedView(walker, dataProvider, locusView); - - // We keep processing while the next reference location is within the interval - GenomeLoc prevLoc = null; - while( locusView.hasNext() ) { - final AlignmentContext locus = locusView.next(); - final GenomeLoc location = locus.getLocation(); - - // Grab all the previously unseen reads from this pileup and add them to the massive read list - // Note that this must occur before we leave because we are outside the intervals because - // reads may occur outside our intervals but overlap them in the future - final Collection reads = locusView.getLIBS().transferReadsFromAllPreviousPileups(); - for( final GATKSAMRecord read : reads ) { - notifyOfCurrentPosition(read); - // most of the time maybeDuplicatedReads is empty - // TODO -- I believe that because of the ordering of reads that as soon as we don't find a read in the - // TODO -- potential list of duplicates we can clear the hashset - if ( ! maybeDuplicatedReads.isEmpty() && maybeDuplicatedReads.contains(read) ) { - if ( DEBUG ) logger.warn("Skipping duplicated " + read.getReadName()); - } else { - if ( DEBUG ) logger.warn("Adding read " + read.getReadName() + " at " + engine.getGenomeLocParser().createGenomeLoc(read) + " from provider " + dataProvider); - myReads.add((GATKSAMRecord)read); - } - } - - // skip this location -- it's not part of our engine intervals - if ( outsideEngineIntervals(location) ) - continue; - - if ( prevLoc != null && location.getStart() != prevLoc.getStop() + 1 ) { - // we've move across some interval boundary, restart profile - profile = incorporateActiveRegions(profile, activeRegions); - } - - dataProvider.getShard().getReadMetrics().incrementNumIterations(); - - // create reference context. Note that if we have a pileup of "extended events", the context will - // hold the (longest) stretch of deleted reference bases (if deletions are present in the pileup). - final ReferenceContext refContext = referenceView.getReferenceContext(location); - - // Iterate forward to get all reference ordered data covering this location - final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation(), refContext); - - // Call the walkers isActive function for this locus and add them to the list to be integrated later - profile.add(walkerActiveProb(walker, tracker, refContext, locus, location)); - - prevLoc = location; - - printProgress(locus.getLocation()); - } - - updateCumulativeMetrics(dataProvider.getShard()); - - if ( ! profile.isEmpty() ) - incorporateActiveRegions(profile, activeRegions); - - // add active regions to queue of regions to process - // first check if can merge active regions over shard boundaries - if( !activeRegions.isEmpty() ) { - if( !workQueue.isEmpty() ) { - final ActiveRegion last = workQueue.getLast(); - final ActiveRegion first = activeRegions.get(0); - if( last.isActive == first.isActive && last.getLocation().contiguousP(first.getLocation()) && last.getLocation().size() + first.getLocation().size() <= getMaxRegionSize() ) { - workQueue.removeLast(); - activeRegions.remove(first); - workQueue.add( new ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), getActiveRegionExtension()) ); - } - } - workQueue.addAll( activeRegions ); - } - - logger.debug("Integrated " + profile.size() + " isActive calls into " + activeRegions.size() + " regions." ); - - // now go and process all of the active regions - sum = processActiveRegions(walker, sum, false); - - return sum; - } - - private GenomeLoc startOfLiveRegion = null; - - protected void notifyOfCurrentPosition(final GATKSAMRecord read) { - notifyOfCurrentPosition(engine.getGenomeLocParser().createGenomeLoc(read)); - } - - protected void notifyOfCurrentPosition(final GenomeLoc currentLocation) { - if ( startOfLiveRegion == null ) - startOfLiveRegion = currentLocation; - else - startOfLiveRegion = startOfLiveRegion.max(currentLocation.getStartLocation()); - } - - protected GenomeLoc getStartOfLiveRegion() { - return startOfLiveRegion; - } - - protected boolean regionCompletelyWithinDeadZone(final GenomeLoc region, final boolean includeExtension) { - return (region.getStop() < (getStartOfLiveRegion().getStart() - (includeExtension ? getActiveRegionExtension() : 0))) - || ! region.onSameContig(getStartOfLiveRegion()); - } - - private T processActiveRegions(final ActiveRegionWalker walker, T sum, final boolean forceRegionsToBeActive) { - if( walker.activeRegionOutStream != null ) { - writeActiveRegionsToStream(walker); - return sum; - } else { - return callWalkerMapOnActiveRegions(walker, sum, forceRegionsToBeActive); - } - } - - private T callWalkerMapOnActiveRegions(final ActiveRegionWalker walker, T sum, final boolean forceRegionsToBeActive) { - // Since we've traversed sufficiently past this point (or this contig!) in the workQueue we can unload those regions and process them - // TODO can implement parallel traversal here - while( workQueue.peek() != null ) { - final GenomeLoc extendedLoc = workQueue.peek().getExtendedLoc(); - if ( forceRegionsToBeActive || regionCompletelyWithinDeadZone(extendedLoc, false) ) { - final ActiveRegion activeRegion = workQueue.remove(); - if ( DEBUG ) logger.warn("Processing active region " + activeRegion + " dead zone " + getStartOfLiveRegion()); - sum = processActiveRegion( activeRegion, sum, walker ); - } else { - break; - } - } - - return sum; - } - - @Override - public String toString() { - return "TraverseActiveRegionsOptimized"; - } - - private boolean readIsDead(final GATKSAMRecord read, final GenomeLoc readLoc, final ActiveRegion activeRegion) { - return readLoc.getStop() < activeRegion.getLocation().getStart() && regionCompletelyWithinDeadZone(readLoc, true); - } - - @Override - protected T processActiveRegion(final ActiveRegion activeRegion, final T sum, final ActiveRegionWalker walker) { - final Iterator liveReads = myReads.iterator(); - while ( liveReads.hasNext() ) { - boolean killed = false; - final GATKSAMRecord read = liveReads.next(); - final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read ); - - if( activeRegion.getLocation().overlapsP( readLoc ) ) { - activeRegion.add(read); - - if ( ! walker.wantsNonPrimaryReads() ) { - if ( DEBUG ) logger.warn("Removing read " + read.getReadName() + " at " + readLoc + " with dead zone start " + getStartOfLiveRegion()); - liveReads.remove(); - killed = true; - } - } else if( walker.wantsExtendedReads() && activeRegion.getExtendedLoc().overlapsP( readLoc )) { - activeRegion.add( read ); - } - - if ( ! killed && readIsDead(read, readLoc, activeRegion) ) { - if ( DEBUG ) logger.warn("Removing read " + read.getReadName() + " at " + readLoc + " with dead zone start " + getStartOfLiveRegion()); - liveReads.remove(); - } - } - - logger.debug(">> Map call with " + activeRegion.getReads().size() + " " + (activeRegion.isActive ? "active" : "inactive") + " reads @ " + activeRegion.getLocation() + " with full extent: " + activeRegion.getReferenceLoc()); - final M x = walker.map(activeRegion, null); - return walker.reduce( x, sum ); - } - - - /** - * Special function called in LinearMicroScheduler to empty out the work queue. - * Ugly for now but will be cleaned up when we push this functionality more into the engine - */ - @Override - public T endTraversal(final Walker walker, T sum) { - return processActiveRegions((ActiveRegionWalker)walker, sum, true); - } - -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOriginal.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOriginal.java deleted file mode 100644 index 0786bc800..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOriginal.java +++ /dev/null @@ -1,262 +0,0 @@ -/* - * Copyright (c) 2012 The Broad Institute - * - * 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.sting.gatk.traversals; - -import org.apache.log4j.Logger; -import org.broadinstitute.sting.gatk.WalkerManager; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.providers.*; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; -import org.broadinstitute.sting.gatk.walkers.DataSource; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.activeregion.ActivityProfile; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; - -import java.util.*; - -/** - * Created by IntelliJ IDEA. - * User: rpoplin - * Date: 12/9/11 - */ - -public class TraverseActiveRegionsOriginal extends TraverseActiveRegions { - private final LinkedHashSet myReads = new LinkedHashSet(); - - @Override - public T traverse( final ActiveRegionWalker walker, - final LocusShardDataProvider dataProvider, - T sum) { - logger.debug(String.format("TraverseActiveRegions.traverse: Shard is %s", dataProvider)); - - final LocusView locusView = new AllLocusView(dataProvider); - - final LocusReferenceView referenceView = new LocusReferenceView( walker, dataProvider ); - final int activeRegionExtension = walker.getClass().getAnnotation(ActiveRegionExtension.class).extension(); - final int maxRegionSize = walker.getClass().getAnnotation(ActiveRegionExtension.class).maxRegion(); - - int minStart = Integer.MAX_VALUE; - final List activeRegions = new LinkedList(); - ActivityProfile profile = new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions() ); - - ReferenceOrderedView referenceOrderedDataView = getReferenceOrderedView(walker, dataProvider, locusView); - - // We keep processing while the next reference location is within the interval - GenomeLoc prevLoc = null; - while( locusView.hasNext() ) { - final AlignmentContext locus = locusView.next(); - final GenomeLoc location = locus.getLocation(); - - // Grab all the previously unseen reads from this pileup and add them to the massive read list - // Note that this must occur before we leave because we are outside the intervals because - // reads may occur outside our intervals but overlap them in the future - // TODO -- this whole HashSet logic should be changed to a linked list of reads with - // TODO -- subsequent pass over them to find the ones overlapping the active regions - for( final PileupElement p : locus.getBasePileup() ) { - final GATKSAMRecord read = p.getRead(); - if( !myReads.contains(read) ) { - myReads.add(read); - } - - // If this is the last pileup for this shard calculate the minimum alignment start so that we know - // which active regions in the work queue are now safe to process - minStart = Math.min(minStart, read.getAlignmentStart()); - } - - // skip this location -- it's not part of our engine intervals - if ( outsideEngineIntervals(location) ) - continue; - - if ( prevLoc != null && location.getStart() != prevLoc.getStop() + 1 ) { - // we've move across some interval boundary, restart profile - profile = incorporateActiveRegions(profile, activeRegions, activeRegionExtension, maxRegionSize); - } - - dataProvider.getShard().getReadMetrics().incrementNumIterations(); - - // create reference context. Note that if we have a pileup of "extended events", the context will - // hold the (longest) stretch of deleted reference bases (if deletions are present in the pileup). - final ReferenceContext refContext = referenceView.getReferenceContext(location); - - // Iterate forward to get all reference ordered data covering this location - final RefMetaDataTracker tracker = referenceOrderedDataView.getReferenceOrderedDataAtLocus(locus.getLocation(), refContext); - - // Call the walkers isActive function for this locus and add them to the list to be integrated later - profile.add(walkerActiveProb(walker, tracker, refContext, locus, location)); - - prevLoc = location; - - printProgress(locus.getLocation()); - } - - updateCumulativeMetrics(dataProvider.getShard()); - - if ( ! profile.isEmpty() ) - incorporateActiveRegions(profile, activeRegions, activeRegionExtension, maxRegionSize); - - // add active regions to queue of regions to process - // first check if can merge active regions over shard boundaries - if( !activeRegions.isEmpty() ) { - if( !workQueue.isEmpty() ) { - final ActiveRegion last = workQueue.getLast(); - final ActiveRegion first = activeRegions.get(0); - if( last.isActive == first.isActive && last.getLocation().contiguousP(first.getLocation()) && last.getLocation().size() + first.getLocation().size() <= maxRegionSize ) { - workQueue.removeLast(); - activeRegions.remove(first); - workQueue.add( new ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), activeRegionExtension) ); - } - } - workQueue.addAll( activeRegions ); - } - - logger.debug("Integrated " + profile.size() + " isActive calls into " + activeRegions.size() + " regions." ); - - // now go and process all of the active regions - sum = processActiveRegions(walker, sum, minStart, dataProvider.getLocus().getContig()); - - return sum; - } - - /** - * Take the individual isActive calls and integrate them into contiguous active regions and - * add these blocks of work to the work queue - * band-pass filter the list of isActive probabilities and turn into active regions - * - * @param profile - * @param activeRegions - * @param activeRegionExtension - * @param maxRegionSize - * @return - */ - private ActivityProfile incorporateActiveRegions(final ActivityProfile profile, - final List activeRegions, - final int activeRegionExtension, - final int maxRegionSize) { - if ( profile.isEmpty() ) - throw new IllegalStateException("trying to incorporate an empty active profile " + profile); - - final ActivityProfile bandPassFiltered = profile.bandPassFilter(); - activeRegions.addAll(bandPassFiltered.createActiveRegions( activeRegionExtension, maxRegionSize )); - return new ActivityProfile( engine.getGenomeLocParser(), profile.hasPresetRegions() ); - } - - // -------------------------------------------------------------------------------- - // - // code to handle processing active regions - // - // -------------------------------------------------------------------------------- - - private T processActiveRegions( final ActiveRegionWalker walker, T sum, final int minStart, final String currentContig ) { - if( walker.activeRegionOutStream != null ) { - writeActiveRegionsToStream(walker); - return sum; - } else { - return callWalkerMapOnActiveRegions(walker, sum, minStart, currentContig); - } - } - - private T callWalkerMapOnActiveRegions( final ActiveRegionWalker walker, T sum, final int minStart, final String currentContig ) { - // Since we've traversed sufficiently past this point (or this contig!) in the workQueue we can unload those regions and process them - // TODO can implement parallel traversal here - while( workQueue.peek() != null ) { - final GenomeLoc extendedLoc = workQueue.peek().getExtendedLoc(); - if ( extendedLoc.getStop() < minStart || (currentContig != null && !workQueue.peek().getExtendedLoc().getContig().equals(currentContig))) { - final ActiveRegion activeRegion = workQueue.remove(); - sum = processActiveRegion( activeRegion, sum, walker ); - } else { - break; - } - } - - return sum; - } - - @Override - protected T processActiveRegion( final ActiveRegion activeRegion, final T sum, final ActiveRegionWalker walker ) { - final ArrayList placedReads = new ArrayList(); - for( final GATKSAMRecord read : myReads ) { - final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read ); - if( activeRegion.getLocation().overlapsP( readLoc ) ) { - // The region which the highest amount of overlap is chosen as the primary region for the read (tie breaking is done as right most region) - long maxOverlap = activeRegion.getLocation().sizeOfOverlap( readLoc ); - ActiveRegion bestRegion = activeRegion; - for( final ActiveRegion otherRegionToTest : workQueue ) { - if( otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap ) { - maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap( readLoc ); - bestRegion = otherRegionToTest; - } - } - bestRegion.add( read ); - - // The read is also added to all other regions in which it overlaps but marked as non-primary - if( walker.wantsNonPrimaryReads() ) { - if( !bestRegion.equals(activeRegion) ) { - activeRegion.add( read ); - } - for( final ActiveRegion otherRegionToTest : workQueue ) { - if( !bestRegion.equals(otherRegionToTest) ) { - // check for non-primary vs. extended - if ( otherRegionToTest.getLocation().overlapsP( readLoc ) ) { - otherRegionToTest.add( read ); - } else if ( walker.wantsExtendedReads() && otherRegionToTest.getExtendedLoc().overlapsP( readLoc ) ) { - otherRegionToTest.add( read ); - } - } - } - } - placedReads.add( read ); - // check for non-primary vs. extended - } else if( activeRegion.getLocation().overlapsP( readLoc ) ) { - if ( walker.wantsNonPrimaryReads() ) { - activeRegion.add( read ); - } - } else if( walker.wantsExtendedReads() && activeRegion.getExtendedLoc().overlapsP( readLoc )) { - activeRegion.add( read ); - } - } - myReads.removeAll( placedReads ); // remove all the reads which have been placed into their active region - // WARNING: This hashset relies on reads being exactly equal when they are placed in the list as when they are removed. So the ActiveRegionWalker can't modify the reads in any way. - - logger.debug(">> Map call with " + activeRegion.getReads().size() + " " + (activeRegion.isActive ? "active" : "inactive") + " reads @ " + activeRegion.getLocation() + " with full extent: " + activeRegion.getReferenceLoc()); - final M x = walker.map( activeRegion, null ); - return walker.reduce( x, sum ); - } - - /** - * Special function called in LinearMicroScheduler to empty out the work queue. - * Ugly for now but will be cleaned up when we push this functionality more into the engine - */ - public T endTraversal( final Walker walker, T sum) { - return processActiveRegions((ActiveRegionWalker) walker, sum, Integer.MAX_VALUE, null); - } -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionTraversalParameters.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionTraversalParameters.java new file mode 100644 index 000000000..cdb45db7b --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionTraversalParameters.java @@ -0,0 +1,81 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers; + +import org.broadinstitute.sting.utils.activeregion.BandPassActivityProfile; + +import java.lang.annotation.Documented; +import java.lang.annotation.Inherited; +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; + +/** + * Describes the parameters that this walker requires of the active region traversal + * + * User: rpoplin + * Date: 1/18/12 + */ +@Documented +@Inherited +@Retention(RetentionPolicy.RUNTIME) + +public @interface ActiveRegionTraversalParameters { + /** + * How far to either side of the active region itself should we include reads? + * + * That is, if the active region is 10 bp wide, and extension is 5, ART will provide + * the walker with active regions 10 bp, with 5 bp of extension on either side, and + * all reads that cover the 20 bp of the region + extension. + * + * @return the size of the active region extension we'd like + */ + public int extension() default 0; + + /** + * The minimum number of bp for an active region, when we need to chop it up into pieces because + * it's become too big. This only comes into effect when there's literally no good place to chop + * that does make the region smaller than this value. + * + * @return the min size in bp of regions + */ + public int minRegion() default 50; + + /** + * The maximum size in bp of active regions wanted by this walker + * + * Active regions larger than this value are automatically cut up by ART into smaller + * regions of size <= this value. + * + * @return the max size in bp of regions + */ + public int maxRegion() default 1500; + + /** + * The variance value for the Gaussian kernel of the band pass filter employed by ART + * @return the breadth of the band pass gaussian kernel we want for our traversal + */ + public double bandPassSigma() default BandPassActivityProfile.DEFAULT_SIGMA; +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java index f937c2458..e14e50b1a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java @@ -28,9 +28,7 @@ package org.broadinstitute.sting.gatk.walkers; import com.google.java.contract.Ensures; import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broad.tribble.Feature; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.IntervalBinding; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.filters.*; @@ -40,7 +38,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; +import org.broadinstitute.sting.utils.activeregion.ActivityProfileState; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalSetRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; @@ -57,22 +55,48 @@ import java.util.*; @By(DataSource.READS) @Requires({DataSource.READS, DataSource.REFERENCE}) @PartitionBy(PartitionType.READ) -@ActiveRegionExtension(extension=50,maxRegion=1500) +@ActiveRegionTraversalParameters(extension=50,maxRegion=1500) @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, MappingQualityUnavailableFilter.class}) @RemoveProgramRecords public abstract class ActiveRegionWalker extends Walker { + /** + * If provided, this walker will write out its activity profile (per bp probabilities of being active) + * to this file in the IGV formatted TAB deliminated output: + * + * http://www.broadinstitute.org/software/igv/IGV + * + * Intended to make debugging the activity profile calculations easier + */ + @Output(fullName="activityProfileOut", shortName="APO", doc="Output the raw activity profile results in IGV format", required = false) + public PrintStream activityProfileOutStream = null; - @Output(fullName="activeRegionOut", shortName="ARO", doc="Output the active region to this interval list file", required = false) + /** + * If provided, this walker will write out its active and inactive regions + * to this file in the IGV formatted TAB deliminated output: + * + * http://www.broadinstitute.org/software/igv/IGV + * + * Intended to make debugging the active region calculations easier + */ + @Output(fullName="activeRegionOut", shortName="ARO", doc="Output the active region to this IGV formatted file", required = false) public PrintStream activeRegionOutStream = null; @Input(fullName="activeRegionIn", shortName="AR", doc="Use this interval list file as the active regions to process", required = false) protected List> activeRegionBindings = null; - public GenomeLocSortedSet presetActiveRegions = null; + @Advanced + @Argument(fullName="activeRegionExtension", shortName="activeRegionExtension", doc="The active region extension; if not provided defaults to Walker annotated default", required = false) + public Integer activeRegionExtension = null; - public boolean hasPresetActiveRegions() { - return presetActiveRegions != null; - } + @Advanced + @Argument(fullName="activeRegionMaxSize", shortName="activeRegionMaxSize", doc="The active region maximum size; if not provided defaults to Walker annotated default", required = false) + public Integer activeRegionMaxSize = null; + + @Advanced + @Argument(fullName="bandPassSigma", shortName="bandPassSigma", doc="The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default", required = false) + public Double bandPassSigma = null; + + private GenomeLocSortedSet presetActiveRegions = null; @Override public void initialize() { @@ -91,6 +115,22 @@ public abstract class ActiveRegionWalker extends Walker extends Walker= 0.0", "result.isActiveProb <= 1.0"}) - public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context); + public abstract ActivityProfileState isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context); // Map over the ActiveRegion public abstract MapType map(final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker); public final GenomeLocSortedSet extendIntervals( final GenomeLocSortedSet intervals, final GenomeLocParser genomeLocParser, IndexedFastaSequenceFile reference ) { - final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionExtension.class).extension(); + final int activeRegionExtension = this.getClass().getAnnotation(ActiveRegionTraversalParameters.class).extension(); final List allIntervals = new ArrayList(); for( final GenomeLoc interval : intervals.toList() ) { final int start = Math.max( 1, interval.getStart() - activeRegionExtension ); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java new file mode 100644 index 000000000..73c31ef66 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -0,0 +1,155 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypesContext; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + + +/** + * The allele balance (fraction of ref bases over ref + alt bases) across all bialleleic het-called samples + */ +public class AlleleBalance extends InfoFieldAnnotation { + + + char[] BASES = {'A','C','G','T'}; + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map stratifiedPerReadAlleleLikelihoodMap) { + if ( stratifiedContexts.size() == 0 ) + return null; + + if ( !vc.isBiallelic() ) + return null; + final GenotypesContext genotypes = vc.getGenotypes(); + if ( !vc.hasGenotypes() ) + return null; + + double ratioHom = 0.0; + double ratioHet = 0.0; + double weightHom = 0.0; + double weightHet = 0.0; + double overallNonDiploid = 0.0; + for ( Genotype genotype : genotypes ) { + // we care only about het calls + + AlignmentContext context = stratifiedContexts.get(genotype.getSampleName()); + if ( context == null ) + continue; + + final ReadBackedPileup pileup = context.getBasePileup(); + if ( vc.isSNP() ) { + final String bases = new String(pileup.getBases()); + if ( bases.length() == 0 ) + return null; + + double pTrue = 1.0 - Math.pow(10.0,genotype.getLog10PError()); + if ( genotype.isHet() ) { + final char refChr = vc.getReference().toString().charAt(0); + final char altChr = vc.getAlternateAllele(0).toString().charAt(0); + + final int refCount = MathUtils.countOccurrences(refChr, bases); + final int altCount = MathUtils.countOccurrences(altChr, bases); + final int otherCount = bases.length()-refCount-altCount; + + // sanity check + if ( refCount + altCount == 0 ) + continue; + + // weight the allele balance by genotype quality so that e.g. mis-called homs don't affect the ratio too much + ratioHet += pTrue * ((double)refCount / (double)(refCount + altCount)); + weightHet += pTrue; + overallNonDiploid += ( (double) otherCount )/(bases.length()*genotypes.size()); + } else if ( genotype.isHom() ) { + char alleleChr; + if ( genotype.isHomRef() ) { + alleleChr = vc.getReference().toString().charAt(0); + } else { + alleleChr = vc.getAlternateAllele(0).toString().charAt(0); + } + final int alleleCount = MathUtils.countOccurrences(alleleChr,bases); + int bestOtherCount = 0; + for ( char b : BASES ) { + if ( b == alleleChr ) + continue; + int count = MathUtils.countOccurrences(b,bases); + if ( count > bestOtherCount ) + bestOtherCount = count; + } + final int otherCount = bases.length() - alleleCount; + ratioHom += pTrue*( (double) alleleCount)/(alleleCount+bestOtherCount); + weightHom += pTrue; + overallNonDiploid += ((double ) otherCount)/(bases.length()*genotypes.size()); + } + // Allele Balance for indels was not being computed correctly (since there was no allele matching). Instead of + // prolonging the life of imperfect code, I've decided to delete it. If someone else wants to try again from + // scratch, be my guest - but make sure it's done correctly! [EB] + } + } + + // make sure we had a het genotype + + Map map = new HashMap(); + if ( weightHet > 0.0 ) { + map.put("ABHet",ratioHet/weightHet); + } + + if ( weightHom > 0.0 ) { + map.put("ABHom",ratioHom/weightHom); + } + + if ( overallNonDiploid > 0.0 ) { + map.put("OND",overallNonDiploid); + } + return map; + } + + + public List getKeyNames() { return Arrays.asList("ABHet","ABHom","OND"); } + + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("ABHet", 1, VCFHeaderLineType.Float, "Allele Balance for hets (ref/(ref+alt))"), + new VCFInfoHeaderLine("ABHom", 1, VCFHeaderLineType.Float, "Allele Balance for homs (A/(A+O))"), + new VCFInfoHeaderLine("OND", 1, VCFHeaderLineType.Float, "Overall non-diploid ratio (alleles/(alleles+non-alleles))")); } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java new file mode 100644 index 000000000..fbba6722e --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java @@ -0,0 +1,110 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeBuilder; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.Collection; +import java.util.List; + + +/** + * The allele balance (fraction of ref bases over ref + alt bases) separately for each bialleleic het-called sample + */ +public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation { + + public void annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final AlignmentContext stratifiedContext, + final VariantContext vc, + final Genotype g, + final GenotypeBuilder gb, + final PerReadAlleleLikelihoodMap alleleLikelihoodMap){ + if ( stratifiedContext == null ) + return; + + Double ratio = annotateSNP(stratifiedContext, vc, g); + if (ratio == null) + return; + + gb.attribute(getKeyNames().get(0), Double.valueOf(String.format("%.2f", ratio.doubleValue()))); + } + + private Double annotateSNP(AlignmentContext stratifiedContext, VariantContext vc, Genotype g) { + double ratio = -1; + + if ( !vc.isSNP() ) + return null; + + if ( !vc.isBiallelic() ) + return null; + + if ( g == null || !g.isCalled() ) + return null; + + if (!g.isHet()) + return null; + + Collection altAlleles = vc.getAlternateAlleles(); + if ( altAlleles.size() == 0 ) + return null; + + final String bases = new String(stratifiedContext.getBasePileup().getBases()); + if ( bases.length() == 0 ) + return null; + char refChr = vc.getReference().toString().charAt(0); + char altChr = vc.getAlternateAllele(0).toString().charAt(0); + + int refCount = MathUtils.countOccurrences(refChr, bases); + int altCount = MathUtils.countOccurrences(altChr, bases); + + // sanity check + if ( refCount + altCount == 0 ) + return null; + + ratio = ((double)refCount / (double)(refCount + altCount)); + return ratio; + } + + public List getKeyNames() { return Arrays.asList("AB"); } + + public List getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java new file mode 100644 index 000000000..17a33bdca --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java @@ -0,0 +1,117 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypesContext; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +/** + * Created by IntelliJ IDEA. + * User: chartl + * Date: 1/3/13 + * Time: 11:36 AM + * To change this template use File | Settings | File Templates. + */ +public class AverageAltAlleleLength extends InfoFieldAnnotation implements ActiveRegionBasedAnnotation, ExperimentalAnnotation { + + public List getDescriptions() { + return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Average Allele Length")); + } + + public List getKeyNames() { return Arrays.asList("AAL"); } + + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map perReadAlleleLikelihoodMap ) { + if ( !vc.hasLog10PError() ) + return null; + + final GenotypesContext genotypes = vc.getGenotypes(); + if ( genotypes == null || genotypes.size() == 0 ) + return null; + + Map map = new HashMap(); + + double length = getMeanAltAlleleLength(vc); + map.put(getKeyNames().get(0),String.format("%.2f",length)); + return map; + } + + public static double getMeanAltAlleleLength(VariantContext vc) { + double averageLength = 1.0; + if ( ! vc.isSNP() && ! vc.isSymbolic() ) { + // adjust for the event length + int averageLengthNum = 0; + int averageLengthDenom = 0; + int refLength = vc.getReference().length(); + for ( Allele a : vc.getAlternateAlleles() ) { + int numAllele = vc.getCalledChrCount(a); + int alleleSize; + if ( a.length() == refLength ) { + // SNP or MNP + byte[] a_bases = a.getBases(); + byte[] ref_bases = vc.getReference().getBases(); + int n_mismatch = 0; + for ( int idx = 0; idx < a_bases.length; idx++ ) { + if ( a_bases[idx] != ref_bases[idx] ) + n_mismatch++; + } + alleleSize = n_mismatch; + } + else if ( a.isSymbolic() ) { + alleleSize = 1; + } else { + alleleSize = Math.abs(refLength-a.length()); + } + averageLengthNum += alleleSize*numAllele; + averageLengthDenom += numAllele; + } + averageLength = ( (double) averageLengthNum )/averageLengthDenom; + } + + return averageLength; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java new file mode 100644 index 000000000..da0634dd2 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java @@ -0,0 +1,76 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + + +/** + * Count of A, C, G, T bases across all samples + */ +public class BaseCounts extends InfoFieldAnnotation { + + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map stratifiedPerReadAlleleLikelihoodMap) { + if ( stratifiedContexts.size() == 0 ) + return null; + + int[] counts = new int[4]; + + for ( Map.Entry sample : stratifiedContexts.entrySet() ) { + for (byte base : sample.getValue().getBasePileup().getBases() ) { + int index = BaseUtils.simpleBaseToBaseIndex(base); + if ( index != -1 ) + counts[index]++; + } + } + Map map = new HashMap(); + map.put(getKeyNames().get(0), counts); + return map; + } + + public List getKeyNames() { return Arrays.asList("BaseCounts"); } + + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseCounts", 4, VCFHeaderLineType.Integer, "Counts of each base")); } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java new file mode 100644 index 000000000..8ed9a9fe0 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java @@ -0,0 +1,79 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + + +/** + * Triplet annotation: fraction of MAQP == 0, MAPQ < 10, and count of all mapped reads + */ +public class LowMQ extends InfoFieldAnnotation { + + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map stratifiedPerReadAlleleLikelihoodMap) { + if ( stratifiedContexts.size() == 0 ) + return null; + + double mq0 = 0; + double mq10 = 0; + double total = 0; + for ( Map.Entry sample : stratifiedContexts.entrySet() ) + { + for ( PileupElement p : sample.getValue().getBasePileup() ) + { + if ( p.getMappingQual() == 0 ) { mq0 += 1; } + if ( p.getMappingQual() <= 10 ) { mq10 += 1; } + total += 1; + } + } + Map map = new HashMap(); + map.put(getKeyNames().get(0), String.format("%.04f,%.04f,%.00f", mq0/total, mq10/total, total)); + return map; + } + + public List getKeyNames() { return Arrays.asList("LowMQ"); } + + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 3, VCFHeaderLineType.Float, "3-tuple: ,,")); } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java new file mode 100644 index 000000000..fa1a5dde5 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java @@ -0,0 +1,78 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeBuilder; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.List; + +/** + * Count for each sample of mapping quality zero reads + */ +public class MappingQualityZeroBySample extends GenotypeAnnotation { + public void annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final AlignmentContext stratifiedContext, + final VariantContext vc, + final Genotype g, + final GenotypeBuilder gb, + final PerReadAlleleLikelihoodMap alleleLikelihoodMap){ + if ( g == null || !g.isCalled() || stratifiedContext == null ) + return; + + int mq0 = 0; + final ReadBackedPileup pileup = stratifiedContext.getBasePileup(); + for (PileupElement p : pileup ) { + if ( p.getMappingQual() == 0 ) + mq0++; + } + + gb.attribute(getKeyNames().get(0), mq0); + } + + public List getKeyNames() { return Arrays.asList(VCFConstants.MAPPING_QUALITY_ZERO_KEY); } + + public List getDescriptions() { return Arrays.asList( + new VCFFormatHeaderLine(getKeyNames().get(0), 1, + VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample")); } + + +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java new file mode 100644 index 000000000..65d2f0757 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java @@ -0,0 +1,85 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +/** + * Fraction of all reads across samples that have mapping quality zero + */ +public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation { + + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map stratifiedPerReadAlleleLikelihoodMap) { + if ( stratifiedContexts.size() == 0 ) + return null; + + int mq0 = 0; + int depth = 0; + for ( Map.Entry sample : stratifiedContexts.entrySet() ) { + AlignmentContext context = sample.getValue(); + depth += context.size(); + final ReadBackedPileup pileup = context.getBasePileup(); + for (PileupElement p : pileup ) { + if ( p.getMappingQual() == 0 ) + mq0++; + } + } + if (depth > 0) { + double mq0f = (double)mq0 / (double )depth; + + Map map = new HashMap(); + map.put(getKeyNames().get(0), String.format("%1.4f", mq0f)); + return map; + } + else + return null; + } + + public List getKeyNames() { return Arrays.asList("MQ0Fraction"); } + + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Fraction of Mapping Quality Zero Reads")); } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java new file mode 100644 index 000000000..4a8c95dd1 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java @@ -0,0 +1,81 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +/** + * The number of N bases, counting only SOLiD data + */ +public class NBaseCount extends InfoFieldAnnotation { + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map stratifiedPerReadAlleleLikelihoodMap) { + if( stratifiedContexts.size() == 0 ) + return null; + + int countNBaseSolid = 0; + int countRegularBaseSolid = 0; + + for( final AlignmentContext context : stratifiedContexts.values() ) { + for( final PileupElement p : context.getBasePileup()) { + final String platform = p.getRead().getReadGroup().getPlatform(); + if( platform != null && platform.toUpperCase().contains("SOLID") ) { + if( BaseUtils.isNBase( p.getBase() ) ) { + countNBaseSolid++; + } else if( BaseUtils.isRegularBase( p.getBase() ) ) { + countRegularBaseSolid++; + } + } + } + } + final Map map = new HashMap(); + map.put(getKeyNames().get(0), String.format("%.4f", (double)countNBaseSolid / (double)(countNBaseSolid + countRegularBaseSolid + 1))); + return map; + } + + public List getKeyNames() { return Arrays.asList("PercentNBaseSolid"); } + + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("PercentNBaseSolid", 1, VCFHeaderLineType.Float, "Percentage of N bases in the pileup (counting only SOLiD reads)")); } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java similarity index 76% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java index 58f606066..17002ba39 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java new file mode 100644 index 000000000..dbaafb1ed --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java @@ -0,0 +1,101 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.commandline.Hidden; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.sam.ReadUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +/** + * Counts of bases from Illumina, 454, and SOLiD at this site + */ +@Hidden +public class TechnologyComposition extends InfoFieldAnnotation implements ExperimentalAnnotation { + private String nIllumina = "NumIllumina"; + private String n454 ="Num454"; + private String nSolid = "NumSOLiD"; + private String nOther = "NumOther"; + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map stratifiedPerReadAlleleLikelihoodMap) { + if ( stratifiedContexts.size() == 0 ) + return null; + + int readsIllumina = 0; + int readsSolid = 0; + int reads454 = 0; + int readsOther = 0; + + for ( Map.Entry sample : stratifiedContexts.entrySet() ) { + AlignmentContext context = sample.getValue(); + final ReadBackedPileup pileup = context.getBasePileup(); + for ( PileupElement p : pileup ) { + if(ReadUtils.is454Read(p.getRead())) + reads454++; + else if (ReadUtils.isSOLiDRead(p.getRead())) + readsSolid++; + else if (ReadUtils.isIlluminaRead(p.getRead())) + readsIllumina++; + else + readsOther++; + } + } + + Map map = new HashMap(); + map.put(nIllumina, String.format("%d", readsIllumina)); + map.put(n454, String.format("%d", reads454)); + map.put(nSolid, String.format("%d", readsSolid)); + map.put(nOther, String.format("%d", readsOther)); + return map; + } + + public List getKeyNames() { return Arrays.asList(nIllumina,n454,nSolid,nOther); } + + public List getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(nIllumina, 1, VCFHeaderLineType.Integer, "Number of Illumina reads"), + new VCFInfoHeaderLine(n454, 1, VCFHeaderLineType.Integer, "Number of 454 reads"), + new VCFInfoHeaderLine(nSolid, 1, VCFHeaderLineType.Integer, "Number of SOLiD reads"), + new VCFInfoHeaderLine(nOther, 1, VCFHeaderLineType.Integer, "Number of Other technology reads")); } + +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java similarity index 64% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index c3f738c92..b03b5327f 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; @@ -57,7 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.variant.vcf.*; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java similarity index 60% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 99dadea54..c5a6fd624 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator; @@ -52,7 +31,9 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; +import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.variant.variantcontext.*; @@ -214,10 +195,10 @@ public class VariantAnnotatorEngine { Map infoAnnotations = new LinkedHashMap(vc.getAttributes()); // annotate db occurrences - vc = annotateDBs(tracker, ref, vc, infoAnnotations); + vc = annotateDBs(tracker, ref.getLocus(), vc, infoAnnotations); // annotate expressions where available - annotateExpressions(tracker, ref, infoAnnotations); + annotateExpressions(tracker, ref.getLocus(), infoAnnotations); // go through all the requested info annotationTypes for ( InfoFieldAnnotation annotationType : requestedInfoAnnotations ) { @@ -254,10 +235,22 @@ public class VariantAnnotatorEngine { return builder.genotypes(annotateGenotypes(null, null, null, vc, perReadAlleleLikelihoodMap)).make(); } - private VariantContext annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map infoAnnotations) { + public VariantContext annotateDBs(final RefMetaDataTracker tracker, final GenomeLoc loc, VariantContext vc) { + final Map newInfoAnnotations = new HashMap(0); + vc = annotateDBs(tracker, loc, vc, newInfoAnnotations); + + if ( !newInfoAnnotations.isEmpty() ) { + final VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(newInfoAnnotations); + vc = builder.make(); + } + + return vc; + } + + private VariantContext annotateDBs(final RefMetaDataTracker tracker, final GenomeLoc loc, VariantContext vc, final Map infoAnnotations) { for ( Map.Entry, String> dbSet : dbAnnotations.entrySet() ) { if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) { - final String rsID = VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType()); + final String rsID = GATKVCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), loc), vc.getType()); // add the ID if appropriate if ( rsID != null ) { @@ -273,7 +266,7 @@ public class VariantAnnotatorEngine { } } else { boolean overlapsComp = false; - for ( VariantContext comp : tracker.getValues(dbSet.getKey(), ref.getLocus()) ) { + for ( VariantContext comp : tracker.getValues(dbSet.getKey(), loc) ) { if ( !comp.isFiltered() && ( !requireStrictAlleleMatch || comp.getAlleles().equals(vc.getAlleles()) ) ) { overlapsComp = true; break; @@ -287,9 +280,9 @@ public class VariantAnnotatorEngine { return vc; } - private void annotateExpressions(RefMetaDataTracker tracker, ReferenceContext ref, Map infoAnnotations) { + private void annotateExpressions(final RefMetaDataTracker tracker, final GenomeLoc loc, final Map infoAnnotations) { for ( VAExpression expression : requestedExpressions ) { - Collection VCs = tracker.getValues(expression.binding, ref.getLocus()); + Collection VCs = tracker.getValues(expression.binding, loc); if ( VCs.size() == 0 ) continue; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java new file mode 100644 index 000000000..bc725815d --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java @@ -0,0 +1,42 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.List; +import java.util.Map; + +// TODO -- make this an abstract class when we move away from InfoFieldAnnotation +public interface ActiveRegionBasedAnnotation extends AnnotationType { + // return annotations for the given contexts split by sample and then read likelihood + public abstract Map annotate(final Map stratifiedContexts, final VariantContext vc); + + // return the descriptions used for the VCF INFO meta field + public abstract List getDescriptions(); +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java new file mode 100644 index 000000000..221887158 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java @@ -0,0 +1,127 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +import org.broadinstitute.sting.utils.classloader.PluginManager; +import org.broadinstitute.sting.utils.exceptions.UserException; + +import java.util.*; + +public class AnnotationInterfaceManager { + private static PluginManager infoFieldAnnotationPluginManager = new PluginManager(InfoFieldAnnotation.class); + private static PluginManager genotypeAnnotationPluginManager = new PluginManager(GenotypeAnnotation.class); + private static PluginManager annotationTypePluginManager = new PluginManager(AnnotationType.class); + + public static List createAllInfoFieldAnnotations() { + return infoFieldAnnotationPluginManager.createAllTypes(); + } + + public static List createAllGenotypeAnnotations() { + return genotypeAnnotationPluginManager.createAllTypes(); + } + + public static void validateAnnotations(List annotationGroupsToUse, List annotationsToUse) { + HashMap classMap = new HashMap(); + for ( Class c : infoFieldAnnotationPluginManager.getPlugins() ) + classMap.put(c.getSimpleName(), c); + for ( Class c : genotypeAnnotationPluginManager.getPlugins() ) + classMap.put(c.getSimpleName(), c); + for ( Class c : annotationTypePluginManager.getInterfaces() ) + classMap.put(c.getSimpleName(), c); + + if ( annotationGroupsToUse.size() != 1 || !"none".equals(annotationGroupsToUse.get(0)) ) { + for ( String group : annotationGroupsToUse ) { + Class interfaceClass = classMap.get(group); + if ( interfaceClass == null ) + interfaceClass = classMap.get(group + "Annotation"); + if ( interfaceClass == null ) + throw new UserException.BadArgumentValue("group", "Class " + group + " is not found; please check that you have specified the class name correctly"); + } + } + + // validate the specific classes provided + for ( String annotation : annotationsToUse ) { + Class annotationClass = classMap.get(annotation); + if ( annotationClass == null ) + annotationClass = classMap.get(annotation + "Annotation"); + if ( annotationClass == null ) + throw new UserException.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly"); + } + } + + public static List createInfoFieldAnnotations(List annotationGroupsToUse, List annotationsToUse) { + return createAnnotations(infoFieldAnnotationPluginManager, annotationGroupsToUse, annotationsToUse); + } + + public static List createGenotypeAnnotations(List annotationGroupsToUse, List annotationsToUse) { + return createAnnotations(genotypeAnnotationPluginManager, annotationGroupsToUse, annotationsToUse); + } + + private static List createAnnotations(PluginManager pluginManager, List annotationGroupsToUse, List annotationsToUse) { + // get the instances + List annotations = new ArrayList(); + + // get the classes from the provided groups (interfaces) + // create a map for all annotation classes which implement our top-level interfaces + HashMap classMap = new HashMap(); + for ( Class c : pluginManager.getPlugins() ) + classMap.put(c.getSimpleName(), c); + for ( Class c : annotationTypePluginManager.getInterfaces() ) + classMap.put(c.getSimpleName(), c); + + // use a TreeSet so that classes are returned deterministically (the plugin manager apparently isn't deterministic) + TreeSet classes = new TreeSet(new Comparator() { + public int compare(Class o1, Class o2) { + return o1.getSimpleName().compareTo(o2.getSimpleName()); + } + }); + + if ( annotationGroupsToUse.size() != 1 || !"none".equals(annotationGroupsToUse.get(0)) ) { + for ( String group : annotationGroupsToUse ) { + Class interfaceClass = classMap.get(group); + if ( interfaceClass == null ) + interfaceClass = classMap.get(group + "Annotation"); + if ( interfaceClass != null ) + classes.addAll(pluginManager.getPluginsImplementing(interfaceClass)); + } + } + + // get the specific classes provided + for ( String annotation : annotationsToUse ) { + Class annotationClass = classMap.get(annotation); + if ( annotationClass == null ) + annotationClass = classMap.get(annotation + "Annotation"); + if ( annotationClass != null ) + classes.add(annotationClass); + } + + // note that technically an annotation can work on both the INFO and FORMAT fields + for ( Class c : classes ) + annotations.add(pluginManager.createByType(c)); + + return annotations; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java new file mode 100644 index 000000000..515efab5b --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java @@ -0,0 +1,28 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +public interface AnnotationType {} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java new file mode 100644 index 000000000..98b7cad9c --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java @@ -0,0 +1,41 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.List; + +public interface AnnotatorCompatible { + + // getter methods for various used bindings + public abstract RodBinding getSnpEffRodBinding(); + public abstract RodBinding getDbsnpRodBinding(); + public abstract List> getCompRodBindings(); + public abstract List> getResourceRodBindings(); + public abstract boolean alwaysAppendDbsnpId(); +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java new file mode 100644 index 000000000..4161f6c22 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java @@ -0,0 +1,28 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +public interface ExperimentalAnnotation extends AnnotationType {} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java new file mode 100644 index 000000000..ec058708c --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -0,0 +1,54 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeBuilder; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.List; + +public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation { + + // return annotations for the given contexts/genotype split by sample + public abstract void annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final AlignmentContext stratifiedContext, + final VariantContext vc, + final Genotype g, + final GenotypeBuilder gb, + final PerReadAlleleLikelihoodMap alleleLikelihoodMap); + + // return the descriptions used for the VCF FORMAT meta field + public abstract List getDescriptions(); + +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java new file mode 100644 index 000000000..ce1bb47e5 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -0,0 +1,62 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.List; +import java.util.Map; + +public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation { + // return annotations for the given contexts split by sample + public Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc) { + return annotate(tracker, walker, ref, stratifiedContexts, vc, null); + } + + public Map annotate(Map perReadAlleleLikelihoodMap, VariantContext vc) { + return annotate(null, null, null, null, vc, perReadAlleleLikelihoodMap); + } + + + public abstract Map annotate(final RefMetaDataTracker tracker, + final AnnotatorCompatible walker, + final ReferenceContext ref, + final Map stratifiedContexts, + final VariantContext vc, + final Map stratifiedPerReadAlleleLikelihoodMap); + + // return the descriptions used for the VCF INFO meta field + public abstract List getDescriptions(); +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java new file mode 100644 index 000000000..4a6a47418 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java @@ -0,0 +1,28 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +public interface RodRequiringAnnotation extends AnnotationType {} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java new file mode 100644 index 000000000..62734fe6c --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java @@ -0,0 +1,28 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +public interface StandardAnnotation extends AnnotationType {} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/LegacyDownsampleIterator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java similarity index 50% rename from public/java/src/org/broadinstitute/sting/gatk/iterators/LegacyDownsampleIterator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java index d0992149e..1415c1d7c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/iterators/LegacyDownsampleIterator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java @@ -23,55 +23,20 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; -import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import java.util.Iterator; +import java.util.List; +import java.util.Set; +@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations") +public abstract class VariantAnnotatorAnnotation { + // return the INFO keys + public abstract List getKeyNames(); -public class LegacyDownsampleIterator implements StingSAMIterator { - - StingSAMIterator it; - int cutoff; - SAMRecord next; - - public LegacyDownsampleIterator(StingSAMIterator it, double fraction) { - this.it = it; - cutoff = (int)(fraction * 10000); - next = getNextRecord(); - } - - public boolean hasNext() { - return next != null; - } - - public SAMRecord next() { - SAMRecord result = next; - next = getNextRecord(); - return result; - } - - public void remove() { - throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!"); - } - - private SAMRecord getNextRecord() { - while ( true ) { - if ( !it.hasNext() ) - return null; - SAMRecord rec = it.next(); - if ( GenomeAnalysisEngine.getRandomGenerator().nextInt(10000) < cutoff ) - return rec; - } - } - - public void close() { - it.close(); - } - - public Iterator iterator() { - return this; - } + // initialization method (optional for subclasses, and therefore non-abstract) + public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set headerLines ) { } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java new file mode 100644 index 000000000..14f39de17 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java @@ -0,0 +1,28 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.annotator.interfaces; + +public interface WorkInProgressAnnotation extends AnnotationType {} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java similarity index 66% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index 03df03a14..09b2cba80 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.beagle; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java similarity index 69% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java index 409c8dca8..15527d34a 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.beagle; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java new file mode 100644 index 000000000..3ef688d02 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java @@ -0,0 +1,183 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.beagle; + +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Input; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.CommandLineGATK; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; + +import java.io.PrintStream; +import java.util.Arrays; +import java.util.Set; + +/** + * Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample + * in input variant file. Will additionally hold back a fraction of the sites for evaluation, marking the + * genotypes at that sites as missing, and writing the truth of these sites to a second VCF file + */ +@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) +public class VariantsToBeagleUnphased extends RodWalker { + @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) + public RodBinding variants; + + @Output(doc="File to which BEAGLE unphased genotypes should be written",required=true) + protected PrintStream beagleWriter = null; + + @Argument(fullName = "bootstrap_fraction", shortName = "bs", doc = "Proportion of records to be used in bootstrap set", required = false) + public double bootstrap = 0.0; + + @Argument(fullName = "bootstrap_vcf",shortName = "bsvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false) + VariantContextWriter bootstrapVCFOutput = null; + + @Argument(fullName = "missing", shortName = "missing", doc = "String to identify missing data in beagle output", required = false) + public String MISSING = "?"; + + private Set samples = null; + private int bootstrapSetSize = 0; + private int testSetSize = 0; + + public void initialize() { + samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName())); + + beagleWriter.print("I marker alleleA alleleB"); + for ( String sample : samples ) + beagleWriter.print(String.format(" %s %s", sample, sample)); + + beagleWriter.println(); + + if ( bootstrap < 0.0 | bootstrap > 1.0 ) + throw new UserException.BadArgumentValue("bootstrap", "Bootstrap value must be fraction between 0 and 1"); + + if ( bootstrapVCFOutput != null ) { + Set hInfo = GATKVCFUtils.getHeaderFields(getToolkit()); + bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit()))); + } + } + + /** + * Iterate over each site, emitting the BEAGLE unphased genotypes file format + * @param tracker + * @param ref + * @param context + * @return + */ + public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) { + if( tracker != null ) { + GenomeLoc loc = context.getLocation(); + VariantContext vc = tracker.getFirstValue(variants, loc); + + if ( ProduceBeagleInput.canBeOutputToBeagle(vc) ) { + // do we want to hold back this site? + boolean makeMissing = dropSite(vc); + + // if we are holding it back and we are writing a bootstrap VCF, write it out + if ( makeMissing && bootstrapVCFOutput != null ) { + bootstrapVCFOutput.add(vc); + } + + // regardless, all sites are written to the unphased genotypes file, marked as missing if appropriate + writeUnphasedBeagleOutput(vc, makeMissing); + } + } + + return 0; + } + + /** + * Do we want to hold back this site for bootstrap? Considers the bootstrap fraction member variable + * + * @param vc + * @return + */ + public boolean dropSite(VariantContext vc) { + if ( (bootstrapSetSize+1.0)/(1.0+bootstrapSetSize+testSetSize) <= bootstrap ) { + bootstrapSetSize++; + return true; + } else { + testSetSize++; + return false; + } + } + + public void writeUnphasedBeagleOutput(VariantContext vc, boolean makeMissing) { + GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc); + StringBuffer beagleOut = new StringBuffer(); + + String marker = String.format("%s:%d ",currentLoc.getContig(), currentLoc.getStart()); + beagleOut.append("M ").append(marker); + + // write out the alleles at this site + for ( Allele allele : vc.getAlleles() ) { + beagleOut.append(allele.isNoCall() ? "-" : allele.getBaseString()).append(" "); + } + + // write out sample level genotypes + for ( String sample : samples ) { + Genotype genotype = vc.getGenotype(sample); + if ( ! makeMissing && genotype.isCalled() ) { + addAlleles(beagleOut, genotype); + } else { + addAlleles(beagleOut, MISSING, MISSING); + } + } + + beagleWriter.println(beagleOut.toString()); + } + + private void addAlleles(StringBuffer buf, Genotype g) { + addAlleles(buf, g.getAllele(0).getBaseString(), g.getAllele(1).getBaseString()); + + } + + private void addAlleles(StringBuffer buf, String a, String b) { + buf.append(a).append(" ").append(b); + } + + public Integer reduceInit() { return 0; } + public Integer reduce( Integer value, Integer sum ) { return value + sum; } + + public void onTraversalDone( Integer includedSites ) { + logger.info("Sites included in beagle genotypes file : " + includedSites); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java index 566aac6b5..79ff97333 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java @@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java index 573291d06..f0d6f7301 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage; import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fragments.FragmentCollection; @@ -217,9 +217,9 @@ public class CoverageUtils { private static void updateCounts(int[] counts, PileupElement e) { if ( e.isDeletion() ) { - counts[BaseUtils.DELETION_INDEX] += e.getRepresentativeCount(); - } else if ( BaseUtils.basesAreEqual((byte) 'N', e.getBase()) ) { - counts[BaseUtils.NO_CALL_INDEX] += e.getRepresentativeCount(); + counts[BaseUtils.Base.D.ordinal()] += e.getRepresentativeCount(); + } else if ( BaseUtils.basesAreEqual(BaseUtils.Base.N.base, e.getBase()) ) { + counts[BaseUtils.Base.N.ordinal()] += e.getRepresentativeCount(); } else { try { counts[BaseUtils.simpleBaseToBaseIndex(e.getBase())] += e.getRepresentativeCount(); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java similarity index 85% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java index 1e4c55e0d..d9e5e3e98 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.coverage; @@ -62,7 +41,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec; @@ -938,7 +917,7 @@ public class DepthOfCoverage extends LocusWalker { if (tracker == null) return null; int baseIndex = ref.getBaseIndex(); - return (baseIndex == BaseUtils.gIndex || baseIndex == BaseUtils.cIndex) ? 1L : 0L; + return (baseIndex == BaseUtils.Base.G.ordinal() || baseIndex == BaseUtils.Base.C.ordinal()) ? 1L : 0L; } public Long reduce(Long toAdd, Long runningCount) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java index 0ad6e9d3b..a5a8edb0c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java @@ -26,7 +26,6 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics; -import ca.mcgill.mcb.pcingola.interval.Intron; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; @@ -36,17 +35,13 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.variant.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.GenotypesContext; import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.*; -import java.util.ArrayList; import java.util.Collection; -import java.util.List; /** * print intervals file with all the variant sites that have "most" ( >= 90% by default) of the samples with "good" (>= 10 by default)coverage ("most" and "good" can be set in the command line). diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java index 8a7f2bcc3..13dc238cd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java @@ -34,7 +34,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java new file mode 100644 index 000000000..57d903f4d --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java @@ -0,0 +1,118 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.diffengine; + +import net.sf.samtools.SAMFileReader; +import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMRecordIterator; +import net.sf.samtools.util.BlockCompressedInputStream; + +import java.io.*; +import java.util.Arrays; + + +/** + * Created by IntelliJ IDEA. + * User: depristo + * Date: 7/4/11 + * Time: 1:09 PM + * + * Class implementing diffnode reader for VCF + */ +public class BAMDiffableReader implements DiffableReader { + @Override + public String getName() { return "BAM"; } + + @Override + public DiffElement readFromFile(File file, int maxElementsToRead) { + final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index + reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT); + + DiffNode root = DiffNode.rooted(file.getName()); + SAMRecordIterator iterator = reader.iterator(); + + int count = 0; + while ( iterator.hasNext() ) { + final SAMRecord record = iterator.next(); + + // name is the read name + first of pair + String name = record.getReadName().replace('.', '_'); + if ( record.getReadPairedFlag() ) { + name += record.getFirstOfPairFlag() ? "_1" : "_2"; + } + + DiffNode readRoot = DiffNode.empty(name, root); + + // add fields + readRoot.add("NAME", record.getReadName()); + readRoot.add("FLAGS", record.getFlags()); + readRoot.add("RNAME", record.getReferenceName()); + readRoot.add("POS", record.getAlignmentStart()); + readRoot.add("MAPQ", record.getMappingQuality()); + readRoot.add("CIGAR", record.getCigarString()); + readRoot.add("RNEXT", record.getMateReferenceName()); + readRoot.add("PNEXT", record.getMateAlignmentStart()); + readRoot.add("TLEN", record.getInferredInsertSize()); + readRoot.add("SEQ", record.getReadString()); + readRoot.add("QUAL", record.getBaseQualityString()); + + for ( SAMRecord.SAMTagAndValue xt : record.getAttributes() ) { + readRoot.add(xt.tag, xt.value); + } + + // add record to root + if ( ! root.hasElement(name) ) + // protect ourselves from malformed files + root.add(readRoot); + count += readRoot.size(); + if ( count > maxElementsToRead && maxElementsToRead != -1) + break; + } + + reader.close(); + + return root.getBinding(); + } + + @Override + public boolean canRead(File file) { + final byte[] BAM_MAGIC = "BAM\1".getBytes(); + final byte[] buffer = new byte[BAM_MAGIC.length]; + try { + InputStream fstream = new BufferedInputStream(new FileInputStream(file)); + if ( !BlockCompressedInputStream.isValidFile(fstream) ) + return false; + final BlockCompressedInputStream BCIS = new BlockCompressedInputStream(fstream); + BCIS.read(buffer, 0, BAM_MAGIC.length); + BCIS.close(); + return Arrays.equals(buffer, BAM_MAGIC); + } catch ( IOException e ) { + return false; + } catch ( net.sf.samtools.FileTruncatedException e ) { + return false; + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java new file mode 100644 index 000000000..55f52a32a --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java @@ -0,0 +1,104 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.diffengine; + +import org.broadinstitute.sting.gatk.report.GATKReport; +import org.broadinstitute.sting.gatk.report.GATKReportColumn; +import org.broadinstitute.sting.gatk.report.GATKReportTable; + +import java.io.File; +import java.io.FileReader; +import java.io.IOException; + + +/** + * Class implementing diffnode reader for GATKReports + */ + +// TODO Version check to be added at the report level + +public class GATKReportDiffableReader implements DiffableReader { + @Override + public String getName() { + return "GATKReport"; + } + + @Override + public DiffElement readFromFile(File file, int maxElementsToRead) { + DiffNode root = DiffNode.rooted(file.getName()); + try { + // one line reads the whole thing into memory + GATKReport report = new GATKReport(file); + + for (GATKReportTable table : report.getTables()) { + root.add(tableToNode(table, root)); + } + + return root.getBinding(); + } catch (Exception e) { + return null; + } + } + + private DiffNode tableToNode(GATKReportTable table, DiffNode root) { + DiffNode tableRoot = DiffNode.empty(table.getTableName(), root); + + tableRoot.add("Description", table.getTableDescription()); + tableRoot.add("NumberOfRows", table.getNumRows()); + + for ( GATKReportColumn column : table.getColumnInfo() ) { + DiffNode columnRoot = DiffNode.empty(column.getColumnName(), tableRoot); + + columnRoot.add("Width", column.getColumnFormat().getWidth()); + // NOTE: as the values are trimmed during parsing left/right alignment is not currently preserved + columnRoot.add("Displayable", true); + + for ( int i = 0; i < table.getNumRows(); i++ ) { + String name = column.getColumnName() + (i+1); + columnRoot.add(name, table.get(i, column.getColumnName()).toString()); + } + + tableRoot.add(columnRoot); + } + + return tableRoot; + } + + @Override + public boolean canRead(File file) { + try { + final String HEADER = GATKReport.GATKREPORT_HEADER_PREFIX; + final char[] buff = new char[HEADER.length()]; + final FileReader FR = new FileReader(file); + FR.read(buff, 0, HEADER.length()); + FR.close(); + String firstLine = new String(buff); + return firstLine.startsWith(HEADER); + } catch (IOException e) { + return false; + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java new file mode 100644 index 000000000..59f3d512c --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java @@ -0,0 +1,145 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.diffengine; + +import org.apache.log4j.Logger; +import org.broad.tribble.AbstractFeatureReader; +import org.broad.tribble.FeatureReader; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.variant.vcf.*; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.io.*; +import java.util.Iterator; +import java.util.Map; + + +/** + * Created by IntelliJ IDEA. + * User: depristo + * Date: 7/4/11 + * Time: 1:09 PM + * + * Class implementing diffnode reader for VCF + */ +public class VCFDiffableReader implements DiffableReader { + private static Logger logger = Logger.getLogger(VCFDiffableReader.class); + + @Override + public String getName() { return "VCF"; } + + @Override + public DiffElement readFromFile(File file, int maxElementsToRead) { + DiffNode root = DiffNode.rooted(file.getName()); + try { + // read the version line from the file + BufferedReader br = new BufferedReader(new FileReader(file)); + final String version = br.readLine(); + root.add("VERSION", version); + br.close(); + + final VCFCodec vcfCodec = new VCFCodec(); + vcfCodec.disableOnTheFlyModifications(); // must be read as state is stored in reader itself + + FeatureReader reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), vcfCodec, false); + VCFHeader header = (VCFHeader)reader.getHeader(); + for ( VCFHeaderLine headerLine : header.getMetaDataInInputOrder() ) { + String key = headerLine.getKey(); + if ( headerLine instanceof VCFIDHeaderLine) + key += "_" + ((VCFIDHeaderLine) headerLine).getID(); + if ( root.hasElement(key) ) + logger.warn("Skipping duplicate header line: file=" + file + " line=" + headerLine.toString()); + else + root.add(key, headerLine.toString()); + } + + int count = 0, nRecordsAtPos = 1; + String prevName = ""; + Iterator it = reader.iterator(); + while ( it.hasNext() ) { + VariantContext vc = it.next(); + String name = vc.getChr() + ":" + vc.getStart(); + if ( name.equals(prevName) ) { + name += "_" + ++nRecordsAtPos; + } else { + prevName = name; + } + DiffNode vcRoot = DiffNode.empty(name, root); + + // add fields + vcRoot.add("CHROM", vc.getChr()); + vcRoot.add("POS", vc.getStart()); + vcRoot.add("ID", vc.getID()); + vcRoot.add("REF", vc.getReference()); + vcRoot.add("ALT", vc.getAlternateAlleles()); + vcRoot.add("QUAL", vc.hasLog10PError() ? vc.getLog10PError() * -10 : VCFConstants.MISSING_VALUE_v4); + vcRoot.add("FILTER", ! vc.filtersWereApplied() // needs null to differentiate between PASS and . + ? VCFConstants.MISSING_VALUE_v4 + : ( vc.getFilters().isEmpty() ? VCFConstants.PASSES_FILTERS_v4 : vc.getFilters()) ); + + // add info fields + for (Map.Entry attribute : vc.getAttributes().entrySet()) { + if ( ! attribute.getKey().startsWith("_") ) + vcRoot.add(attribute.getKey(), attribute.getValue()); + } + + for (Genotype g : vc.getGenotypes() ) { + DiffNode gRoot = DiffNode.empty(g.getSampleName(), vcRoot); + gRoot.add("GT", g.getGenotypeString()); + if ( g.hasGQ() ) gRoot.add("GQ", g.getGQ() ); + if ( g.hasDP() ) gRoot.add("DP", g.getDP() ); + if ( g.hasAD() ) gRoot.add("AD", Utils.join(",", g.getAD())); + if ( g.hasPL() ) gRoot.add("PL", Utils.join(",", g.getPL())); + if ( g.getFilters() != null ) gRoot.add("FT", g.getFilters()); + + for (Map.Entry attribute : g.getExtendedAttributes().entrySet()) { + if ( ! attribute.getKey().startsWith("_") ) + gRoot.add(attribute.getKey(), attribute.getValue()); + } + + vcRoot.add(gRoot); + } + + root.add(vcRoot); + count += vcRoot.size(); + if ( count > maxElementsToRead && maxElementsToRead != -1) + break; + } + + reader.close(); + } catch ( IOException e ) { + return null; + } + + return root.getBinding(); + } + + @Override + public boolean canRead(File file) { + return AbstractVCFCodec.canDecodeFile(file.getPath(), VCFCodec.VCF4_MAGIC_HEADER); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java new file mode 100644 index 000000000..8a5b3530e --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java @@ -0,0 +1,139 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.fasta; + +import org.broadinstitute.sting.commandline.Input; +import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.CommandLineGATK; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Collections; +import java.util.List; + + +/** + * Generates an alternative reference sequence over the specified interval. + * + *

+ * Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). + * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'. + * + * The output format can be partially controlled using the provided command-line arguments. + * Specify intervals with the usual -L argument to output only the reference bases within your intervals. + * Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a + * separate fasta sequence (named numerically in order). + * + * Several important notes: + * 1) if there are multiple variants that start at a site, it chooses one of them randomly. + * 2) when there are overlapping indels (but with different start positions) only the first will be chosen. + * 3) this tool works only for SNPs and for simple indels (but not for things like complex substitutions). + * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order). + * + *

Input

+ *

+ * The reference, requested intervals, and any number of variant rod files. + *

+ * + *

Output

+ *

+ * A fasta file representing the requested intervals. + *

+ * + *

Examples

+ * 
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T FastaAlternateReferenceMaker \
+ *   -o output.fasta \
+ *   -L input.intervals \
+ *   --variant input.vcf \
+ *   [--snpmask mask.vcf]
+ *
+ * + */ +@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) +@Reference(window=@Window(start=-1,stop=50)) +@Requires(value={DataSource.REFERENCE}) +public class FastaAlternateReferenceMaker extends FastaReferenceMaker { + + /** + * Variants from these input files are used by this tool to construct an alternate reference. + */ + @Input(fullName = "variant", shortName = "V", doc="variants to model", required=false) + public List> variants = Collections.emptyList(); + + /** + * Snps from this file are used as a mask when constructing the alternate reference. + */ + @Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false) + public RodBinding snpmask; + + private int deletionBasesRemaining = 0; + + public Pair map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + + if (deletionBasesRemaining > 0) { + deletionBasesRemaining--; + return new Pair(context.getLocation(), ""); + } + + String refBase = String.valueOf((char)ref.getBase()); + + // Check to see if we have a called snp + for ( VariantContext vc : tracker.getValues(variants, ref.getLocus()) ) { + if ( vc.isFiltered() ) + continue; + + if ( vc.isSimpleDeletion()) { + deletionBasesRemaining = vc.getReference().length() - 1; + // delete the next n bases, not this one + return new Pair(context.getLocation(), refBase); + } else if ( vc.isSimpleInsertion()) { + return new Pair(context.getLocation(), vc.getAlternateAllele(0).toString()); + } else if (vc.isSNP()) { + return new Pair(context.getLocation(), vc.getAlternateAllele(0).toString()); + } + } + + // if we don't have a called site, and we have a mask at this site, mask it + for ( VariantContext vc : tracker.getValues(snpmask) ) { + if ( vc.isSNP()) { + return new Pair(context.getLocation(), "N"); + } + } + + + // if we got here then we're just ref + return new Pair(context.getLocation(), refBase); + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java new file mode 100644 index 000000000..ed3ebe173 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java @@ -0,0 +1,126 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.fasta; + +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RefWalker; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; + +import java.io.PrintStream; + +/** + * Renders a new reference in FASTA format consisting of only those loci provided in the input data set. + * + *

+ * The output format can be partially controlled using the provided command-line arguments. + * Specify intervals with the usual -L argument to output only the reference bases within your intervals. + * Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a + * separate fasta sequence (named numerically in order). + * + *

Input

+ *

+ * The reference and requested intervals. + *

+ * + *

Output

+ *

+ * A fasta file representing the requested intervals. + *

+ * + *

Examples

+ * 
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T FastaReferenceMaker \
+ *   -o output.fasta \
+ *   -L input.intervals
+ *
+ * + */ +@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) +public class FastaReferenceMaker extends RefWalker, GenomeLoc> { + + @Output PrintStream out; + + @Argument(fullName="lineWidth", shortName="lw", doc="Maximum length of sequence to write per line", required=false) + public int fastaLineWidth=60; + + /** + * Please note that when using this argument adjacent intervals will automatically be merged. + */ + @Argument(fullName="rawOnelineSeq", shortName="raw", doc="Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity)", required=false) + public boolean fastaRawSeqs=false; + + protected FastaSequence fasta; + + public void initialize() { + if (fastaRawSeqs) fastaLineWidth = Integer.MAX_VALUE; + fasta = new FastaSequence(out, fastaLineWidth, fastaRawSeqs); + } + + public Pair map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) { + return new Pair(context.getLocation(), String.valueOf((char)ref.getBase())); + } + + public GenomeLoc reduceInit() { + return null; + } + + public GenomeLoc reduce(Pair value, GenomeLoc sum) { + if ( value == null ) + return sum; + + // if there is no interval to the left, then this is the first one + if ( sum == null ) { + sum = value.first; + fasta.append(value.second); + } + // if the intervals don't overlap, print out the leftmost one and start a new one + // (end of contig or new interval) + else if ( value.first.getStart() != sum.getStop() + 1 ) { + fasta.flush(); + sum = value.first; + fasta.append(value.second); + } + // otherwise, merge them + else { + sum = getToolkit().getGenomeLocParser().setStop(sum, value.first.getStop()); + fasta.append(value.second); + } + return sum; + } + + public void onTraversalDone(GenomeLoc sum) { + fasta.flush(); + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java new file mode 100644 index 000000000..41f701f1a --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java @@ -0,0 +1,101 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.fasta; + +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.io.PrintStream; + +// fasta sequence holder class + +public class FastaSequence { + + private PrintStream out; + private StringBuffer sb = new StringBuffer(); + private long sequenceCounter = 1; + private boolean printedHeader = false; + private String name = null; + private int lineWidth = -1; + private boolean noHeader = false; + + public FastaSequence(PrintStream out, int lineWidth, boolean noHeader) { + this.out = out; + this.lineWidth = lineWidth; + this.noHeader = noHeader; + } + + public void setName(String name) { + if ( printedHeader ) throw new ReviewedStingException("Can not set name for FASTA record: header is already printed."); + this.name = name; + } + + public String getName() { + if ( name != null ) return name; + else return getCurrentID(); + } + + public void append(String s) { + sb.append(s); + printFasta(false); + } + + public void flush() { + printFasta(true); + printedHeader = false; + name = null; + sequenceCounter++; + } + + public long getCurrentCount() { + return sequenceCounter; + } + + public String getCurrentID() { + return String.valueOf(sequenceCounter); + } + + private void printFasta(boolean printAll) { + if ( sb.length() == 0 || (!printAll && sb.length() < lineWidth) ) + return; + if ( !printedHeader && !noHeader) { + if ( name == null ) out.println(">" + sequenceCounter); + else out.println(">" + name); + printedHeader = true; + } + int lines = sb.length() / lineWidth; + int currentStart = 0; + for (int i=0; i < lines; i++) { + out.println(sb.substring(currentStart, currentStart+lineWidth)); + currentStart += lineWidth; + } + if ( printAll ) { + out.println(sb.substring(currentStart)); + sb.setLength(0); + } else { + sb.delete(0, currentStart); + } + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java index ad7d85031..ee2530e8b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RefWalker; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java new file mode 100644 index 000000000..f186fc73d --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java @@ -0,0 +1,81 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.filters; + +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; + +public class ClusteredSnps { + private GenomeLocParser genomeLocParser; + private int window = 10; + private int snpThreshold = 3; + + public ClusteredSnps(GenomeLocParser genomeLocParser,int snpThreshold, int window) { + this.genomeLocParser = genomeLocParser; + this.window = window; + this.snpThreshold = snpThreshold; + if ( window < 1 || snpThreshold < 1 ) + throw new IllegalArgumentException("Window and threshold values need to be positive values"); + } + + public boolean filter(FiltrationContextWindow contextWindow) { + + FiltrationContext[] variants = contextWindow.getWindow(snpThreshold-1, snpThreshold-1); + for (int i = 0; i < snpThreshold; i++) { + // ignore positions at the beginning or end of the overall interval (where there aren't enough records) + if ( variants[i] == null || variants[i+snpThreshold-1] == null ) + continue; + + // note: the documentation tells users we'll blow up if ref calls are present. + // if we ever get a windowed rod context that isn't a hack, we can actually allow this... + if ( !variants[i].getVariantContext().isVariant() ) + throw new UserException.BadInput("The clustered SNPs filter does not work in the presence of non-variant records; see the documentation for more details"); + + // find the nth variant + GenomeLoc left = GATKVariantContextUtils.getLocation(genomeLocParser, variants[i].getVariantContext()); + GenomeLoc right = null; + int snpsSeen = 1; + + int currentIndex = i; + while ( ++currentIndex < variants.length ) { + if ( variants[currentIndex] != null && variants[currentIndex].getVariantContext() != null && variants[currentIndex].getVariantContext().isVariant() ) { + if ( ++snpsSeen == snpThreshold ) { + right = GATKVariantContextUtils.getLocation(genomeLocParser, variants[currentIndex].getVariantContext()); + break; + } + } + } + + if ( right != null && + left.getContigIndex() == right.getContigIndex() && + Math.abs(right.getStart() - left.getStart()) <= window ) + return true; + } + return false; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java new file mode 100644 index 000000000..bce20d31a --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java @@ -0,0 +1,47 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.filters; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.variant.variantcontext.VariantContext; + + +public class FiltrationContext { + + private ReferenceContext ref; + private VariantContext vc; + + public FiltrationContext(ReferenceContext ref, VariantContext vc) { + this.ref = ref; + this.vc = vc; + } + + public ReferenceContext getReferenceContext() { return ref; } + + public VariantContext getVariantContext() { return vc; } + + public void setVariantContext(VariantContext newVC) { vc = newVC; } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java new file mode 100644 index 000000000..f41053f75 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java @@ -0,0 +1,104 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.filters; + +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.util.LinkedList; +import java.util.List; +import java.util.ListIterator; + +/** + * A window of variants surrounding the current variant being investigated + * + * @author ebanks + * @version 0.1 + */ + +public class FiltrationContextWindow { + + /** + * The variants. + */ + private LinkedList window = new LinkedList(); + private int currentContext; + + /** + * Contructor for a variant context. + * @param firstVariants the first set of variants, comprising the right half of the window + */ + public FiltrationContextWindow(List firstVariants) { + int windowSize = (firstVariants == null ? 1 : 2 * firstVariants.size() + 1); + currentContext = (firstVariants == null ? 0 : firstVariants.size()); + window.addAll(firstVariants); + while ( window.size() < windowSize ) + window.addFirst(null); + } + + /** + * The context currently being examined. + * @return The current context. + */ + public FiltrationContext getContext() { + return window.get(currentContext); + } + + /** + * The maximum number of elements that can be requested on either end of the current context. + * @return max. + */ + public int maxWindowElements() { + return currentContext; + } + + /** + * The window around the context currently being examined. + * @param elementsToLeft number of earlier contexts to return () + * @param elementsToRight number of later contexts to return () + * @return The current context window. + */ + public FiltrationContext[] getWindow(int elementsToLeft, int elementsToRight) { + if ( elementsToLeft > maxWindowElements() || elementsToRight > maxWindowElements() ) + throw new ReviewedStingException("Too large a window requested"); + if ( elementsToLeft < 0 || elementsToRight < 0 ) + throw new ReviewedStingException("Window size cannot be negative"); + + FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1]; + ListIterator iter = window.listIterator(currentContext - elementsToLeft); + for (int i = 0; i < elementsToLeft + elementsToRight + 1; i++) + array[i] = iter.next(); + return array; + } + + /** + * Move the window along to the next context + * @param context The new rightmost context + */ + public void moveWindow(FiltrationContext context) { + window.removeFirst(); + window.addLast(context); + } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java similarity index 65% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java index 461afd049..091d5e428 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.filters; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java index b4d8dd564..84a28b05a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RefWalker; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java index fe2b75464..91059edfd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java @@ -40,7 +40,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.Requires; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.clipping.ClippingOp; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java similarity index 75% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 9ba74b98a..78c55d1c4 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.validation; @@ -62,7 +41,7 @@ import org.broadinstitute.sting.utils.codecs.table.TableFeature; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; @@ -376,7 +355,7 @@ public class ValidationAmplicons extends RodWalker { if ( lowerCaseSNPs ) { sequence.append(Character.toLowerCase((char) ref.getBase())); } else { - sequence.append((char) BaseUtils.N); + sequence.append((char) BaseUtils.Base.N.base); } rawSequence.append(Character.toUpperCase((char) ref.getBase())); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java similarity index 79% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index e1450a428..e24c725a6 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval; @@ -307,7 +286,7 @@ public class VariantEval extends RodWalker implements TreeRedu // Now that we have all the rods categorized, determine the sample list from the eval rods. Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), evals); - Set vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); + Set vcfSamples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); // Load the sample list, using an intermediate tree set to sort the samples final Set allSampleNames = SampleUtils.getSamplesFromCommandLineInput(vcfSamples); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java similarity index 52% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java index 77459a0de..a63f32485 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java new file mode 100644 index 000000000..c0b87b5b7 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -0,0 +1,109 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; + +/** + * The Broad Institute + * SOFTWARE COPYRIGHT NOTICE AGREEMENT + * This software and its documentation are copyright 2009 by the + * Broad Institute/Massachusetts Institute of Technology. All rights are reserved. + *

+ * This software is supplied without any warranty or guaranteed support whatsoever. Neither + * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. + */ +@Analysis(description = "The overlap between eval and comp sites") +public class CompOverlap extends VariantEvaluator implements StandardEval { + @DataPoint(description = "number of eval variant sites", format = "%d") + public long nEvalVariants = 0; + + @DataPoint(description = "number of eval sites outside of comp sites", format = "%d") + public long novelSites = 0; + + @DataPoint(description = "number of eval sites at comp sites", format = "%d") + public long nVariantsAtComp = 0; + + @DataPoint(description = "percentage of eval sites at comp sites", format = "%.2f" ) + public double compRate = 0.0; + + @DataPoint(description = "number of concordant sites", format = "%d") + public long nConcordant = 0; + + @DataPoint(description = "the concordance rate", format = "%.2f") + public double concordantRate = 0.0; + + public int getComparisonOrder() { + return 2; // we need to see each eval track and each comp track + } + + public long nNovelSites() { return nEvalVariants - nVariantsAtComp; } + public double compRate() { return rate(nVariantsAtComp, nEvalVariants); } + public double concordanceRate() { return rate(nConcordant, nVariantsAtComp); } + + public void finalizeEvaluation() { + compRate = 100 * compRate(); + concordantRate = 100 * concordanceRate(); + novelSites = nNovelSites(); + } + + /** + * Returns true if every allele in eval is also in comp + * + * @param eval eval context + * @param comp db context + * @return true if eval and db are discordant + */ + public boolean discordantP(VariantContext eval, VariantContext comp) { + for (Allele a : eval.getAlleles()) { + if (!comp.hasAllele(a, true)) + return true; + } + + return false; + } + + public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + boolean evalIsGood = eval != null && eval.isPolymorphicInSamples(); + boolean compIsGood = comp != null && comp.isNotFiltered(); + + if (evalIsGood) nEvalVariants++; // count the number of eval events + + if (compIsGood && evalIsGood) { + nVariantsAtComp++; + + if (!discordantP(eval, comp)) { // count whether we're concordant or not with the comp value + nConcordant++; + } + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java new file mode 100644 index 000000000..33a5a9fc9 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -0,0 +1,217 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; + +@Analysis(description = "Counts different classes of variants in the sample") +public class CountVariants extends VariantEvaluator implements StandardEval { + // the following fields are in output order: + + // basic counts on various rates found + @DataPoint(description = "Number of processed loci", format = "%d") + public long nProcessedLoci = 0; + @DataPoint(description = "Number of called loci", format = "%d") + public long nCalledLoci = 0; + @DataPoint(description = "Number of reference loci", format = "%d") + public long nRefLoci = 0; + @DataPoint(description = "Number of variant loci", format = "%d") + public long nVariantLoci = 0; + + // the following two calculations get set in the finalizeEvaluation + @DataPoint(description = "Variants per loci rate", format = "%.8f") + public double variantRate = 0; + @DataPoint(description = "Number of variants per base", format = "%.8f") + public double variantRatePerBp = 0; + + @DataPoint(description = "Number of snp loci", format = "%d") + public long nSNPs = 0; + @DataPoint(description = "Number of mnp loci", format = "%d") + public long nMNPs = 0; + @DataPoint(description = "Number of insertions", format = "%d") + public long nInsertions = 0; + @DataPoint(description = "Number of deletions", format = "%d") + public long nDeletions = 0; + @DataPoint(description = "Number of complex indels", format = "%d") + public long nComplex = 0; + @DataPoint(description = "Number of symbolic events", format = "%d") + public long nSymbolic = 0; + + @DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)", format = "%d") + public long nMixed = 0; + + @DataPoint(description = "Number of no calls loci", format = "%d") + public long nNoCalls = 0; + @DataPoint(description = "Number of het loci", format = "%d") + public long nHets = 0; + @DataPoint(description = "Number of hom ref loci", format = "%d") + public long nHomRef = 0; + @DataPoint(description = "Number of hom var loci", format = "%d") + public long nHomVar = 0; + @DataPoint(description = "Number of singletons", format = "%d") + public long nSingletons = 0; + @DataPoint(description = "Number of derived homozygotes", format = "%d") + public long nHomDerived = 0; + + // calculations that get set in the finalizeEvaluation method + @DataPoint(description = "heterozygosity per locus rate", format = "%.2e") + public double heterozygosity = 0; + @DataPoint(description = "heterozygosity per base pair", format = "%.2f") + public double heterozygosityPerBp = 0; + @DataPoint(description = "heterozygosity to homozygosity ratio", format = "%.2f") + public double hetHomRatio = 0; + @DataPoint(description = "indel rate (insertion count + deletion count)", format = "%.2e") + public double indelRate = 0; + @DataPoint(description = "indel rate per base pair", format = "%.2f") + public double indelRatePerBp = 0; + @DataPoint(description = "insertion to deletion ratio", format = "%.2f") + public double insertionDeletionRatio = 0; + + private double perLocusRate(long n) { + return rate(n, nProcessedLoci); + } + + private long perLocusRInverseRate(long n) { + return inverseRate(n, nProcessedLoci); + } + + + public int getComparisonOrder() { + return 1; // we only need to see each eval track + } + + public void update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + nCalledLoci++; + + // Note from Eric: + // This is really not correct. What we really want here is a polymorphic vs. monomorphic count (i.e. on the Genotypes). + // So in order to maintain consistency with the previous implementation (and the intention of the original author), I've + // added in a proxy check for monomorphic status here. + // Protect against case when vc only as no-calls too - can happen if we strafity by sample and sample as a single no-call. + if ( getWalker().ignoreAC0Sites() && vc1.isMonomorphicInSamples() ) { + nRefLoci++; + } else { + switch (vc1.getType()) { + case NO_VARIATION: + // shouldn't get here + break; + case SNP: + nVariantLoci++; + nSNPs++; + if (variantWasSingleton(vc1)) nSingletons++; + break; + case MNP: + nVariantLoci++; + nMNPs++; + if (variantWasSingleton(vc1)) nSingletons++; + break; + case INDEL: + nVariantLoci++; + if (vc1.isSimpleInsertion()) + nInsertions++; + else if (vc1.isSimpleDeletion()) + nDeletions++; + else + nComplex++; + break; + case MIXED: + nVariantLoci++; + nMixed++; + break; + case SYMBOLIC: + nSymbolic++; + break; + default: + throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType()); + } + } + + // these operations are ordered to ensure that we don't get the base string of the ref unless we need it + final String aaStr = vc1.hasAttribute("ANCESTRALALLELE") ? vc1.getAttributeAsString("ANCESTRALALLELE", null).toUpperCase() : null; + final String refStr = aaStr != null ? vc1.getReference().getBaseString().toUpperCase() : null; + + // ref aa alt class + // A C A der homozygote + // A C C anc homozygote + + // A A A ref homozygote + // A A C + // A C A + // A C C + + for (final Genotype g : vc1.getGenotypes()) { + final String altStr = vc1.getAlternateAlleles().size() > 0 ? vc1.getAlternateAllele(0).getBaseString().toUpperCase() : null; + + switch (g.getType()) { + case NO_CALL: + nNoCalls++; + break; + case HOM_REF: + nHomRef++; + + if ( aaStr != null && altStr != null && !refStr.equalsIgnoreCase(aaStr) ) { + nHomDerived++; + } + + break; + case HET: + nHets++; + break; + case HOM_VAR: + nHomVar++; + + if ( aaStr != null && altStr != null && !altStr.equalsIgnoreCase(aaStr) ) { + nHomDerived++; + } + + break; + case MIXED: + break; + default: + throw new ReviewedStingException("BUG: Unexpected genotype type: " + g); + } + } + } + + public void finalizeEvaluation() { + nProcessedLoci = getWalker().getnProcessedLoci(); + variantRate = perLocusRate(nVariantLoci); + variantRatePerBp = perLocusRInverseRate(nVariantLoci); + heterozygosity = perLocusRate(nHets); + heterozygosityPerBp = perLocusRInverseRate(nHets); + hetHomRatio = ratio(nHets, nHomVar); + indelRate = perLocusRate(nDeletions + nInsertions + nComplex); + indelRatePerBp = perLocusRInverseRate(nDeletions + nInsertions + nComplex); + insertionDeletionRatio = ratio(nInsertions, nDeletions); + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java new file mode 100644 index 000000000..643948b45 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -0,0 +1,123 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.*; + +/** + * Simple utility for histogramming indel lengths + * + * Based on code from chartl + * + * @author Mark DePristo + * @since 3/21/12 + */ +@Analysis(description = "Indel length histogram", molten = true) +public class IndelLengthHistogram extends VariantEvaluator implements StandardEval { + private final Map counts = new HashMap(); + private final static boolean asFrequencies = true; + int nIndels = 0; + + @Molten(variableName = "Length", valueName = "Freq", variableFormat = "%d", valueFormat = "%.2f") + public TreeMap results; + + public final static int MAX_SIZE_FOR_HISTOGRAM = 10; + private final static boolean INCLUDE_LONG_EVENTS_AT_MAX_SIZE = false; + + public IndelLengthHistogram() { + initializeCounts(MAX_SIZE_FOR_HISTOGRAM); + } + + private void initializeCounts(int size) { + for ( int i = -size; i <= size; i++ ) { + if ( i != 0 ) counts.put(i, 0); + } + } + + @Override + public void finalizeEvaluation() { + if ( asFrequencies ) { + results = new TreeMap(); + for ( final int len : counts.keySet() ) { + final double value = nIndels == 0 ? 0.0 : counts.get(len) / (1.0 * nIndels); + results.put(len, value); + } + } else { + results = new TreeMap(results); + } + } + + @Override + public int getComparisonOrder() { + return 1; + } + + @Override + public void update1(final VariantContext eval, final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { + if ( eval.isIndel() && ! eval.isComplexIndel() ) { + if ( ! ( getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples() )) { + // only if we are actually polymorphic in the subsetted samples should we count the allele + for ( Allele alt : eval.getAlternateAlleles() ) { + final int alleleSize = alt.length() - eval.getReference().length(); + if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference()); + updateLengthHistogram(eval.getReference(), alt); + } + } + } + } + + /** + * Update the histogram with the implied length of the indel allele between ref and alt (alt.len - ref.len). + * + * If this size is outside of MAX_SIZE_FOR_HISTOGRAM, the size is capped to MAX_SIZE_FOR_HISTOGRAM, + * if INCLUDE_LONG_EVENTS_AT_MAX_SIZE is set. + * + * @param ref + * @param alt + */ + public void updateLengthHistogram(final Allele ref, final Allele alt) { + int len = alt.length() - ref.length(); + if ( INCLUDE_LONG_EVENTS_AT_MAX_SIZE ) { + if ( len > MAX_SIZE_FOR_HISTOGRAM ) len = MAX_SIZE_FOR_HISTOGRAM; + if ( len < -MAX_SIZE_FOR_HISTOGRAM ) len = -MAX_SIZE_FOR_HISTOGRAM; + } + + if ( Math.abs(len) > MAX_SIZE_FOR_HISTOGRAM ) + return; + + nIndels++; + counts.put(len, counts.get(len) + 1); + } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java similarity index 55% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java index 4793aa390..68fcc6aba 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java new file mode 100644 index 000000000..3d082f23c --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -0,0 +1,187 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.samples.Sample; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.sting.utils.MendelianViolation; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Map; +import java.util.Set; + +/** + * Mendelian violation detection and counting + *

+ * a violation looks like: + * Suppose dad = A/B and mom = C/D + * The child can be [A or B] / [C or D]. + * If the child doesn't match this, the site is a violation + *

+ * Some examples: + *

+ * mom = A/A, dad = C/C + * child can be A/C only + *

+ * mom = A/C, dad = C/C + * child can be A/C or C/C + *

+ * mom = A/C, dad = A/C + * child can be A/A, A/C, C/C + *

+ * The easiest way to do this calculation is to: + *

+ * Get alleles for mom => A/B + * Get alleles for dad => C/D + * Make allowed genotypes for child: A/C, A/D, B/C, B/D + * Check that the child is one of these. + */ +@Analysis(name = "Mendelian Violation Evaluator", description = "Mendelian Violation Evaluator") +public class MendelianViolationEvaluator extends VariantEvaluator { + + @DataPoint(description = "Number of variants found with at least one family having genotypes", format = "%d") + public long nVariants; + @DataPoint(description = "Number of variants found with no family having genotypes -- these sites do not count in the nNoCall", format = "%d") + public long nSkipped; + @DataPoint(description="Number of variants x families called (no missing genotype or lowqual)", format = "%d") + public long nFamCalled; + @DataPoint(description="Number of variants x families called (no missing genotype or lowqual) that contain at least one var allele.", format = "%d") + public long nVarFamCalled; + @DataPoint(description="Number of variants x families discarded as low quality", format = "%d") + public long nLowQual; + @DataPoint(description="Number of variants x families discarded as no call", format = "%d") + public long nNoCall; + @DataPoint(description="Number of loci with mendelian violations", format = "%d") + public long nLociViolations; + @DataPoint(description = "Number of mendelian violations found", format = "%d") + public long nViolations; + + @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_REF -> HOM_VAR", format = "%d") + public long mvRefRef_Var; + @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_REF -> HET", format = "%d") + public long mvRefRef_Het; + @DataPoint(description="Number of mendelian violations of the type HOM_REF/HET -> HOM_VAR", format = "%d") + public long mvRefHet_Var; + @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_VAR -> HOM_VAR", format = "%d") + public long mvRefVar_Var; + @DataPoint(description="Number of mendelian violations of the type HOM_REF/HOM_VAR -> HOM_REF", format = "%d") + public long mvRefVar_Ref; + @DataPoint(description="Number of mendelian violations of the type HOM_VAR/HET -> HOM_REF", format = "%d") + public long mvVarHet_Ref; + @DataPoint(description="Number of mendelian violations of the type HOM_VAR/HOM_VAR -> HOM_REF", format = "%d") + public long mvVarVar_Ref; + @DataPoint(description="Number of mendelian violations of the type HOM_VAR/HOM_VAR -> HET", format = "%d") + public long mvVarVar_Het; + + @DataPoint(description="Number of HomRef/HomRef/HomRef trios", format = "%d") + public long HomRefHomRef_HomRef; + @DataPoint(description="Number of Het/Het/Het trios", format = "%d") + public long HetHet_Het; + @DataPoint(description="Number of Het/Het/HomRef trios", format = "%d") + public long HetHet_HomRef; + @DataPoint(description="Number of Het/Het/HomVar trios", format = "%d") + public long HetHet_HomVar; + @DataPoint(description="Number of HomVar/HomVar/HomVar trios", format = "%d") + public long HomVarHomVar_HomVar; + @DataPoint(description="Number of HomRef/HomVar/Het trios", format = "%d") + public long HomRefHomVAR_Het; + @DataPoint(description="Number of ref alleles inherited from het/het parents", format = "%d") + public long HetHet_inheritedRef; + @DataPoint(description="Number of var alleles inherited from het/het parents", format = "%d") + public long HetHet_inheritedVar; + @DataPoint(description="Number of ref alleles inherited from homRef/het parents", format = "%d") + public long HomRefHet_inheritedRef; + @DataPoint(description="Number of var alleles inherited from homRef/het parents", format = "%d") + public long HomRefHet_inheritedVar; + @DataPoint(description="Number of ref alleles inherited from homVar/het parents", format = "%d") + public long HomVarHet_inheritedRef; + @DataPoint(description="Number of var alleles inherited from homVar/het parents", format = "%d") + public long HomVarHet_inheritedVar; + + MendelianViolation mv; + Map> families; + + public void initialize(VariantEval walker) { + super.initialize(walker); + mv = new MendelianViolation(walker.getMendelianViolationQualThreshold(),false); + families = walker.getSampleDB().getFamilies(); + } + + public String getName() { + return "mendelian_violations"; + } + + public int getComparisonOrder() { + return 1; // we only need to see each eval track + } + + public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if (vc.isBiallelic() && vc.hasGenotypes()) { // todo -- currently limited to biallelic loci + + if(mv.countViolations(families,vc)>0){ + nLociViolations++; + nViolations += mv.getViolationsCount(); + mvRefRef_Var += mv.getParentsRefRefChildVar(); + mvRefRef_Het += mv.getParentsRefRefChildHet(); + mvRefHet_Var += mv.getParentsRefHetChildVar(); + mvRefVar_Var += mv.getParentsRefVarChildVar(); + mvRefVar_Ref += mv.getParentsRefVarChildRef(); + mvVarHet_Ref += mv.getParentsVarHetChildRef(); + mvVarVar_Ref += mv.getParentsVarVarChildRef(); + mvVarVar_Het += mv.getParentsVarVarChildHet(); + + } + HomRefHomRef_HomRef += mv.getRefRefRef(); + HetHet_Het += mv.getHetHetHet(); + HetHet_HomRef += mv.getHetHetHomRef(); + HetHet_HomVar += mv.getHetHetHomVar(); + HomVarHomVar_HomVar += mv.getVarVarVar(); + HomRefHomVAR_Het += mv.getRefVarHet(); + HetHet_inheritedRef += mv.getParentsHetHetInheritedRef(); + HetHet_inheritedVar += mv.getParentsHetHetInheritedVar(); + HomRefHet_inheritedRef += mv.getParentsRefHetInheritedRef(); + HomRefHet_inheritedVar += mv.getParentsRefHetInheritedVar(); + HomVarHet_inheritedRef += mv.getParentsVarHetInheritedRef(); + HomVarHet_inheritedVar += mv.getParentsVarHetInheritedVar(); + + if(mv.getFamilyCalledCount()>0){ + nVariants++; + nFamCalled += mv.getFamilyCalledCount(); + nLowQual += mv.getFamilyLowQualsCount(); + nNoCall += mv.getFamilyNoCallCount(); + nVarFamCalled += mv.getVarFamilyCalledCount(); + } + else{ + nSkipped++; + } + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java new file mode 100644 index 000000000..2a7e29583 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java @@ -0,0 +1,164 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.apache.log4j.Logger; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; + +@Analysis(description = "Evaluation summary for multi-allelic variants") +public class MultiallelicSummary extends VariantEvaluator implements StandardEval { + final protected static Logger logger = Logger.getLogger(MultiallelicSummary.class); + + public enum Type { + SNP, INDEL + } + + // basic counts on various rates found + @DataPoint(description = "Number of processed loci", format = "%d") + public long nProcessedLoci = 0; + + @DataPoint(description = "Number of SNPs", format = "%d") + public int nSNPs = 0; + @DataPoint(description = "Number of multi-allelic SNPs", format = "%d") + public int nMultiSNPs = 0; + @DataPoint(description = "% processed sites that are multi-allelic SNPs", format = "%.5f") + public double processedMultiSnpRatio = 0; + @DataPoint(description = "% SNP sites that are multi-allelic", format = "%.3f") + public double variantMultiSnpRatio = 0; + + @DataPoint(description = "Number of Indels", format = "%d") + public int nIndels = 0; + @DataPoint(description = "Number of multi-allelic Indels", format = "%d") + public int nMultiIndels = 0; + @DataPoint(description = "% processed sites that are multi-allelic Indels", format = "%.5f") + public double processedMultiIndelRatio = 0; + @DataPoint(description = "% Indel sites that are multi-allelic", format = "%.3f") + public double variantMultiIndelRatio = 0; + + @DataPoint(description = "Number of Transitions", format = "%d") + public int nTi = 0; + @DataPoint(description = "Number of Transversions", format = "%d") + public int nTv = 0; + @DataPoint(description = "Overall TiTv ratio", format = "%.2f") + public double TiTvRatio = 0; + + @DataPoint(description = "Multi-allelic SNPs partially known", format = "%d") + public int knownSNPsPartial = 0; + @DataPoint(description = "Multi-allelic SNPs completely known", format = "%d") + public int knownSNPsComplete = 0; + @DataPoint(description = "Multi-allelic SNP Novelty Rate") + public String SNPNoveltyRate = "NA"; + + //TODO -- implement me + //@DataPoint(description = "Multi-allelic Indels partially known", format = "%d") + public int knownIndelsPartial = 0; + //@DataPoint(description = "Multi-allelic Indels completely known", format = "%d") + public int knownIndelsComplete = 0; + //@DataPoint(description = "Multi-allelic Indel Novelty Rate") + public String indelNoveltyRate = "NA"; + + + @Override public int getComparisonOrder() { return 2; } + + public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if ( eval == null || (getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples()) ) + return; + + // update counts + switch ( eval.getType() ) { + case SNP: + nSNPs++; + if ( !eval.isBiallelic() ) { + nMultiSNPs++; + calculatePairwiseTiTv(eval); + calculateSNPPairwiseNovelty(eval, comp); + } + break; + case INDEL: + nIndels++; + if ( !eval.isBiallelic() ) { + nMultiIndels++; + calculateIndelPairwiseNovelty(eval, comp); + } + break; + default: + //throw new UserException.BadInput("Unexpected variant context type: " + eval); + break; + } + + return; + } + + private void calculatePairwiseTiTv(VariantContext vc) { + for ( Allele alt : vc.getAlternateAlleles() ) { + if ( GATKVariantContextUtils.isTransition(vc.getReference(), alt) ) + nTi++; + else + nTv++; + } + } + + private void calculateSNPPairwiseNovelty(VariantContext eval, VariantContext comp) { + if ( comp == null ) + return; + + int knownAlleles = 0; + for ( Allele alt : eval.getAlternateAlleles() ) { + if ( comp.getAlternateAlleles().contains(alt) ) + knownAlleles++; + } + + if ( knownAlleles == eval.getAlternateAlleles().size() ) + knownSNPsComplete++; + else if ( knownAlleles > 0 ) + knownSNPsPartial++; + } + + private void calculateIndelPairwiseNovelty(VariantContext eval, VariantContext comp) { + // TODO -- implement me + } + + public void finalizeEvaluation() { + nProcessedLoci = getWalker().getnProcessedLoci(); + processedMultiSnpRatio = (double)nMultiSNPs / (double)nProcessedLoci; + variantMultiSnpRatio = (double)nMultiSNPs / (double)nSNPs; + processedMultiIndelRatio = (double)nMultiIndels / (double)nProcessedLoci; + variantMultiIndelRatio = (double)nMultiIndels / (double)nIndels; + + TiTvRatio = (double)nTi / (double)nTv; + + SNPNoveltyRate = Utils.formattedNoveltyRate(knownSNPsPartial + knownSNPsComplete, nMultiSNPs); + indelNoveltyRate = Utils.formattedNoveltyRate(knownIndelsPartial + knownIndelsComplete, nMultiSNPs); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java new file mode 100644 index 000000000..8553ed376 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java @@ -0,0 +1,57 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.variant.variantcontext.VariantContext; + +@Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites") +public class PrintMissingComp extends VariantEvaluator { + @DataPoint(description = "number of eval sites outside of comp sites", format = "%d") + public long nMissing = 0; + + public String getName() { + return "PrintMissingComp"; + } + + public int getComparisonOrder() { + return 2; // we need to see each eval track and each comp track + } + + public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + final boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP(); + final boolean evalIsGood = eval != null && eval.isSNP(); + + if ( compIsGood & ! evalIsGood ) { + nMissing++; + super.getWalker().getLogger().info("MissingFrom" + eval.toString() + " is missing from " + comp.getSource()); + } + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java new file mode 100644 index 000000000..206fc9560 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java @@ -0,0 +1,28 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +public interface StandardEval {} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java new file mode 100644 index 000000000..c5e73a875 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -0,0 +1,143 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.concurrent.ConcurrentHashMap; +import java.util.concurrent.ConcurrentMap; + +@Analysis(description = "Computes different estimates of theta based on variant sites and genotypes") +public class ThetaVariantEvaluator extends VariantEvaluator { + @DataPoint(description = "Average heterozygosity at variant sites; note that missing genotypes are ignored when computing this value", format = "%.8f") + public double avgHet = 0.0; + @DataPoint(description = "Average pairwise differences at aligned sequences; averaged over both number of sequeneces and number of variant sites; note that missing genotypes are ignored when computing this value", format = "%.8f") + public double avgAvgDiffs = 0.0; + @DataPoint(description = "Sum of heterozygosity over all variant sites; divide this by total target to get estimate of per base theta", format = "%.8f") + public double totalHet = 0.0; + @DataPoint(description = "Sum of pairwise diffs over all variant sites; divide this by total target to get estimate of per base theta", format = "%.8f") + public double totalAvgDiffs = 0.0; + @DataPoint(description = "Theta for entire region estimated based on number of segregating sites; divide ths by total target to get estimate of per base theta", format = "%.8f") + public double thetaRegionNumSites = 0.0; + + //helper variables + double numSites = 0; + + public int getComparisonOrder() { + return 1; + } + + public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if (vc == null || !vc.isSNP() || (getWalker().ignoreAC0Sites() && vc.isMonomorphicInSamples())) { + return; + } + + //this maps allele to a count + ConcurrentMap alleleCounts = new ConcurrentHashMap(); + + int numHetsHere = 0; + int numGenosHere = 0; + int numIndsHere = 0; + + for (final Genotype genotype : vc.getGenotypes()) { + numIndsHere++; + if (!genotype.isNoCall()) { + //increment stats for heterozygosity + if (genotype.isHet()) { + numHetsHere++; + } + + numGenosHere++; + //increment stats for pairwise mismatches + + for (Allele allele : genotype.getAlleles()) { + if (allele.isCalled()) { + String alleleString = allele.toString(); + alleleCounts.putIfAbsent(alleleString, 0); + alleleCounts.put(alleleString, alleleCounts.get(alleleString) + 1); + } + } + } + } + if (numGenosHere > 0) { + //only if have one called genotype at least + this.numSites++; + + this.totalHet += numHetsHere / (double)numGenosHere; + + //compute based on num sites + float harmonicFactor = 0; + for (int i = 1; i <= numIndsHere; i++) { + harmonicFactor += 1.0 / i; + } + this.thetaRegionNumSites += 1.0 / harmonicFactor; + + //now compute pairwise mismatches + float numPairwise = 0; + int numDiffs = 0; + for (String allele1 : alleleCounts.keySet()) { + int allele1Count = alleleCounts.get(allele1); + + for (String allele2 : alleleCounts.keySet()) { + if (allele1.compareTo(allele2) < 0) { + continue; + } + if (allele1 .compareTo(allele2) == 0) { + numPairwise += allele1Count * (allele1Count - 1) * .5; + + } + else { + int allele2Count = alleleCounts.get(allele2); + numPairwise += allele1Count * allele2Count; + numDiffs += allele1Count * allele2Count; + } + } + } + + if (numPairwise > 0) { + this.totalAvgDiffs += numDiffs / numPairwise; + } + } + } + + @Override + public void finalizeEvaluation() { + + if (this.numSites > 0) { + + this.avgHet = this.totalHet / this.numSites; + this.avgAvgDiffs = this.totalAvgDiffs / this.numSites; + + } + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java new file mode 100644 index 000000000..5618f607f --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -0,0 +1,100 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; + +@Analysis(description = "Ti/Tv Variant Evaluator") +public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval { + @DataPoint(description = "number of transition loci", format = "%d") + public long nTi = 0; + @DataPoint(description = "number of transversion loci", format = "%d") + public long nTv = 0; + @DataPoint(description = "the transition to transversion ratio", format = "%.2f") + public double tiTvRatio = 0.0; + @DataPoint(description = "number of comp transition sites", format = "%d") + public long nTiInComp = 0; + @DataPoint(description = "number of comp transversion sites", format = "%d") + public long nTvInComp = 0; + @DataPoint(description = "the transition to transversion ratio for comp sites", format = "%.2f") + public double TiTvRatioStandard = 0.0; + @DataPoint(description = "number of derived transition loci", format = "%d") + public long nTiDerived = 0; + @DataPoint(description = "number of derived transversion loci", format = "%d") + public long nTvDerived = 0; + @DataPoint(description = "the derived transition to transversion ratio", format = "%.2f") + public double tiTvDerivedRatio = 0.0; + + public int getComparisonOrder() { + return 2; // we only need to see each eval track + } + + public void updateTiTv(VariantContext vc, boolean updateStandard) { + if (vc != null && vc.isSNP() && vc.isBiallelic() && vc.isPolymorphicInSamples()) { + if ( GATKVariantContextUtils.isTransition(vc)) { + if (updateStandard) nTiInComp++; + else nTi++; + } else { + if (updateStandard) nTvInComp++; + else nTv++; + } + + if (vc.hasAttribute("ANCESTRALALLELE")) { + final String aaStr = vc.getAttributeAsString("ANCESTRALALLELE", "null").toUpperCase(); + if ( ! aaStr.equals(".") ) { + switch ( BaseUtils.SNPSubstitutionType(aaStr.getBytes()[0], vc.getAlternateAllele(0).getBases()[0] ) ) { + case TRANSITION: nTiDerived++; break; + case TRANSVERSION: nTvDerived++; break; + default: break; + } + } + } + } + } + + @Override + public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if (eval != null) + updateTiTv(eval, false); + if (comp != null) + updateTiTv(comp, true); + } + + @Override + public void finalizeEvaluation() { + // the ti/tv ratio needs to be set (it's not calculated per-variant). + this.tiTvRatio = rate(nTi,nTv); + this.tiTvDerivedRatio = rate(nTiDerived,nTvDerived); + this.TiTvRatioStandard = rate(nTiInComp, nTvInComp); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java new file mode 100644 index 000000000..c31cf9f86 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -0,0 +1,183 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Collection; +import java.util.Set; + +/** + * The Broad Institute + * SOFTWARE COPYRIGHT NOTICE AGREEMENT + * This software and its documentation are copyright 2009 by the + * Broad Institute/Massachusetts Institute of Technology. All rights are reserved. + *

+ * This software is supplied without any warranty or guaranteed support whatsoever. Neither + * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. + */ +@Analysis(description = "Assess site accuracy and sensitivity of callset against follow-up validation assay") +public class ValidationReport extends VariantEvaluator implements StandardEval { + // todo -- note this isn't strictly allele away. It's really focused on sites. A/T call at a validated A/G site is currently counted as a TP + @DataPoint(description = "nComp", format = "%d") public int nComp = 0; + @DataPoint(description = "TP", format = "%d") public int TP = 0; + @DataPoint(description = "FP", format = "%d") public int FP = 0; + @DataPoint(description = "FN", format = "%d") public int FN = 0; + @DataPoint(description = "TN", format = "%d") public int TN = 0; + + @DataPoint(description = "Sensitivity", format = "%.2f") public double sensitivity = 0; + @DataPoint(description = "Specificity", format = "%.2f") public double specificity = 0; + @DataPoint(description = "PPV", format = "%.2f") public double PPV = 0; + @DataPoint(description = "FDR", format = "%.2f") public double FDR = 0; + + @DataPoint(description = "CompMonoEvalNoCall", format = "%d") public int CompMonoEvalNoCall = 0; + @DataPoint(description = "CompMonoEvalFiltered", format = "%d") public int CompMonoEvalFiltered = 0; + @DataPoint(description = "CompMonoEvalMono", format = "%d") public int CompMonoEvalMono = 0; + @DataPoint(description = "CompMonoEvalPoly", format = "%d") public int CompMonoEvalPoly = 0; + + @DataPoint(description = "CompPolyEvalNoCall", format = "%d") public int CompPolyEvalNoCall = 0; + @DataPoint(description = "CompPolyEvalFiltered", format = "%d") public int CompPolyEvalFiltered = 0; + @DataPoint(description = "CompPolyEvalMono", format = "%d") public int CompPolyEvalMono = 0; + @DataPoint(description = "CompPolyEvalPoly", format = "%d") public int CompPolyEvalPoly = 0; + + @DataPoint(description = "CompFiltered", format = "%d") public int CompFiltered = 0; + @DataPoint(description = "Eval and comp have different alleles", format = "%d") public int nDifferentAlleleSites = 0; + + private static final boolean TREAT_ALL_SITES_IN_EVAL_VCF_AS_CALLED = true; + private static final boolean REQUIRE_IDENTICAL_ALLELES = false; + + private enum SiteStatus { NO_CALL, FILTERED, MONO, POLY } + + // Counts of ValidationSiteStatus x CallSiteStatus + final int[][] counts = new int[SiteStatus.values().length][SiteStatus.values().length]; + + @Override public int getComparisonOrder() { return 2; } + + @Override + public void finalizeEvaluation() { + for ( SiteStatus x : SiteStatus.values() ) + CompFiltered += getCounts(SiteStatus.FILTERED, x); + + CompMonoEvalNoCall = getCounts(SiteStatus.MONO, SiteStatus.NO_CALL); + CompMonoEvalFiltered = getCounts(SiteStatus.MONO, SiteStatus.FILTERED); + CompMonoEvalMono = getCounts(SiteStatus.MONO, SiteStatus.MONO); + CompMonoEvalPoly = getCounts(SiteStatus.MONO, SiteStatus.POLY); + + CompPolyEvalNoCall = getCounts(SiteStatus.POLY, SiteStatus.NO_CALL); + CompPolyEvalFiltered = getCounts(SiteStatus.POLY, SiteStatus.FILTERED); + CompPolyEvalMono = getCounts(SiteStatus.POLY, SiteStatus.MONO); + CompPolyEvalPoly = getCounts(SiteStatus.POLY, SiteStatus.POLY); + + TP = CompPolyEvalPoly; + FN = CompPolyEvalNoCall + CompPolyEvalFiltered + CompPolyEvalMono; + FP = CompMonoEvalPoly; + TN = CompMonoEvalNoCall + CompMonoEvalFiltered + CompMonoEvalMono; + + for ( SiteStatus x : SiteStatus.values() ) + for ( SiteStatus y : SiteStatus.values() ) + nComp += getCounts(x, y); + + if ( nComp != TP + FN + FP + TN + CompFiltered ) + throw new ReviewedStingException("BUG: nComp != TP + FN + FP + TN + CompFiltered!"); + + sensitivity = (100.0 * TP) / (TP + FN); + specificity = (TN+FP > 0) ? (100.0 * TN) / (TN + FP) : 100.0; + PPV = (100.0 * TP) / (TP + FP); + FDR = (100.0 * FP) / (FP + TP); + } + + private int getCounts(SiteStatus comp, SiteStatus eval) { + return counts[comp.ordinal()][eval.ordinal()]; + } + + @Override + public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if ( comp != null ) { // we only need to consider sites in comp + if ( REQUIRE_IDENTICAL_ALLELES && (eval != null && haveDifferentAltAlleles(eval, comp))) + nDifferentAlleleSites++; + else { + SiteStatus evalStatus = calcSiteStatus(eval); + final Set evalSamples = getWalker().getSampleNamesForEvaluation(); + if ( comp.hasGenotypes() && ! evalSamples.isEmpty() && comp.hasGenotypes(evalSamples) ) + // if we have genotypes in both eval and comp, subset comp down just the samples in eval + comp = comp.subContextFromSamples(evalSamples, false); + SiteStatus compStatus = calcSiteStatus(comp); + counts[compStatus.ordinal()][evalStatus.ordinal()]++; + } + } + } + + // + // helper routines + // + private SiteStatus calcSiteStatus(VariantContext vc) { + if ( vc == null ) return SiteStatus.NO_CALL; + if ( vc.isFiltered() ) return SiteStatus.FILTERED; + if ( vc.isMonomorphicInSamples() ) return SiteStatus.MONO; + if ( vc.hasGenotypes() ) return SiteStatus.POLY; // must be polymorphic if isMonomorphicInSamples was false and there are genotypes + + if ( vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) { + int ac = 0; + if ( vc.getNAlleles() > 2 ) { + return SiteStatus.POLY; + } + else + ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0); + return ac > 0 ? SiteStatus.POLY : SiteStatus.MONO; + } else { + return TREAT_ALL_SITES_IN_EVAL_VCF_AS_CALLED ? SiteStatus.POLY : SiteStatus.NO_CALL; // we can't figure out what to do + } + } + + + + private boolean haveDifferentAltAlleles(VariantContext eval, VariantContext comp) { + Collection evalAlts = eval.getAlternateAlleles(); + Collection compAlts = comp.getAlternateAlleles(); + if ( evalAlts.size() != compAlts.size() ) { + return true; + } else { + // same size => every alt from eval must be in comp + for ( Allele a : evalAlts ) { + if ( ! compAlts.contains(a) ) { +// System.out.printf("Different alleles: %s:%d eval=%s comp=%s\n\t\teval=%s\n\t\tcomp=%s%n", +// eval.getChr(), eval.getStart(), eval.getAlleles(), comp.getAlleles(), eval, comp); + return true; + } + } + + return false; + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java new file mode 100644 index 000000000..13130ccb0 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java @@ -0,0 +1,133 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.variantcontext.VariantContext; + +public abstract class VariantEvaluator implements Comparable { + private VariantEval walker; + private final String simpleName; + + protected VariantEvaluator() { + this.simpleName = getClass().getSimpleName(); + } + + public void initialize(VariantEval walker) { + this.walker = walker; + } + + public VariantEval getWalker() { + return walker; + } + + // Should return the number of VariantContexts expected as inputs to update. Can be 1 or 2 + public abstract int getComparisonOrder(); + + // called at all sites, regardless of eval context itself; useful for counting processed bases + // No longer available. The processed bp is kept in VEW itself for performance reasons + // public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + + public void update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + } + + public void update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + } + + public void finalizeEvaluation() {} + + protected double rate(long n, long d) { + return n / (1.0 * Math.max(d, 1)); + } + + protected long inverseRate(long n, long d) { + return n == 0 ? 0 : d / Math.max(n, 1); + } + + protected double ratio(long num, long denom) { + return ((double)num) / (Math.max(denom, 1)); + } + + /** + * Returns true if the variant in vc was a singleton in the original input evaluation + * set, regardless of variant context subsetting that has occurred. + * @param eval the VariantContext being assessed for this previous status as a singleton + * @return true if eval was originally a singleton site + */ + protected static boolean variantWasSingleton(final VariantContext eval) { + return eval.getAttributeAsBoolean(VariantEval.IS_SINGLETON_KEY, false); + } + + public final String getSimpleName() { + return simpleName; + } + + @Override + public int compareTo(final VariantEvaluator variantEvaluator) { + return getSimpleName().compareTo(variantEvaluator.getSimpleName()); + } + + /** + * Evaluation modules that override this function to indicate that they support + * combining the results of two independent collections of eval data into + * a single meaningful result. The purpose of this interface is to + * allow us to cut up the input data into many independent stratifications, and then + * at the end of the eval run decide which stratifications to combine. This is + * important in the case of AC, where you may have thousands of distinct AC + * values that chop up the number of variants to too small a number of variants, + * and you'd like to combine the AC values into ranges containing some percent + * of the data. + * + * For example, suppose you have an eval that + * counts variants in a variable nVariants. If you want to be able to combine + * multiple evaluations of this type, overload the combine function + * with a function that sets this.nVariants += other.nVariants. + * + * Add in the appropriate fields of the VariantEvaluator T + * (of the same type as this object) to the values of this object. + * + * The values in this and other are implicitly independent, so that + * the values can be added together. + * + * @param other a VariantEvaluator of the same type of this object + */ + public void combine(final VariantEvaluator other) { + throw new ReviewedStingException(getSimpleName() + " doesn't support combining results, sorry"); + } + + /** + * Must be overloaded to return true for evaluation modules that support the combine operation + * + * @return + */ + public boolean supportsCombine() { + return false; + } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java similarity index 54% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java index d5aedaf04..48d926115 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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. 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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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.evaluators; @@ -56,11 +35,11 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.variant.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.util.*; @@ -214,7 +193,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval { private boolean overlapsKnownCNV(VariantContext cnv) { if ( knownCNVs != null ) { - final GenomeLoc loc = getWalker().getToolkit().getGenomeLocParser().createGenomeLoc(cnv, true); + final GenomeLoc loc = getWalker().getToolkit().getGenomeLocParser().createGenomeLoc(cnv); IntervalTree intervalTree = knownCNVs.get(loc.getContig()); final Iterator> nodeIt = intervalTree.overlappers(loc.getStart(), loc.getStop()); @@ -247,7 +226,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval { // type specific calculations if ( type == Type.SNP && eval.isBiallelic() ) { - titvTable = VariantContextUtils.isTransition(eval) ? transitionsPerSample : transversionsPerSample; + titvTable = GATKVariantContextUtils.isTransition(eval) ? transitionsPerSample : transversionsPerSample; titvTable.inc(type, ALL); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java new file mode 100644 index 000000000..f18f73bac --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java @@ -0,0 +1,114 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; +import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.*; + +/** + * Stratifies the eval RODs by the allele count of the alternate allele + * + * Looks first at the MLEAC value in the INFO field, and uses that value if present. + * If not present, it then looks for the AC value in the INFO field. If both are absent, + * it computes the AC from the genotypes themselves. If no AC can be computed, 0 is used. + */ +public class AlleleCount extends VariantStratifier { + int nchrom; + + @Override + public void initialize() { + // we can only work with a single eval VCF, and it must have genotypes + if ( getVariantEvalWalker().getEvals().size() != 1 && !getVariantEvalWalker().mergeEvals ) + throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification only works with a single eval vcf"); + + // There are ploidy x n sample chromosomes + // TODO -- generalize to handle multiple ploidy + nchrom = getVariantEvalWalker().getNumberOfSamplesForEvaluation() * getVariantEvalWalker().getSamplePloidy(); + if ( nchrom < 2 ) + throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification requires an eval vcf with at least one sample"); + + // create an array containing each of the allele counts + for( int ac = 0; ac <= nchrom; ac++ ) { + states.add(ac); + } + + getVariantEvalWalker().getLogger().info("AlleleCount using " + nchrom + " chromosomes"); + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if (eval != null) { + int AC = 0; // by default, the site is considered monomorphic + + try { + if ( eval.isBiallelic() ) { + if ( eval.hasAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY) ) { + // the MLEAC is allowed to be larger than the AN (e.g. in the case of all PLs being 0, the GT is ./. but the exact model may arbitrarily choose an AC>1) + AC = Math.min(eval.getAttributeAsInt(VCFConstants.MLE_ALLELE_COUNT_KEY, 0), nchrom); + } else if ( eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) { + AC = eval.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0); + } + } + } catch ( ClassCastException e ) { + // protect ourselves from bad inputs + // TODO -- fully decode VC + } + + if ( AC == 0 && eval.isVariant() ) { + // fall back to the direct calculation + for (Allele allele : eval.getAlternateAlleles()) + AC = Math.max(AC, eval.getCalledChrCount(allele)); + } + + // make sure that the AC isn't invalid + if ( AC > nchrom ) + throw new UserException.MalformedVCF(String.format("The AC value (%d) at position %s:%d " + + "is larger than the number of chromosomes over all samples (%d)", AC, + eval.getChr(), eval.getStart(), nchrom)); + + return Collections.singletonList((Object) AC); + } else { + return Collections.emptyList(); + } + } + + @Override + public Set> getIncompatibleEvaluators() { + return new HashSet>(Arrays.asList(VariantSummary.class)); + } + + @Override + public String getFormat() { + return "%d"; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java new file mode 100644 index 000000000..179161ee2 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java @@ -0,0 +1,61 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Collections; +import java.util.List; + +/** + * Stratifies the eval RODs by the allele frequency of the alternate allele + * + * Uses a constant 0.005 frequency grid, and projects the AF INFO field value. Requires + * that AF be present in every ROD, otherwise this stratification throws an exception + */ +public class AlleleFrequency extends VariantStratifier { + @Override + public void initialize() { + for( double a = 0.000; a <= 1.005; a += 0.005 ) { + states.add(String.format("%.3f", a)); + } + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if (eval != null) { + try { + return Collections.singletonList((Object)String.format("%.3f", (5.0 * MathUtils.round(eval.getAttributeAsDouble("AF", 0.0) / 5.0, 3)))); + } catch (Exception e) { + return Collections.emptyList(); + } + } + + return Collections.emptyList(); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java new file mode 100644 index 000000000..202f6528a --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java @@ -0,0 +1,51 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Collections; +import java.util.List; + + +/** + * Required stratification grouping output by each comp ROD + */ +public class CompRod extends VariantStratifier implements RequiredStratification { + @Override + public void initialize() { + for ( RodBinding rod : getVariantEvalWalker().getComps() ) { + states.add(rod.getName()); + } + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + return Collections.singletonList((Object)compName); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java new file mode 100644 index 000000000..411aed94f --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java @@ -0,0 +1,54 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +/** + * Stratifies the evaluation by each contig in the reference sequence + */ +public class Contig extends VariantStratifier { + @Override + public void initialize() { + states.addAll(getVariantEvalWalker().getContigNames()); + states.add("all"); + } + + @Override + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if (eval != null) { + return Arrays.asList((Object)"all", eval.getChr()); + } else { + return Collections.emptyList(); + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java new file mode 100644 index 000000000..bba431ab4 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java @@ -0,0 +1,76 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.ArrayList; +import java.util.List; + +/** + * CpG is a stratification module for VariantEval that divides the input data by within/not within a CpG site + * + *

+ * It is a three-state stratification: + *

    + *
  • The locus is a CpG site ("CpG") + *
  • The locus is not a CpG site ("non_CpG") + *
  • The locus is either a CpG or not a CpG site ("all") + *
+ * A CpG site is defined as a site where the reference base at a locus is a C and the adjacent reference base in the 3' direction is a G. + */ +public class CpG extends VariantStratifier { + @Override + public void initialize() { + states.add("all"); + states.add("CpG"); + states.add("non_CpG"); + } + + @Override + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + boolean isCpG = false; + if (ref != null && ref.getBases() != null) { + String fwRefBases = new String(ref.getBases()); + + //String leftFlank = fwRefBases.substring((fwRefBases.length()/2) - 1, (fwRefBases.length()/2) + 1); + String rightFlank = fwRefBases.substring((fwRefBases.length()/2), (fwRefBases.length()/2) + 2); + + //if (leftFlank.equalsIgnoreCase("CG") || leftFlank.equalsIgnoreCase("GC") || rightFlank.equalsIgnoreCase("CG") || rightFlank.equalsIgnoreCase("GC")) { + if (rightFlank.equalsIgnoreCase("CG")) { + isCpG = true; + } + } + + ArrayList relevantStates = new ArrayList(2); + relevantStates.add("all"); + relevantStates.add(isCpG ? "CpG" : "non_CpG"); + + return relevantStates; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java new file mode 100644 index 000000000..120bd3cf0 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java @@ -0,0 +1,158 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; + +/** + * Experimental stratification by the degeneracy of an amino acid, according to VCF annotation. Not safe + */ +public class Degeneracy extends VariantStratifier { + private HashMap> degeneracies; + + @Override + public void initialize() { + states.add("1-fold"); + states.add("2-fold"); + states.add("3-fold"); + states.add("4-fold"); + states.add("6-fold"); + states.add("all"); + + HashMap aminoAcids = new HashMap(); + aminoAcids.put("Ile", new String[]{"ATT", "ATC", "ATA"}); + aminoAcids.put("Leu", new String[]{"CTT", "CTC", "CTA", "CTG", "TTA", "TTG"}); + aminoAcids.put("Val", new String[]{"GTT", "GTC", "GTA", "GTG"}); + aminoAcids.put("Phe", new String[]{"TTT", "TTC"}); + aminoAcids.put("Met", new String[]{"ATG"}); + aminoAcids.put("Cys", new String[]{"TGT", "TGC"}); + aminoAcids.put("Ala", new String[]{"GCT", "GCC", "GCA", "GCG"}); + aminoAcids.put("Gly", new String[]{"GGT", "GGC", "GGA", "GGG"}); + aminoAcids.put("Pro", new String[]{"CCT", "CCC", "CCA", "CCG"}); + aminoAcids.put("Thr", new String[]{"ACT", "ACC", "ACA", "ACG"}); + aminoAcids.put("Ser", new String[]{"TCT", "TCC", "TCA", "TCG", "AGT", "AGC"}); + aminoAcids.put("Tyr", new String[]{"TAT", "TAC"}); + aminoAcids.put("Trp", new String[]{"TGG"}); + aminoAcids.put("Glu", new String[]{"CAA", "CAG"}); + aminoAcids.put("Asn", new String[]{"AAT", "AAC"}); + aminoAcids.put("His", new String[]{"CAT", "CAC"}); + aminoAcids.put("Gln", new String[]{"GAA", "GAG"}); + aminoAcids.put("Asp", new String[]{"GAT", "GAC"}); + aminoAcids.put("Lys", new String[]{"AAA", "AAG"}); + aminoAcids.put("Arg", new String[]{"CGT", "CGC", "CGA", "CGG", "AGA", "AGG"}); + aminoAcids.put("Stop", new String[]{"TAA", "TAG", "TGA"}); + + degeneracies = new HashMap>(); + + for (String aminoAcid : aminoAcids.keySet()) { + String[] codons = aminoAcids.get(aminoAcid); + + for (int pos = 0; pos < 3; pos++) { + HashSet alleles = new HashSet(); + + for (String codon : codons) { + alleles.add(codon.charAt(pos)); + } + + String degeneracy; + switch (alleles.size()) { + case 1: degeneracy = "1-fold"; break; + case 2: degeneracy = "2-fold"; break; + case 3: degeneracy = "3-fold"; break; + case 4: degeneracy = "4-fold"; break; + case 6: degeneracy = "6-fold"; break; + default: degeneracy = "1-fold"; break; + } + + if (!degeneracies.containsKey(aminoAcid)) { + degeneracies.put(aminoAcid, new HashMap()); + } + + degeneracies.get(aminoAcid).put(pos, degeneracy); + } + } + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + ArrayList relevantStates = new ArrayList(); + + relevantStates.add("all"); + + if (eval != null && eval.isVariant()) { + String type = null; + String aa = null; + Integer frame = null; + + if (eval.hasAttribute("refseq.functionalClass")) { + aa = eval.getAttributeAsString("refseq.variantAA", null); + frame = eval.getAttributeAsInt("refseq.frame", 0); + } else if (eval.hasAttribute("refseq.functionalClass_1")) { + int annotationId = 1; + String key; + + do { + key = String.format("refseq.functionalClass_%d", annotationId); + + String newtype = eval.getAttributeAsString(key, null); + + if ( newtype != null && + ( type == null || + ( type.equals("silent") && !newtype.equals("silent") ) || + ( type.equals("missense") && newtype.equals("nonsense") ) ) + ) { + type = newtype; + + String aakey = String.format("refseq.variantAA_%d", annotationId); + aa = eval.getAttributeAsString(aakey, null); + + if (aa != null) { + String framekey = String.format("refseq.frame_%d", annotationId); + + if (eval.hasAttribute(framekey)) { + frame = eval.getAttributeAsInt(framekey, 0); + } + } + } + + annotationId++; + } while (eval.hasAttribute(key)); + } + + if (aa != null && degeneracies.containsKey(aa) && frame != null) { + relevantStates.add(degeneracies.get(aa).get(frame)); + } + } + + return relevantStates; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java new file mode 100644 index 000000000..afb36cdc6 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java @@ -0,0 +1,66 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.variant.variantcontext.VariantContext; + +/** + * Tag this stratification as dynamically determining the final strat based on the input data + * + * The paradigm here is simple. We upfront create a strat with N states that reflect the finest grained + * possible division of the data. The data is processed, and statistics collected for each of the N states. + * An update call is made to the stratification for evaluation VariantContext during each map call, + * allowing the strat to collect data about the usage of each state. A final call requests that + * the stratification map down the N states into M states (typically less than N, not necessarily + * a subset of N). This is provided by returning a map from each of M state -> N states and + * the VariantEval walker will combine all of the evaluations for N into a single value for + * each M. + * + * For example, suppose I have a dynamic strat called AC, adopting 7 possible values 0,1,2,3,4,5,6. This + * strats tracks the number of eval vcs for each state, with final counts 0=1, 1=100, 2=10, 3=5, 4=3, 5=2, 6=1. + * The stratification attempts to combine the strats down to so that each state has approximately the same + * fraction of the data in each bin. Overall there is 1+100+10+5+3+2+1=124 observations and 7 bins so we really + * want ~ 18 observations in each bin. So we merge 3-6 with 5+3+2+1 = 11 and keep 2, 1, and 0 as distinct bins. We + * return a map from 0 -> 0, 1 -> 1, 2 -> 2, 3-6 -> {3,4,5,6}. + * + * TODO - some open implementation questions + * -- We should only create one stratifier overall. How do we track this? When we create the stratifiers + * perhaps we can look at them and create a tracker? + * -- How do we create a new stratifier based on the finalStratifications() given the framework? Conceptually + * this new thing is itself a stratifier, just like before, but it's states are determined at the end. We'd + * then like to call not getRelevantStates but a different function that accepts an old state and returns + * the new state. Perhaps the process should look like: + * finalizeStratification -> new Stratifier whose states are the final ones + * getNewState(old state) -> new state (one of those in getFinalStratification) + * + * @author Mark DePristo + * @since 4/9/12 + */ +public interface DynamicStratification { + public void update(final VariantContext eval); + public VariantStratifier finalizeStratification(); + public Object getFinalState(final Object oldState); +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java new file mode 100644 index 000000000..6d00bf16a --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java @@ -0,0 +1,52 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.List; + +/** + * Required stratification grouping output by each eval ROD + */ +public class EvalRod extends VariantStratifier implements RequiredStratification { + @Override + public void initialize() { + for ( RodBinding rod : getVariantEvalWalker().getEvals() ) { + states.add(rod.getName()); + if ( getVariantEvalWalker().mergeEvals ) + break; + } + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + return Arrays.asList((Object)evalName); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java new file mode 100644 index 000000000..49c2a8808 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java @@ -0,0 +1,56 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.ArrayList; +import java.util.List; + +/** + * Stratifies by the FILTER status (PASS, FAIL) of the eval records + */ +public class Filter extends VariantStratifier { + @Override + public void initialize() { + states.add("called"); + states.add("filtered"); + states.add("raw"); + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + ArrayList relevantStates = new ArrayList(); + + relevantStates.add("raw"); + if (eval != null) { + relevantStates.add(eval.isFiltered() ? "filtered" : "called"); + } + + return relevantStates; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java new file mode 100644 index 000000000..d43db70fa --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java @@ -0,0 +1,110 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.ArrayList; +import java.util.List; + +/** + * Stratifies by nonsense, missense, silent, and all annotations in the input ROD, from the INFO field annotation. + */ +public class FunctionalClass extends VariantStratifier { + + public enum FunctionalType { + silent, + missense, + nonsense + } + + + @Override + public void initialize() { + states.add("all"); + for ( FunctionalType type : FunctionalType.values() ) + states.add(type.name()); + } + + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + ArrayList relevantStates = new ArrayList(); + + relevantStates.add("all"); + + if (eval != null && eval.isVariant()) { + FunctionalType type = null; + + if (eval.hasAttribute("refseq.functionalClass")) { + try { + type = FunctionalType.valueOf(eval.getAttributeAsString("refseq.functionalClass", null)); + } catch ( Exception e ) {} // don't error out if the type isn't supported + } else if (eval.hasAttribute("refseq.functionalClass_1")) { + int annotationId = 1; + String key; + + do { + key = String.format("refseq.functionalClass_%d", annotationId); + + String newtypeStr = eval.getAttributeAsString(key, null); + if ( newtypeStr != null && !newtypeStr.equalsIgnoreCase("null") ) { + try { + FunctionalType newType = FunctionalType.valueOf(newtypeStr); + if ( type == null || + ( type == FunctionalType.silent && newType != FunctionalType.silent ) || + ( type == FunctionalType.missense && newType == FunctionalType.nonsense ) ) { + type = newType; + } + } catch ( Exception e ) {} // don't error out if the type isn't supported + } + + annotationId++; + } while (eval.hasAttribute(key)); + + } else if ( eval.hasAttribute(SnpEff.InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName()) ) { + try { + SnpEff.EffectFunctionalClass snpEffFunctionalClass = SnpEff.EffectFunctionalClass.valueOf(eval.getAttribute(SnpEff.InfoFieldKey.FUNCTIONAL_CLASS_KEY.getKeyName()).toString()); + if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.NONSENSE ) + type = FunctionalType.nonsense; + else if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.MISSENSE ) + type = FunctionalType.missense; + else if ( snpEffFunctionalClass == SnpEff.EffectFunctionalClass.SILENT ) + type = FunctionalType.silent; + } + catch ( Exception e ) {} // don't error out if the type isn't supported + } + + if ( type != null ) { + relevantStates.add(type.name()); + } + } + + return relevantStates; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java new file mode 100644 index 000000000..3e10d3b98 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java @@ -0,0 +1,78 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Collections; +import java.util.List; + +/** + * Stratifies the eval RODs by the indel size + * + * Indel sizes are stratified from sizes -100 to +100. Sizes greater than this are lumped in the +/- 100 bin + * This stratification ignores multi-allelic indels (whose size is not defined uniquely) + */ +public class IndelSize extends VariantStratifier { + static final int MAX_INDEL_SIZE = 100; + + @Override + public void initialize() { + for( int a=-MAX_INDEL_SIZE; a <=MAX_INDEL_SIZE; a++ ) { + states.add(a); + } + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if (eval != null && eval.isIndel() && eval.isBiallelic()) { + try { + int eventLength = 0; + if ( eval.isSimpleInsertion() ) { + eventLength = eval.getAlternateAllele(0).length(); + } else if ( eval.isSimpleDeletion() ) { + eventLength = -eval.getReference().length(); + } + + if (eventLength > MAX_INDEL_SIZE) + eventLength = MAX_INDEL_SIZE; + else if (eventLength < -MAX_INDEL_SIZE) + eventLength = -MAX_INDEL_SIZE; + + return Collections.singletonList((Object)eventLength); + } catch (Exception e) { + return Collections.emptyList(); + } + } + + return Collections.emptyList(); + } + @Override + public String getFormat() { + return "%d"; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java new file mode 100644 index 000000000..312e506a2 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java @@ -0,0 +1,92 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import net.sf.picard.util.IntervalTree; +import org.apache.log4j.Logger; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.interval.IntervalUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.*; + +/** + * Stratifies the variants by whether they overlap an interval in the set provided on the command line. + * + * The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up + * by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring + * in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like: + * + * -T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification + * + * Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to + * safely use this module you should provide entire contigs worth of variants, and let the interval strat decide + * overlap, as opposed to using -L which will not properly work with symbolic variants. + */ +public class IntervalStratification extends VariantStratifier { + final protected static Logger logger = Logger.getLogger(IntervalStratification.class); + Map> intervalTreeByContig = null; + + final List OVERLAPPING = Arrays.asList((Object)"all", (Object)"overlaps.intervals"); + final List NOT_OVERLAPPING = Arrays.asList((Object)"all", (Object)"outside.intervals"); + + + @Override + public void initialize() { + if ( getVariantEvalWalker().intervalsFile == null ) + throw new UserException.MissingArgument("stratIntervals", "Must be provided when IntervalStratification is enabled"); + + final List locs = getVariantEvalWalker().intervalsFile.getIntervals(getVariantEvalWalker().getToolkit()); + + if ( locs.isEmpty() ) + throw new UserException.BadArgumentValue("stratIntervals", "Contains no intervals. Perhaps the file is malformed or empty?"); + + intervalTreeByContig = getVariantEvalWalker().createIntervalTreeByContig(getVariantEvalWalker().intervalsFile); + + logger.info(String.format("Creating IntervalStratification %s containing %d intervals covering %d bp", + getVariantEvalWalker().intervalsFile.getSource(), locs.size(), IntervalUtils.intervalSize(locs))); + + states.addAll(Arrays.asList("all", "overlaps.intervals", "outside.intervals")); + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if (eval != null) { + final GenomeLoc loc = getVariantEvalWalker().getToolkit().getGenomeLocParser().createGenomeLoc(eval); + IntervalTree intervalTree = intervalTreeByContig.get(loc.getContig()); + IntervalTree.Node node = intervalTree.minOverlapper(loc.getStart(), loc.getStop()); + //logger.info(String.format("Overlap %s found %s", loc, node)); + if ( node != null ) + return OVERLAPPING; + else + return NOT_OVERLAPPING; + } + + return Collections.emptyList(); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java new file mode 100644 index 000000000..a1a10294f --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java @@ -0,0 +1,69 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; + +import java.util.List; +import java.util.ArrayList; +import java.util.Set; + +/** + * Stratifies the eval RODs by user-supplied JEXL expressions + * + * See http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk for more details + */ +public class JexlExpression extends VariantStratifier implements StandardStratification { + // needs to know the jexl expressions + private Set jexlExpressions; + + @Override + public void initialize() { + jexlExpressions = getVariantEvalWalker().getJexlExpressions(); + + states.add("none"); + for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) { + states.add(jexlExpression.name); + } + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + ArrayList relevantStates = new ArrayList(); + relevantStates.add("none"); + + for ( SortableJexlVCMatchExp jexlExpression : jexlExpressions ) { + if (eval != null && VariantContextUtils.match(eval, jexlExpression)) { + relevantStates.add(jexlExpression.name); + } + } + + return relevantStates; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java new file mode 100644 index 000000000..ef077c678 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java @@ -0,0 +1,64 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.*; + +/** + * Stratifies by whether a site in in the list of known RODs (e.g., dbsnp by default) + */ +public class Novelty extends VariantStratifier implements StandardStratification { + // needs the variant contexts and known names + private List> knowns; + + private final static List KNOWN_STATES = Arrays.asList((Object)"all", (Object)"known"); + private final static List NOVEL_STATES = Arrays.asList((Object)"all", (Object)"novel"); + + @Override + public void initialize() { + states.addAll(Arrays.asList("all", "known", "novel")); + knowns = getVariantEvalWalker().getKnowns(); + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if (tracker != null && eval != null) { + final Collection knownComps = tracker.getValues(knowns, ref.getLocus()); + for ( final VariantContext c : knownComps ) { + // loop over sites, looking for something that matches the type eval + if ( eval.getType() == c.getType() || eval.getType() == VariantContext.Type.NO_VARIATION ) { + return KNOWN_STATES; + } + } + } + + return NOVEL_STATES; + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java new file mode 100644 index 000000000..65fb2dd11 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java @@ -0,0 +1,59 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.List; + +/** + * Stratifies the eval RODs into sites where the indel is 1 bp in length and those where the event is 2+. + * all non indel events go into all bins, so that SNP counts can be used as contrasts in eval modules. + */ +public class OneBPIndel extends VariantStratifier { + private final static List ALL = Arrays.asList((Object)"all", (Object)"one.bp", (Object)"two.plus.bp"); + private final static List ONE_BP = Arrays.asList((Object)"all", (Object)"one.bp"); + private final static List TWO_PLUS_BP = Arrays.asList((Object)"all", (Object)"two.plus.bp"); + + @Override + public void initialize() { + states.addAll(ALL); + } + + @Override + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if (eval != null && eval.isIndel()) { + for ( int l : eval.getIndelLengths() ) + if ( Math.abs(l) > 1 ) + return TWO_PLUS_BP; // someone is too long + return ONE_BP; // all lengths are one + } else + return ALL; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java new file mode 100644 index 000000000..de4ab5db8 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java @@ -0,0 +1,28 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +public interface RequiredStratification {} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java new file mode 100644 index 000000000..ca9a1df85 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java @@ -0,0 +1,57 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; +import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.*; + +/** + * Stratifies the eval RODs by each sample in the eval ROD. + * + * This allows the system to analyze each sample separately. Since many evaluations + * only consider non-reference sites, stratifying by sample results in meaningful + * calculations for CompOverlap + */ +public class Sample extends VariantStratifier { + @Override + public void initialize() { + states.addAll(getVariantEvalWalker().getSampleNamesForStratification()); + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + return Collections.singletonList((Object) sampleName); + } + + @Override + public Set> getIncompatibleEvaluators() { + return new HashSet>(Arrays.asList(VariantSummary.class)); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java new file mode 100644 index 000000000..5267513ad --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java @@ -0,0 +1,29 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +public interface StandardStratification { +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java new file mode 100644 index 000000000..de82b18cc --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java @@ -0,0 +1,67 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Arrays; +import java.util.List; + +/** + * Stratifies the eval RODs into sites that are tandem repeats + */ +public class TandemRepeat extends VariantStratifier { + private final static List JUST_ALL = Arrays.asList((Object)"all"); + private final static List ALL = Arrays.asList((Object)"all", (Object)"is.repeat", (Object)"not.repeat"); + private final static List REPEAT = Arrays.asList((Object)"all", (Object)"is.repeat"); + private final static List NOT_REPEAT = Arrays.asList((Object)"all", (Object)"not.repeat"); + + @Override + public void initialize() { + states.addAll(ALL); + } + + @Override + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + if ( eval == null || ! eval.isIndel() ) + return ALL; + else if ( GATKVariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) { + print("REPEAT", eval, ref); + return REPEAT; + } else { + print("NOT A REPEAT", eval, ref); + return NOT_REPEAT; + } + } + + private final void print(String prefix, VariantContext eval, ReferenceContext ref) { +// String alleles = ParsingUtils.sortList(eval.getAlleles()).toString(); +// this.getVariantEvalWalker().getLogger().info(prefix + ": " + "pos=" + eval.getStart() + " alleles=" + alleles + " ref=" + new String(ref.getForwardBases())); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java new file mode 100644 index 000000000..3ca8c0bdc --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java @@ -0,0 +1,110 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; +import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; +import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.Stratifier; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.Set; + +public abstract class VariantStratifier implements Comparable, Stratifier { + private VariantEval variantEvalWalker; + final private String name; + final protected ArrayList states = new ArrayList(); + + protected VariantStratifier() { + name = this.getClass().getSimpleName(); + } + + // ------------------------------------------------------------------------------------- + // + // to be overloaded + // + // ------------------------------------------------------------------------------------- + + public abstract void initialize(); + + public abstract List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName); + + // ------------------------------------------------------------------------------------- + // + // final capabilities + // + // ------------------------------------------------------------------------------------- + + /** + * @return a reference to the parent VariantEvalWalker running this stratification + */ + public final VariantEval getVariantEvalWalker() { + return variantEvalWalker; + } + + /** + * Should only be called by VariantEvalWalker itself + * @param variantEvalWalker + */ + public final void setVariantEvalWalker(VariantEval variantEvalWalker) { + this.variantEvalWalker = variantEvalWalker; + } + + public final int compareTo(VariantStratifier o1) { + return this.getName().compareTo(o1.getName()); + } + + @Override + public String toString() { + return getName(); + } + + public final String getName() { + return name; + } + + public String getFormat() { return "%s"; } + + public final ArrayList getAllStates() { + return states; + } + + + /** + * The way for a stratifier to specify that it's incompatible with specific evaluations. For + * example, VariantSummary includes a per-sample metric, and so cannot be used safely with Sample + * or AlleleCount stratifications as this introduces an O(n^2) memory and cpu cost. + * + * @return the set of VariantEvaluators that cannot be active with this Stratification + */ + public Set> getIncompatibleEvaluators() { + return Collections.emptySet(); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java new file mode 100644 index 000000000..01862cf3a --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java @@ -0,0 +1,49 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications; + +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.Collections; +import java.util.List; + +/** + * Stratifies the eval variants by their type (SNP, INDEL, ETC) + */ +public class VariantType extends VariantStratifier { + @Override + public void initialize() { + for (VariantContext.Type t : VariantContext.Type.values()) + states.add(t.toString()); + } + + public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { + return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType().toString()); + } + +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java new file mode 100644 index 000000000..4ab6262be --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java @@ -0,0 +1,166 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications.manager; + +import com.google.java.contract.Ensures; +import com.google.java.contract.Invariant; +import com.google.java.contract.Requires; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.util.*; + +/** + * Helper class representing a tree of stratification splits, where leaf nodes + * are given a unique integer key starting at 0 and incrementing up to the + * number of leaves in the tree. This allows you to use this tree to produce + * a key to map into an array index mapped data structure. + * + * Suppose I have to strats, each with two values: A = 1, 2 and B = 3, 4 + * + * This data structure creates a tree such as: + * + * root -> A -> 1 -> B -> 3 : 0 + * |- B -> 4 : 1 + * |- A -> 2 -> B -> 3 : 2 + * |- B -> 4 : 3 + * + * This code allows us to efficiently look up a state key (A=2, B=3) and map it + * to a specific key (an integer) that's unique over the tree + * + * Note the structure of this tree is that the keys are -1 for all internal nodes, and + * leafs are the only nodes with meaningful keys. So for a tree with 2N nodes N of these + * will be internal, with no keys, and meaningful maps from states -> subtrees. The + * other N nodes are leafs, with meaningful keys, empty maps, and null stratification objects + * + * @author Mark DePristo + * @since 3/27/12 + */ +@Invariant({ + "(isLeaf() && stratifier == null && subnodes.isEmpty()) || (!isLeaf() && stratifier != null && !subnodes.isEmpty())"}) +class StratNode implements Iterable> { + int key = -1; + final T stratifier; + final Map> subnodes; // NOTE, because we don't iterate our best option is a HashMap + + protected StratNode() { + this.subnodes = Collections.emptyMap(); + this.stratifier = null; + } + + protected StratNode(final T stratifier, final Map> subnodes) { + this.stratifier = stratifier; + // important to reallocate an unmodififable hashmap with this specific size for space and safety + this.subnodes = Collections.unmodifiableMap(new HashMap>(subnodes)); + } + + @Requires("key >= 0") + public void setKey(final int key) { + if ( ! isLeaf() ) + throw new ReviewedStingException("Cannot set key of non-leaf node"); + this.key = key; + } + + @Requires({ + "states != null", + "offset >= 0", + "offset <= states.size()" + }) + public int find(final List states, int offset) { + if ( isLeaf() ) // we're here! + return key; + else { + final Object state = states.get(offset); + StratNode subnode = subnodes.get(state); + if ( subnode == null ) + return -1; + else + return subnode.find(states, offset+1); + } + } + + @Requires({ + "multipleStates != null", + "offset >= 0", + "offset <= multipleStates.size()", + "keys != null", + "offset == multipleStates.size() || multipleStates.get(offset) != null"}) + public void find(final List> multipleStates, final int offset, final HashSet keys) { + if ( isLeaf() ) // we're here! + keys.add(key); + else { + for ( final Object state : multipleStates.get(offset) ) { + // loop over all of the states at this offset + final StratNode subnode = subnodes.get(state); + if ( subnode == null ) + throw new ReviewedStingException("Couldn't find state for " + state + " at node " + this); + else + subnode.find(multipleStates, offset+1, keys); + } + } + } + + @Ensures("result >= 0") + public int getKey() { + if ( ! isLeaf() ) + throw new ReviewedStingException("Cannot get key of non-leaf node"); + else + return key; + } + + protected Map> getSubnodes() { + return subnodes; + } + + @Ensures("result >= 0") + public int size() { + if ( isLeaf() ) + return 1; + else { + return subnodes.values().iterator().next().size() * subnodes.size(); + } + } + + public T getSetOfStates() { + return stratifier; + } + + /** + * @return true if this node is a leaf + */ + public boolean isLeaf() { + return stratifier == null; + } + + /** + * Returns an iterator over this node and all subnodes including internal and leaf nodes + * @return + */ + @Override + @Ensures("result != null") + public Iterator> iterator() { + return new StratNodeIterator(this); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java new file mode 100644 index 000000000..87fb3dfa4 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java @@ -0,0 +1,69 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications.manager; + +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.util.*; + +/** + * Helper class for creating iterators over all nodes in the stratification tree + * + * @author Mark DePristo + * @since 3/27/12 + */ +class StratNodeIterator implements Iterator> { + Queue>> iterators = new LinkedList>>(); + Iterator> currentIterator; + + StratNodeIterator(final StratNode root) { + currentIterator = Collections.singleton(root).iterator(); + for ( final StratNode subNode : root.subnodes.values() ) + iterators.add(new StratNodeIterator(subNode)); + } + + @Override + public boolean hasNext() { + return currentIterator.hasNext() || ! iterators.isEmpty(); + } + + @Override + public StratNode next() { + if ( currentIterator.hasNext() ) + return currentIterator.next(); + else if ( ! iterators.isEmpty() ) { + currentIterator = iterators.poll(); + return next(); + } else { + throw new IllegalStateException("Next called on empty iterator"); + } + } + + @Override + public void remove() { + throw new ReviewedStingException("Cannot remove from StratNode iterator"); + } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java similarity index 64% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java index 9d95313a1..681d32f2d 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java @@ -1,54 +1,32 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications.manager; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java new file mode 100644 index 000000000..d211eee50 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java @@ -0,0 +1,41 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.stratifications.manager; + +import java.util.List; + +/** + * A basic interface for a class to be used with the StratificationManager system + * + * @author Mark DePristo + * @since 3/28/12 + */ +public interface Stratifier { + /** + * @return a list of all objects states that may be provided by this States provider + */ + public List getAllStates(); +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionExtension.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java similarity index 74% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionExtension.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java index fdb24e2f6..838500ab8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionExtension.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java @@ -23,23 +23,14 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.varianteval.util; -import java.lang.annotation.Documented; -import java.lang.annotation.Inherited; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; -/** - * Describes the size of the buffer region that is added to each active region when pulling in covered reads. - * User: rpoplin - * Date: 1/18/12 - */ -@Documented -@Inherited @Retention(RetentionPolicy.RUNTIME) - -public @interface ActiveRegionExtension { - public int extension() default 0; - public int maxRegion() default 1500; +public @interface Analysis { + String name() default ""; // its description, required + String description(); // its description, required + boolean molten() default false; // if true we'll look for a @Molten map } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java new file mode 100644 index 000000000..a5c3b125e --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java @@ -0,0 +1,154 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.util; + +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +import java.lang.annotation.Annotation; +import java.lang.reflect.Field; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.Map; + + +/** + * @author aaron + *

+ * Class AnalysisModuleScanner + *

+ * Given an analysis, find the annotated fields and methods. Given this module and + * the object, a Mashalling object can serialize or deserialize a analysis module. + */ +public class AnalysisModuleScanner { + final private static Map annotationCache = new HashMap(); + + // what we extracted from the class + private Map datums = new LinkedHashMap(); // the data we've discovered + private Analysis analysis; // the analysis annotation + + private Field moltenField = null; + private Molten moltenAnnotation = null; + + // private storage of the class type + private final Class cls; + + /** + * create a report scanner from the passed in class + * @param cls the target class, annotated with the @Analysis annotation + */ + public AnalysisModuleScanner(Class cls) { + this.cls = cls; + scan(); // scan the passed in class + } + + /** + * create a report scanner from the passed in class + * @param obj the target object, annotated with the @Analysis annotation + */ + public AnalysisModuleScanner(Object obj) { + this.cls = obj.getClass(); + scan(); // scan the passed in class + } + + /** scan the class and find all appropriate fields and tables */ + public void scan() { + if (cls == null || !cls.isAnnotationPresent(Analysis.class)) + throw new ReviewedStingException("The class passed in cannot be null, " + "" + + "and must contain the @Analysis annotation, class " + cls + " was the input"); + + // get the annotation off of the class + analysis = (Analysis) cls.getAnnotation(Analysis.class); + scanFields(); + } + + /** + * scan the fields of the class, extracting parameters and table annotations and their associated fields + */ + private void scanFields() { + // get the fields from the class, and extract + for ( Class superCls = cls; superCls != null; superCls=superCls.getSuperclass() ) { + for (Field f : superCls.getDeclaredFields()) { + for (Annotation annotation : getAnnotations(f)) { + if (annotation.annotationType().equals(DataPoint.class)) + datums.put(f,(DataPoint) annotation); + if ( annotation.annotationType().equals(Molten.class)) { + if ( hasMoltenField() ) + throw new ReviewedStingException("Analysis " + analysis.name() + " has multiple @Molten fields, which is forbidden"); + moltenField = f; + moltenAnnotation = (Molten)annotation; + } + } + } + } + + if ( hasMoltenField() ) { + if ( datums.size() > 0 ) + throw new ReviewedStingException("Analysis " + analysis.name() + " has an @Molten field as well as @DataPoint fields, which is forbidden"); + } + } + + public Field getMoltenField() { + return moltenField; + } + + public Molten getMoltenAnnotation() { + return moltenAnnotation; + } + + public boolean hasMoltenField() { + return getMoltenField() != null; + } + + private Annotation[] getAnnotations(final Field field) { + final String fieldName = field.toString(); + Annotation[] annotations = annotationCache.get(fieldName); + if ( annotations == null ) { + annotations = field.getAnnotations(); + annotationCache.put(fieldName, annotations); + } + return annotations; + } + + /** + * + * @return a map of the datum annotations found + */ + public Map getData() { + return datums; + } + + /** + * + * @return the analysis annotation found + */ + public Analysis getAnalysis() { + return analysis; + } + + public Class getModuleClass() { + return cls; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java new file mode 100644 index 000000000..34c9368f2 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java @@ -0,0 +1,35 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.util; + +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; + +@Retention(RetentionPolicy.RUNTIME) +public @interface DataPoint { + String description() default ""; // the description, optional + String format() default ""; +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java new file mode 100644 index 000000000..2e9512639 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java @@ -0,0 +1,115 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.util; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; +import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; +import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.ArrayList; +import java.util.Set; +import java.util.TreeSet; + +public final class EvaluationContext { + // NOTE: must be hashset to avoid O(log n) cost of iteration in the very frequently called apply function + final VariantEval walker; + private final ArrayList evaluationInstances; + private final Set> evaluationClasses; + + public EvaluationContext(final VariantEval walker, final Set> evaluationClasses) { + this(walker, evaluationClasses, true); + } + + private EvaluationContext(final VariantEval walker, final Set> evaluationClasses, final boolean doInitialize) { + this.walker = walker; + this.evaluationClasses = evaluationClasses; + this.evaluationInstances = new ArrayList(evaluationClasses.size()); + + for ( final Class c : evaluationClasses ) { + try { + final VariantEvaluator eval = c.newInstance(); + if ( doInitialize ) eval.initialize(walker); + evaluationInstances.add(eval); + } catch (InstantiationException e) { + throw new ReviewedStingException("Unable to instantiate eval module '" + c.getSimpleName() + "'", e); + } catch (IllegalAccessException e) { + throw new ReviewedStingException("Illegal access error when trying to instantiate eval module '" + c.getSimpleName() + "'", e); + } + } + } + + /** + * Returns a sorted set of VariantEvaluators + * + * @return + */ + public final TreeSet getVariantEvaluators() { + return new TreeSet(evaluationInstances); + } + + public final void apply(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext comp, VariantContext eval) { + for ( final VariantEvaluator evaluation : evaluationInstances ) { + // the other updateN methods don't see a null context + if ( tracker == null ) + continue; + + // now call the single or paired update function + switch ( evaluation.getComparisonOrder() ) { + case 1: + if (eval != null) { + evaluation.update1(eval, tracker, ref, context); + } + break; + case 2: + evaluation.update2(eval, comp, tracker, ref, context); + break; + default: + throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation); + } + } + } + + public void combine(final EvaluationContext rhs) { + for ( int i = 0; i < evaluationInstances.size(); i++ ) + evaluationInstances.get(i).combine(rhs.evaluationInstances.get(i)); + } + + public final static EvaluationContextCombiner COMBINER = new EvaluationContext.EvaluationContextCombiner(); + private static class EvaluationContextCombiner implements StratificationManager.Combiner { + @Override + public EvaluationContext combine(EvaluationContext lhs, final EvaluationContext rhs) { + if ( lhs == null ) + lhs = new EvaluationContext(rhs.walker, rhs.evaluationClasses, false); + lhs.combine(rhs); + return lhs; + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java new file mode 100644 index 000000000..d65887090 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java @@ -0,0 +1,64 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.util; + +import java.lang.annotation.Retention; +import java.lang.annotation.RetentionPolicy; + +/** + * Molten for @Analysis modules. + * + * If you are flagged as a molten analysis, then there must be one and + * only one annotation in that evaluation module: @Molten which + * must have time Map. This data set will then + * be represented in the VE output as: + * + * variable value + * key1 value1 + * key2 value1 + * ... + * keyN valueN + * + * in the output table. The names of these two fields can be override via annotation values. + */ +@Retention(RetentionPolicy.RUNTIME) +public @interface Molten { + String description() default ""; // the description, optional + + /** + * The name to use for the molten variable field in the output table. + * @return + */ + String variableName() default "variable"; + String variableFormat() default ""; + + /** + * The name to use for the molten value field in the output table. + * @return + */ + String valueName() default "value"; + String valueFormat() default ""; +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java new file mode 100644 index 000000000..1cd68c610 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java @@ -0,0 +1,45 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.util; + +import org.apache.commons.jexl2.Expression; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; + +public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable { + /** + * Create a new matcher expression with name and JEXL expression exp + * + * @param name name + * @param exp expression + */ + public SortableJexlVCMatchExp(String name, Expression exp) { + super(name, exp); + } + + public int compareTo(SortableJexlVCMatchExp sortableJexlVCMatchExp) { + return this.name.compareTo(sortableJexlVCMatchExp.name); + } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java similarity index 62% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index fc6aaea76..7e751e4a0 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.varianteval.util; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java new file mode 100644 index 000000000..d416d5d16 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java @@ -0,0 +1,160 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantrecalibration; + +import org.apache.log4j.Logger; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.text.XReadLines; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.ArrayList; +import java.util.List; + +/** + * Created by IntelliJ IDEA. + * User: depristo + * Date: 3/11/11 + * Time: 10:33 AM + * To change this template use File | Settings | File Templates. + */ +public class VQSRCalibrationCurve { + private final static boolean DEBUG = false; + List points; + public static final double CERTAIN_FALSE_POSITIVE = -1; + + private static class VQSRRange { + double start, stop, truePositiveRate; + + public double getStart() { + return start; + } + + public double getStop() { + return stop; + } + + public double getTruePositiveRate() { + return truePositiveRate; + } + + private VQSRRange(double start, double stop, double truePositiveRate) { + this.start = start; + this.stop = stop; + this.truePositiveRate = truePositiveRate; + } + } + + public static VQSRCalibrationCurve readFromFile(File source) { + List points = new ArrayList(); + + try { + for ( String line : new XReadLines(source).readLines() ) { + if ( ! line.trim().isEmpty() ) { + String[] parts = line.split("\\s+"); + double fpRate = Double.parseDouble(parts[2]); + double tpRate = fpRate >= 1.0 ? CERTAIN_FALSE_POSITIVE : 1.0 - fpRate; + points.add(new VQSRRange(Double.parseDouble(parts[0]), Double.parseDouble(parts[1]), tpRate)); + } + } + } catch ( FileNotFoundException e ) { + throw new UserException.CouldNotReadInputFile(source, e); + } + + // ensure that the entire range gets caught + points.get(0).start = Double.POSITIVE_INFINITY; + points.get(points.size()-1).stop = Double.NEGATIVE_INFINITY; + + return new VQSRCalibrationCurve(points); + } + + protected VQSRCalibrationCurve(List points) { + this.points = points; + } + + public boolean certainFalsePositive(String VQSRQualKey, VariantContext vc) { + return probTrueVariant(VQSRQualKey, vc) == CERTAIN_FALSE_POSITIVE; + } + + + public double probTrueVariant(double VQSRqual) { + for ( VQSRRange r : points ) { + if ( VQSRqual <= r.getStart() && VQSRqual > r.getStop() ) + return r.getTruePositiveRate(); + } + + throw new ReviewedStingException("BUG: should not be able to reach this code"); + } + + public double probTrueVariant(String VQSRQualKey, VariantContext vc) { + if ( vc.isFiltered() ) + return 0.0; + else if ( vc.hasAttribute(VQSRQualKey) ) { + double qual = vc.getAttributeAsDouble(VQSRQualKey, 0.0); + return probTrueVariant(qual); + } else { + throw new UserException.VariantContextMissingRequiredField(VQSRQualKey, vc); + } + } + + /** + * Returns a likelihoods vector adjusted by the probability that the site is an error. Returns a + * null vector if the probability of the site being real is 0.0 + * @param VQSRQualKey + * @param vc + * @param log10Likelihoods + * @return + */ + public double[] includeErrorRateInLikelihoods(String VQSRQualKey, VariantContext vc, double[] log10Likelihoods) { + double[] updated = new double[log10Likelihoods.length]; + + double alpha = probTrueVariant(VQSRQualKey, vc); + + if ( alpha == CERTAIN_FALSE_POSITIVE ) + return null; + else { + double noInfoPr = 1.0 / 3; + if ( DEBUG ) System.out.printf("------------------------------%n"); + for ( int i = 0; i < log10Likelihoods.length; i++) { + double p = Math.pow(10, log10Likelihoods[i]); + double q = alpha * p + (1-alpha) * noInfoPr; + if ( DEBUG ) System.out.printf(" vqslod = %.2f, p = %.2e, alpha = %.2e, q = %.2e%n", vc.getAttributeAsDouble(VQSRQualKey, 0.0), p, alpha, q); + updated[i] = Math.log10(q); + } + + return updated; + } + } + + + public void printInfo(Logger logger) { + for ( VQSRRange r : points ) { + logger.info(String.format(" start=%f stop=%f TPrate=%.6e", r.getStart(), r.getStop(), r.getTruePositiveRate())); + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 996eab7e9..0d87bb921 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -38,6 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; @@ -135,14 +136,14 @@ public class CombineVariants extends RodWalker implements Tree protected VariantContextWriter vcfWriter = null; @Argument(shortName="genotypeMergeOptions", doc="Determines how we should merge genotype records for samples shared across the ROD files", required=false) - public VariantContextUtils.GenotypeMergeType genotypeMergeOption = null; + public GATKVariantContextUtils.GenotypeMergeType genotypeMergeOption = null; @Argument(shortName="filteredRecordsMergeType", doc="Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields", required=false) - public VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED; + public GATKVariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED; @Hidden @Argument(shortName="multipleAllelesMergeType", doc="Determines how we should handle records seen at the same site in the VCF, but with different allele types (for example, SNP vs. indel)", required=false) - public VariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = VariantContextUtils.MultipleAllelesMergeType.BY_TYPE; + public GATKVariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = GATKVariantContextUtils.MultipleAllelesMergeType.BY_TYPE; /** * Used when taking the union of variants that contain genotypes. A complete priority list MUST be provided. @@ -203,17 +204,21 @@ public class CombineVariants extends RodWalker implements Tree validateAnnotateUnionArguments(); if ( PRIORITY_STRING == null && genotypeMergeOption == null) { - genotypeMergeOption = VariantContextUtils.GenotypeMergeType.UNSORTED; + genotypeMergeOption = GATKVariantContextUtils.GenotypeMergeType.UNSORTED; //PRIORITY_STRING = Utils.join(",", vcfRods.keySet()); Deleted by Ami (7/10/12) logger.info("Priority string is not provided, using arbitrary genotyping order: "+priority); } + if (genotypeMergeOption == GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE && + !SampleUtils.verifyUniqueSamplesNames(vcfRods)) + throw new IllegalStateException("REQUIRE_UNIQUE sample names is true but duplicate names were discovered."); + samples = sitesOnlyVCF ? Collections.emptySet() : SampleUtils.getSampleList(vcfRods, genotypeMergeOption); if ( SET_KEY.toLowerCase().equals("null") ) SET_KEY = null; - Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger); + Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); if ( SET_KEY != null ) headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record in CombineVariants")); if ( !ASSUME_IDENTICAL_SAMPLES ) @@ -223,10 +228,12 @@ public class CombineVariants extends RodWalker implements Tree vcfWriter.writeHeader(vcfHeader); } + + private void validateAnnotateUnionArguments() { Set rodNames = SampleUtils.getRodNamesWithVCFHeader(getToolkit(), null); - if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE && PRIORITY_STRING == null ) + if ( genotypeMergeOption == GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE && PRIORITY_STRING == null ) throw new UserException.MissingArgument("rod_priority_list", "Priority string must be provided if you want to prioritize genotypes"); if ( PRIORITY_STRING != null){ @@ -272,8 +279,8 @@ public class CombineVariants extends RodWalker implements Tree List mergedVCs = new ArrayList(); - if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.BY_TYPE) { - Map> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs); + if (multipleAllelesMergeType == GATKVariantContextUtils.MultipleAllelesMergeType.BY_TYPE) { + Map> VCsByType = GATKVariantContextUtils.separateVariantContextsByType(vcs); // TODO -- clean this up in a refactoring // merge NO_VARIATION into another type of variant (based on the ordering in VariantContext.Type) @@ -290,13 +297,13 @@ public class CombineVariants extends RodWalker implements Tree // iterate over the types so that it's deterministic for (VariantContext.Type type : VariantContext.Type.values()) { if (VCsByType.containsKey(type)) - mergedVCs.add(VariantContextUtils.simpleMerge(VCsByType.get(type), - priority, rodNames.size() , filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges, + mergedVCs.add(GATKVariantContextUtils.simpleMerge(VCsByType.get(type), + priority, rodNames.size(), filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges, SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC)); } } - else if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.MIX_TYPES) { - mergedVCs.add(VariantContextUtils.simpleMerge(vcs, + else if (multipleAllelesMergeType == GATKVariantContextUtils.MultipleAllelesMergeType.MIX_TYPES) { + mergedVCs.add(GATKVariantContextUtils.simpleMerge(vcs, priority, rodNames.size(), filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges, SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC)); } @@ -313,7 +320,7 @@ public class CombineVariants extends RodWalker implements Tree // re-compute chromosome counts VariantContextUtils.calculateChromosomeCounts(builder, false); if ( minimalVCF ) - VariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY)); + GATKVariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY)); vcfWriter.add(builder.make()); } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java similarity index 52% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java index bb76006bf..efb84edef 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java @@ -1,56 +1,33 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. 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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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; -import com.google.java.contract.Ensures; -import com.google.java.contract.Invariant; import com.google.java.contract.Requires; -import org.broad.tribble.util.ParsingUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.variantcontext.*; import org.broadinstitute.variant.vcf.VCFHeader; @@ -272,22 +249,7 @@ public class ConcordanceMetrics { @Requires({"evalVC != null","truthVC != null"}) private SiteConcordanceType getMatchType(VariantContext evalVC, VariantContext truthVC) { - if ( evalVC.isMonomorphicInSamples() ) - return SiteConcordanceType.TRUTH_ONLY; - if ( truthVC.isMonomorphicInSamples() ) - return SiteConcordanceType.EVAL_ONLY; - - boolean evalSusbsetTruth = VariantContextUtils.allelesAreSubset(evalVC,truthVC); - boolean truthSubsetEval = VariantContextUtils.allelesAreSubset(truthVC,evalVC); - - if ( evalSusbsetTruth && truthSubsetEval ) - return SiteConcordanceType.ALLELES_MATCH; - else if ( evalSusbsetTruth ) - return SiteConcordanceType.EVAL_SUBSET_TRUTH; - else if ( truthSubsetEval ) - return SiteConcordanceType.EVAL_SUPERSET_TRUTH; - - return SiteConcordanceType.ALLELES_DO_NOT_MATCH; + return SiteConcordanceType.getConcordanceType(evalVC,truthVC); } public int[] getSiteConcordance() { @@ -305,6 +267,27 @@ public class ConcordanceMetrics { EVAL_SUBSET_TRUTH, ALLELES_DO_NOT_MATCH, EVAL_ONLY, - TRUTH_ONLY + TRUTH_ONLY; + + public static SiteConcordanceType getConcordanceType(VariantContext eval, VariantContext truth) { + if ( eval.isMonomorphicInSamples() ) + return TRUTH_ONLY; + if ( truth.isMonomorphicInSamples() ) + return EVAL_ONLY; + + boolean evalSubsetTruth = GATKVariantContextUtils.allelesAreSubset(eval, truth); + boolean truthSubsetEval = GATKVariantContextUtils.allelesAreSubset(truth, eval); + + if ( evalSubsetTruth && truthSubsetEval ) + return ALLELES_MATCH; + + if ( evalSubsetTruth ) + return EVAL_SUBSET_TRUTH; + + if ( truthSubsetEval ) + return EVAL_SUPERSET_TRUTH; + + return ALLELES_DO_NOT_MATCH; + } } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java new file mode 100644 index 000000000..c2785e920 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -0,0 +1,109 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; + +import org.broadinstitute.sting.commandline.ArgumentCollection; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; +import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.util.*; + +/** + * Filters a lifted-over VCF file for ref bases that have been changed. + */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) +@Reference(window=@Window(start=0,stop=100)) +public class FilterLiftedVariants extends RodWalker { + + @ArgumentCollection + protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + + private static final int MAX_VARIANT_SIZE = 100; + + @Output(doc="File to which variants should be written",required=true) + protected VariantContextWriter writer = null; + + private long failedLocs = 0, totalLocs = 0; + + 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 VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.emptySet(), samples); + writer.writeHeader(vcfHeader); + } + + private void filterAndWrite(byte[] ref, VariantContext vc) { + + totalLocs++; + + boolean failed = false; + byte[] recordRef = vc.getReference().getBases(); + for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) { + if ( recordRef[i] != ref[i] ) { + failed = true; + break; + } + } + + if ( failed ) + failedLocs++; + else + writer.add(vc); + } + + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if ( tracker == null ) + return 0; + + Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation()); + for ( VariantContext vc : VCs ) + filterAndWrite(ref.getBases(), vc); + + return 0; + } + + public Integer reduceInit() { return 0; } + + public Integer reduce(Integer value, Integer sum) { return 0; } + + public void onTraversalDone(Integer result) { + System.out.println("Filtered " + failedLocs + " records out of " + totalLocs + " total records."); + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java new file mode 100644 index 000000000..048c7ef77 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java @@ -0,0 +1,523 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; + +import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.report.GATKReport; +import org.broadinstitute.sting.gatk.report.GATKReportTable; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.vcf.VCFHeader; + +import java.io.PrintStream; +import java.util.*; + +/** + * A simple walker for performing genotype concordance calculations between two callsets. Outputs a GATK table with + * per-sample and aggregate counts and frequencies, a summary table for NRD/NRS, and a table for site allele overlaps. + * + *

+ * Genotype concordance takes in two callsets (vcfs) and tabulates the number of sites which overlap and share alleles, + * and for each sample, the genotype-by-genotype counts (for instance, the number of sites at which a sample was + * called homozygous reference in the EVAL callset, but homozygous variant in the COMP callset). It outputs these + * counts as well as convenient proportions (such as the proportion of het calls in the EVAL which were called REF in + * the COMP) and metrics (such as NRD and NRS). + * + *

INPUT

+ *

+ * Genotype concordance requires two callsets (as it does a comparison): an EVAL and a COMP callset, specified via + * the -eval and -comp arguments + *

+ * (Optional) Jexl expressions for genotype-level filtering of EVAL or COMP genotypes, specified via the -gfe and + * -cfe arguments, respectively. + * + *

OUTPUT

+ * Genotype Concordance writes a GATK report to the specified (via -o) file, consisting of multiple tables of counts + * and proportions. These tables may be optionally moltenized via the -moltenize argument. + * + */ +public class GenotypeConcordance extends RodWalker>,ConcordanceMetrics> { + + /** + * The callset you want to evaluate, typically this is where you'd put 'unassessed' callsets. + */ + @Input(fullName="eval",shortName="eval",doc="The variants and genotypes to evaluate",required=true) + RodBinding evalBinding; + + /** + * The callset you want to treat as 'truth'. Can also be of unknown quality for the sake of callset comparisons. + */ + @Input(fullName="comp",shortName="comp",doc="The variants and genotypes to compare against",required=true) + RodBinding compBinding; + + /** + * The FILTER field of the eval and comp VCFs will be ignored. If this flag is not included, all FILTER sites will + * be treated as not being present in the VCF. (That is, the genotypes will be assigned UNAVAILABLE, as distinct + * from NO_CALL). + */ + @Argument(fullName="ignoreFilters",doc="Filters will be ignored",required=false) + boolean ignoreFilters = false; + + /** + * A genotype level JEXL expression to apply to eval genotypes. Genotypes filtered in this way will be replaced by NO_CALL. + * For instance: -gfe 'GQ<20' will set to no-call any genotype with genotype quality less than 20. + */ + @Argument(shortName="gfe", fullName="genotypeFilterExpressionEval", doc="One or more criteria to use to set EVAL genotypes to no-call. "+ + "These genotype-level filters are only applied to the EVAL rod.", required=false) + public ArrayList genotypeFilterExpressionsEval = new ArrayList(); + + /** + * Identical to -gfe except the filter is applied to genotypes in the comp rod. + */ + @Argument(shortName="gfc", fullName="genotypeFilterExpressionComp", doc="One or more criteria to use to set COMP genotypes to no-call. "+ + "These genotype-level filters are only applied to the COMP rod.", required=false) + public ArrayList genotypeFilterExpressionsComp = new ArrayList(); + + /** + * Moltenize the count and proportion tables. Rather than moltenizing per-sample data into a 2x2 table, it is fully + * moltenized into elements. That is, WITHOUT this argument, each row of the table begins with the sample name and + * proceeds directly with counts/proportions of eval/comp counts (for instance HOM_REF/HOM_REF, HOM_REF/NO_CALL). + * + * If the Moltenize argument is given, the output will begin with a sample name, followed by the contrastive genotype + * type (such as HOM_REF/HOM_REF), followed by the count or proportion. This will significantly increase the number of + * rows. + */ + @Argument(shortName="moltenize",fullName="moltenize",doc="Molten rather than tabular output") + public boolean moltenize = false; + + @Output + PrintStream out; + + private List evalSamples; + private List compSamples; + private List evalJexls = null; + private List compJexls = null; + + // todo -- table with "proportion of overlapping sites" (not just eval/comp margins) [e.g. drop no-calls] + // (this will break all the integration tests of course, due to new formatting) + + public void initialize() { + evalJexls = initializeJexl(genotypeFilterExpressionsEval); + compJexls = initializeJexl(genotypeFilterExpressionsComp); + } + + private List initializeJexl(ArrayList genotypeFilterExpressions) { + ArrayList dummyNames = new ArrayList(genotypeFilterExpressions.size()); + int expCount = 1; + for ( String exp : genotypeFilterExpressions ) { + dummyNames.add(String.format("gfe%d",expCount++)); + } + return VariantContextUtils.initializeMatchExps(dummyNames, genotypeFilterExpressions); + } + + public ConcordanceMetrics reduceInit() { + Map headerMap = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(evalBinding,compBinding)); + VCFHeader evalHeader = headerMap.get(evalBinding.getName()); + evalSamples = evalHeader.getGenotypeSamples(); + VCFHeader compHeader = headerMap.get(compBinding.getName()); + compSamples = compHeader.getGenotypeSamples(); + return new ConcordanceMetrics(evalHeader,compHeader); + } + + + public List> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + List> evalCompPair = new ArrayList>(3); + if ( tracker != null && ( + tracker.getValues(evalBinding,ref.getLocus()).size() > 0 || + tracker.getValues(compBinding,ref.getLocus()).size() > 0 ) ) { + + List eval = tracker.getValues(evalBinding,ref.getLocus()); + List comp = tracker.getValues(compBinding,ref.getLocus()); + if ( eval.size() > 1 || comp.size() > 1 ) { + if ( noDuplicateTypes(eval) && noDuplicateTypes(comp) ) { + logger.info("Eval or Comp Rod at position " + ref.getLocus().toString() + " has multiple records. Resolving."); + evalCompPair = resolveMultipleRecords(eval,comp); + } else { + logger.warn("Eval or Comp Rod at position "+ref.getLocus().toString()+" has multiple records of the same type. This locus will be skipped."); + } + } else { + // if a rod is missing, explicitly create a variant context with 'missing' genotypes. Slow, but correct. + // note that if there is no eval rod there must be a comp rod, and also the reverse + VariantContext evalContext = eval.size() == 1 ? eval.get(0) : createEmptyContext(comp.get(0),evalSamples); + VariantContext compContext = comp.size() == 1 ? comp.get(0) : createEmptyContext(eval.get(0),compSamples); + evalContext = filterGenotypes(evalContext,ignoreFilters,evalJexls); + compContext = filterGenotypes(compContext,ignoreFilters,compJexls); + evalCompPair.add(new Pair(evalContext,compContext)); + } + } + + return evalCompPair; + } + + private boolean noDuplicateTypes(List vcList) { + HashSet types = new HashSet(vcList.size()); + for ( VariantContext vc : vcList ) { + VariantContext.Type type = vc.getType(); + if ( types.contains(type) ) + return false; + types.add(type); + } + + return true; + } + + /** + * The point of this method is to match up pairs of evals and comps by their type (or alternate alleles for mixed). + * Basically multiple records could exist for a site such as: + * Eval: 20 4000 A C + * Eval: 20 4000 A AC + * Comp: 20 4000 A C + * So for each eval, loop through the comps. If the types match, or for mixed types if eval alleles (non-emptily) + * intersect the comp alleles, pair them up and remove that comp records. + * Continue until we're out of evals or comps. This is n^2, but should rarely actually happen. + * + * The remaining unpaired records get paird with an empty contexts. So in the example above we'd get a list of: + * 1 - (20,4000,A/C | 20,4000,A/C) + * 2 - (20,4000,A/AC | Empty ) + * @param evalList - list of eval variant contexts + * @param compList - list of comp variant contexts + * @return resolved pairs of the input lists + */ + private List> resolveMultipleRecords(List evalList, List compList) { + List> resolvedPairs = new ArrayList>(evalList.size()+compList.size()); // oversized but w/e + List pairedEval = new ArrayList(evalList.size()); + for ( VariantContext eval : evalList ) { + VariantContext.Type evalType = eval.getType(); + Set evalAlleles = new HashSet(eval.getAlternateAlleles()); + VariantContext pairedComp = null; + for ( VariantContext comp : compList ) { + if ( evalType.equals(comp.getType()) ) { + pairedComp = comp; + break; + } else if ( eval.isMixed() || comp.isMixed() ) { + for ( Allele compAllele : comp.getAlternateAlleles() ) { + if ( evalAlleles.contains(compAllele) ) { + pairedComp = comp; + break; + } + } + } + } + if ( pairedComp != null ) { + compList.remove(pairedComp); + resolvedPairs.add(new Pair(filterGenotypes(eval,ignoreFilters,evalJexls),filterGenotypes(pairedComp,ignoreFilters,compJexls))); + pairedEval.add(eval); + if ( compList.size() < 1 ) + break; + } + } + evalList.removeAll(pairedEval); + for ( VariantContext unpairedEval : evalList ) { + resolvedPairs.add(new Pair(filterGenotypes(unpairedEval,ignoreFilters,evalJexls),createEmptyContext(unpairedEval,compSamples))); + } + + for ( VariantContext unpairedComp : compList ) { + resolvedPairs.add(new Pair(createEmptyContext(unpairedComp,evalSamples),filterGenotypes(unpairedComp,ignoreFilters,compJexls))); + } + + return resolvedPairs; + } + + public ConcordanceMetrics reduce(List> evalCompList, ConcordanceMetrics metrics) { + for ( Pair evalComp : evalCompList) + metrics.update(evalComp.getFirst(),evalComp.getSecond()); + return metrics; + } + + private static double repairNaN(double d) { + if ( Double.isNaN(d) ) { + return 0.0; + } + return d; + } + + public void onTraversalDone(ConcordanceMetrics metrics) { + // todo -- this is over 200 lines of code just to format the output and could use some serious cleanup + GATKReport report = new GATKReport(); + GATKReportTable concordanceCounts = new GATKReportTable("GenotypeConcordance_Counts","Per-sample concordance tables: comparison counts",2+GenotypeType.values().length*GenotypeType.values().length); + GATKReportTable concordanceEvalProportions = new GATKReportTable("GenotypeConcordance_EvalProportions", "Per-sample concordance tables: proportions of genotypes called in eval",2+GenotypeType.values().length*GenotypeType.values().length); + GATKReportTable concordanceCompProportions = new GATKReportTable("GenotypeConcordance_CompProportions", "Per-sample concordance tables: proportions of genotypes called in comp",2+GenotypeType.values().length*GenotypeType.values().length); + GATKReportTable concordanceSummary = new GATKReportTable("GenotypeConcordance_Summary","Per-sample summary statistics: NRS and NRD",2); + GATKReportTable siteConcordance = new GATKReportTable("SiteConcordance_Summary","Site-level summary statistics",ConcordanceMetrics.SiteConcordanceType.values().length); + if ( moltenize ) { + concordanceCompProportions.addColumn("Sample","%s"); + concordanceCounts.addColumn("Sample","%s"); + concordanceEvalProportions.addColumn("Sample","%s"); + concordanceSummary.addColumn("Sample","%s"); + + concordanceCompProportions.addColumn("Eval_Genotype","%s"); + concordanceCounts.addColumn("Eval_Genotype","%s"); + concordanceEvalProportions.addColumn("Eval_Genotype","%s"); + concordanceSummary.addColumn("Non-Reference_Discrepancy","%.3f"); + + concordanceCompProportions.addColumn("Comp_Genotype","%s"); + concordanceCounts.addColumn("Comp_Genotype","%s"); + concordanceEvalProportions.addColumn("Comp_Genotype","%s"); + concordanceSummary.addColumn("Non-Reference_Sensitivity","%.3f"); + + concordanceCompProportions.addColumn("Proportion","%.3f"); + concordanceCounts.addColumn("Count","%d"); + concordanceEvalProportions.addColumn("Proportion","%.3f"); + + for ( Map.Entry entry : metrics.getPerSampleGenotypeConcordance().entrySet() ) { + ConcordanceMetrics.GenotypeConcordanceTable table = entry.getValue(); + for ( GenotypeType evalType : GenotypeType.values() ) { + for ( GenotypeType compType : GenotypeType.values() ) { + String rowKey = String.format("%s_%s_%s",entry.getKey(),evalType.toString(),compType.toString()); + concordanceCounts.set(rowKey,"Sample",entry.getKey()); + concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString()); + concordanceCounts.set(rowKey,"Comp_Genotype",evalType.toString()); + int count = table.get(evalType, compType); + concordanceCounts.set(rowKey,"Count",count); + if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) { + concordanceEvalProportions.set(rowKey,"Sample",entry.getKey()); + concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString()); + concordanceEvalProportions.set(rowKey,"Comp_Genotype",evalType.toString()); + concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType))); + } + if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) { + concordanceCompProportions.set(rowKey,"Sample",entry.getKey()); + concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString()); + concordanceCompProportions.set(rowKey,"Comp_Genotype",evalType.toString()); + concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType))); + } + } + } + String mismatchKey = String.format("%s_%s",entry.getKey(),"Mismatching"); + concordanceCounts.set(mismatchKey,"Sample",entry.getKey()); + concordanceCounts.set(mismatchKey,"Eval_Genotype","Mismatching_Alleles"); + concordanceCounts.set(mismatchKey,"Comp_Genotype","Mismatching_Alleles"); + concordanceEvalProportions.set(mismatchKey,"Sample",entry.getKey()); + concordanceEvalProportions.set(mismatchKey,"Eval_Genotype","Mismatching_Alleles"); + concordanceEvalProportions.set(mismatchKey,"Comp_Genotype","Mismatching_Alleles"); + concordanceCompProportions.set(mismatchKey,"Sample",entry.getKey()); + concordanceCompProportions.set(mismatchKey,"Eval_Genotype","Mismatching_Alleles"); + concordanceCompProportions.set(mismatchKey,"Comp_Genotype","Mismatching_Alleles"); + concordanceEvalProportions.set(mismatchKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes())); + concordanceCompProportions.set(mismatchKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes())); + concordanceCounts.set(mismatchKey,"Count",table.getnMismatchingAlt()); + } + + String sampleKey = "ALL"; + ConcordanceMetrics.GenotypeConcordanceTable table = metrics.getOverallGenotypeConcordance(); + for ( GenotypeType evalType : GenotypeType.values() ) { + for ( GenotypeType compType : GenotypeType.values() ) { + String rowKey = String.format("%s_%s_%s",sampleKey,evalType.toString(),compType.toString()); + concordanceCounts.set(rowKey,"Sample",sampleKey); + concordanceCounts.set(rowKey,"Eval_Genotype",evalType.toString()); + concordanceCounts.set(rowKey,"Comp_Genotype",evalType.toString()); + int count = table.get(evalType, compType); + concordanceCounts.set(rowKey,"Count",count); + if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) { + concordanceEvalProportions.set(rowKey,"Sample",sampleKey); + concordanceEvalProportions.set(rowKey,"Eval_Genotype",evalType.toString()); + concordanceEvalProportions.set(rowKey,"Comp_Genotype",evalType.toString()); + concordanceEvalProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnEvalGenotypes(evalType))); + } + if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) { + concordanceCompProportions.set(rowKey,"Sample",sampleKey); + concordanceCompProportions.set(rowKey,"Eval_Genotype",evalType.toString()); + concordanceCompProportions.set(rowKey,"Comp_Genotype",evalType.toString()); + concordanceCompProportions.set(rowKey,"Proportion",repairNaN(( (double) count)/table.getnCompGenotypes(compType))); + } + } + } + String rowKey = String.format("%s_%s",sampleKey,"Mismatching"); + concordanceCounts.set(rowKey,"Sample",sampleKey); + concordanceCounts.set(rowKey,"Eval_Genotype","Mismatching_Alleles"); + concordanceCounts.set(rowKey,"Comp_Genotype","Mismatching_Alleles"); + concordanceEvalProportions.set(rowKey,"Sample",sampleKey); + concordanceEvalProportions.set(rowKey,"Eval_Genotype","Mismatching_Alleles"); + concordanceEvalProportions.set(rowKey,"Comp_Genotype","Mismatching_Alleles"); + concordanceCompProportions.set(rowKey,"Sample",sampleKey); + concordanceCompProportions.set(rowKey,"Eval_Genotype","Mismatching_Alleles"); + concordanceCompProportions.set(rowKey,"Comp_Genotype","Mismatching_Alleles"); + concordanceEvalProportions.set(rowKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes())); + concordanceCompProportions.set(rowKey,"Proportion", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes())); + concordanceCounts.set(rowKey,"Count",table.getnMismatchingAlt()); + + for ( Map.Entry nrsEntry : metrics.getPerSampleNRS().entrySet() ) { + concordanceSummary.set(nrsEntry.getKey(),"Sample",nrsEntry.getKey()); + concordanceSummary.set(nrsEntry.getKey(),"Non-Reference_Sensitivity",nrsEntry.getValue()); + } + for ( Map.Entry nrdEntry : metrics.getPerSampleNRD().entrySet() ) { + concordanceSummary.set(nrdEntry.getKey(),"Non-Reference_Discrepancy",nrdEntry.getValue()); + } + concordanceSummary.set("ALL_NRS_NRD","Sample","ALL"); + concordanceSummary.set("ALL_NRS_NRD","Non-Reference_Sensitivity",metrics.getOverallNRS()); + concordanceSummary.set("ALL_NRS_NRD","Non-Reference_Discrepancy",metrics.getOverallNRD()); + + + for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) { + siteConcordance.addColumn(type.toString(),"%d"); + } + + for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) { + siteConcordance.set("Comparison",type.toString(),metrics.getOverallSiteConcordance().get(type)); + } + + } else { + concordanceCompProportions.addColumn("Sample","%s"); + concordanceCounts.addColumn("Sample","%s"); + concordanceEvalProportions.addColumn("Sample","%s"); + concordanceSummary.addColumn("Sample","%s"); + for ( GenotypeType evalType : GenotypeType.values() ) { + for ( GenotypeType compType : GenotypeType.values() ) { + String colKey = String.format("%s_%s", evalType.toString(), compType.toString()); + concordanceCounts.addColumn(colKey,"%d"); + if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) + concordanceEvalProportions.addColumn(colKey,"%.3f"); + if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) + concordanceCompProportions.addColumn(colKey,"%.3f"); + } + } + concordanceEvalProportions.addColumn("Mismatching_Alleles","%.3f"); + concordanceCompProportions.addColumn("Mismatching_Alleles","%.3f"); + concordanceCounts.addColumn("Mismatching_Alleles","%d"); + concordanceSummary.addColumn("Non-Reference Sensitivity","%.3f"); + concordanceSummary.addColumn("Non-Reference Discrepancy","%.3f"); + for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) { + siteConcordance.addColumn(type.toString(),"%d"); + } + + for ( Map.Entry entry : metrics.getPerSampleGenotypeConcordance().entrySet() ) { + ConcordanceMetrics.GenotypeConcordanceTable table = entry.getValue(); + concordanceEvalProportions.set(entry.getKey(),"Sample",entry.getKey()); + concordanceCompProportions.set(entry.getKey(),"Sample",entry.getKey()); + concordanceCounts.set(entry.getKey(),"Sample",entry.getKey()); + for ( GenotypeType evalType : GenotypeType.values() ) { + for ( GenotypeType compType : GenotypeType.values() ) { + String colKey = String.format("%s_%s",evalType.toString(),compType.toString()); + int count = table.get(evalType, compType); + concordanceCounts.set(entry.getKey(),colKey,count); + if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) + concordanceEvalProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType))); + if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) + concordanceCompProportions.set(entry.getKey(),colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType))); + } + } + concordanceEvalProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes())); + concordanceCompProportions.set(entry.getKey(),"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes())); + concordanceCounts.set(entry.getKey(),"Mismatching_Alleles",table.getnMismatchingAlt()); + } + + String rowKey = "ALL"; + concordanceCompProportions.set(rowKey,"Sample",rowKey); + concordanceEvalProportions.set(rowKey,"Sample",rowKey); + concordanceCounts.set(rowKey,"Sample",rowKey); + ConcordanceMetrics.GenotypeConcordanceTable table = metrics.getOverallGenotypeConcordance(); + for ( GenotypeType evalType : GenotypeType.values() ) { + for ( GenotypeType compType : GenotypeType.values() ) { + String colKey = String.format("%s_%s",evalType.toString(),compType.toString()); + int count = table.get(evalType,compType); + concordanceCounts.set(rowKey,colKey,count); + if ( evalType == GenotypeType.HET || evalType == GenotypeType.HOM_REF || evalType == GenotypeType.HOM_VAR) + concordanceEvalProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnEvalGenotypes(evalType))); + if ( compType == GenotypeType.HET || compType == GenotypeType.HOM_VAR || compType == GenotypeType.HOM_REF ) + concordanceCompProportions.set(rowKey,colKey,repairNaN(( (double) count)/table.getnCompGenotypes(compType))); + } + } + concordanceEvalProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledEvalGenotypes())); + concordanceCompProportions.set(rowKey,"Mismatching_Alleles", repairNaN(( (double) table.getnMismatchingAlt() )/table.getnCalledCompGenotypes())); + concordanceCounts.set(rowKey,"Mismatching_Alleles",table.getnMismatchingAlt()); + + for ( Map.Entry nrsEntry : metrics.getPerSampleNRS().entrySet() ) { + concordanceSummary.set(nrsEntry.getKey(),"Sample",nrsEntry.getKey()); + concordanceSummary.set(nrsEntry.getKey(),"Non-Reference Sensitivity",nrsEntry.getValue()); + } + for ( Map.Entry nrdEntry : metrics.getPerSampleNRD().entrySet() ) { + concordanceSummary.set(nrdEntry.getKey(),"Non-Reference Discrepancy",nrdEntry.getValue()); + } + concordanceSummary.set("ALL","Sample","ALL"); + concordanceSummary.set("ALL","Non-Reference Sensitivity",metrics.getOverallNRS()); + concordanceSummary.set("ALL","Non-Reference Discrepancy",metrics.getOverallNRD()); + + for (ConcordanceMetrics.SiteConcordanceType type : ConcordanceMetrics.SiteConcordanceType.values() ) { + siteConcordance.set("Comparison",type.toString(),metrics.getOverallSiteConcordance().get(type)); + } + } + + report.addTable(concordanceCompProportions); + report.addTable(concordanceEvalProportions); + report.addTable(concordanceCounts); + report.addTable(concordanceSummary); + report.addTable(siteConcordance); + + report.print(out); + } + + public VariantContext createEmptyContext(VariantContext other, List samples) { + VariantContextBuilder builder = new VariantContextBuilder(); + // set the alleles to be the same + builder.alleles(other.getAlleles()); + builder.loc(other.getChr(),other.getStart(),other.getEnd()); + // set all genotypes to empty + List genotypes = new ArrayList(samples.size()); + for ( String sample : samples ) + genotypes.add(GenotypeBuilder.create(sample, new ArrayList(0))); + builder.genotypes(genotypes); + return builder.make(); + } + + public VariantContext filterGenotypes(VariantContext context, boolean ignoreSiteFilter, List exps) { + if ( ! context.isFiltered() || ignoreSiteFilter ) { + List filteredGenotypes = new ArrayList(context.getNSamples()); + for ( Genotype g : context.getGenotypes() ) { + Map matchMap = VariantContextUtils.match(context, g, exps); + boolean filtered = false; + for ( Boolean b : matchMap.values() ) { + if ( b ) { + filtered = true; + break; + } + } + if ( filtered ) { + filteredGenotypes.add(GenotypeBuilder.create(g.getSampleName(),Arrays.asList(Allele.NO_CALL,Allele.NO_CALL),g.getExtendedAttributes())); + } else { + filteredGenotypes.add(g); + } + } + VariantContextBuilder builder = new VariantContextBuilder(context); + builder.genotypes(filteredGenotypes); + return builder.make(); + } + + VariantContextBuilder builder = new VariantContextBuilder(); + builder.alleles(Arrays.asList(context.getReference())); + builder.loc(context.getChr(),context.getStart(),context.getEnd()); + List newGeno = new ArrayList(context.getNSamples()); + for ( Genotype g : context.getGenotypes().iterateInSampleNameOrder() ) { + newGeno.add(GenotypeBuilder.create(g.getSampleName(),new ArrayList())); + } + builder.genotypes(newGeno); + return builder.make(); + } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java similarity index 51% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index 7ac36b2f8..17f75229a 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java new file mode 100644 index 000000000..b78038953 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -0,0 +1,168 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; + +import net.sf.picard.liftover.LiftOver; +import net.sf.picard.util.Interval; +import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMFileReader; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.ArgumentCollection; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; +import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.*; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; + +import java.io.File; +import java.util.*; + +/** + * Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted. + */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) +public class LiftoverVariants extends RodWalker { + + @ArgumentCollection + protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + + @Output(doc="File to which variants should be written",required=true) + protected File file = null; + protected VariantContextWriter writer = null; + + @Argument(fullName="chain", shortName="chain", doc="Chain file", required=true) + protected File CHAIN = null; + + @Argument(fullName="newSequenceDictionary", shortName="dict", doc="Sequence .dict file for the new build", required=true) + protected File NEW_SEQ_DICT = null; + + @Argument(fullName="recordOriginalLocation", shortName="recordOriginalLocation", doc="Should we record what the original location was in the INFO field?", required=false) + protected Boolean RECORD_ORIGINAL_LOCATION = false; + + private LiftOver liftOver; + + private long successfulIntervals = 0, failedIntervals = 0; + + public void initialize() { + try { + liftOver = new LiftOver(CHAIN); + } catch (RuntimeException e) { + throw new UserException.BadInput("there is a problem with the chain file you are using: " + e.getMessage()); + } + + liftOver.setLiftOverMinMatch(LiftOver.DEFAULT_LIFTOVER_MINMATCH); + + try { + final SAMFileHeader toHeader = new SAMFileReader(NEW_SEQ_DICT).getFileHeader(); + liftOver.validateToSequences(toHeader.getSequenceDictionary()); + } catch (RuntimeException e) { + throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference"); + } + + String trackName = variantCollection.variants.getName(); + Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)); + Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); + + Set metaData = new HashSet(); + if ( vcfHeaders.containsKey(trackName) ) + metaData.addAll(vcfHeaders.get(trackName).getMetaDataInSortedOrder()); + if ( RECORD_ORIGINAL_LOCATION ) { + metaData.add(new VCFInfoHeaderLine("OriginalChr", 1, VCFHeaderLineType.String, "Original contig name for the record")); + metaData.add(new VCFInfoHeaderLine("OriginalStart", 1, VCFHeaderLineType.Integer, "Original start position for the record")); + } + + + final VCFHeader vcfHeader = new VCFHeader(metaData, samples); + writer = VariantContextWriterFactory.create(file, getMasterSequenceDictionary(), VariantContextWriterFactory.NO_OPTIONS); + writer.writeHeader(vcfHeader); + } + + private void convertAndWrite(VariantContext vc, ReferenceContext ref) { + + final Interval fromInterval = new Interval(vc.getChr(), vc.getStart(), vc.getStart(), false, String.format("%s:%d", vc.getChr(), vc.getStart())); + final int length = vc.getEnd() - vc.getStart(); + final Interval toInterval = liftOver.liftOver(fromInterval); + VariantContext originalVC = vc; + + if ( toInterval != null ) { + // check whether the strand flips, and if so reverse complement everything + if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && vc.isPointEvent() ) { + vc = GATKVariantContextUtils.reverseComplement(vc); + } + + vc = new VariantContextBuilder(vc).loc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length).make(); + + if ( RECORD_ORIGINAL_LOCATION ) { + vc = new VariantContextBuilder(vc) + .attribute("OriginalChr", fromInterval.getSequence()) + .attribute("OriginalStart", fromInterval.getStart()).make(); + } + + if ( originalVC.isSNP() && originalVC.isBiallelic() && GATKVariantContextUtils.getSNPSubstitutionType(originalVC) != GATKVariantContextUtils.getSNPSubstitutionType(vc) ) { + logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s", + originalVC.getChr(), originalVC.getStart(), vc.getChr(), vc.getStart(), + originalVC.getReference(), originalVC.getAlternateAllele(0), vc.getReference(), vc.getAlternateAllele(0))); + } + + writer.add(vc); + successfulIntervals++; + } else { + failedIntervals++; + } + } + + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if ( tracker == null ) + return 0; + + Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation()); + for ( VariantContext vc : VCs ) + convertAndWrite(vc, ref); + + return 0; + } + + public Integer reduceInit() { return 0; } + + public Integer reduce(Integer value, Integer sum) { return 0; } + + public void onTraversalDone(Integer result) { + System.out.println("Converted " + successfulIntervals + " records; failed to convert " + failedIntervals + " records."); + writer.close(); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java new file mode 100644 index 000000000..896f36e6c --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java @@ -0,0 +1,121 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; + +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.ArgumentCollection; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.gatk.CommandLineGATK; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; + +import java.io.File; +import java.util.*; + +/** + * Takes a VCF file, randomly splits variants into two different sets, and outputs 2 new VCFs with the results. + */ +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) +public class RandomlySplitVariants extends RodWalker { + + @ArgumentCollection + protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + + @Output(fullName="out1", shortName="o1", doc="File #1 to which variants should be written", required=true) + protected VariantContextWriter vcfWriter1 = null; + + @Output(fullName="out2", shortName="o2", doc="File #2 to which variants should be written", required=true) + // there's a reported bug in the GATK where we can't have 2 @Output writers + protected File file2 = null; + protected VariantContextWriter vcfWriter2 = null; + + @Argument(fullName="fractionToOut1", shortName="fraction", doc="Fraction of records to be placed in out1 (must be 0 >= fraction <= 1); all other records are placed in out2", required=false) + protected double fraction = 0.5; + + /** + * Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher + */ + public void initialize() { + if ( fraction < 0.0 || fraction > 1.0 ) + throw new UserException.BadArgumentValue("fractionToOut1", "this value needs to be a number between 0 and 1"); + + // setup the header info + final List inputNames = Arrays.asList(variantCollection.variants.getName()); + Set samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames); + Set hInfo = new HashSet(); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames)); + + vcfWriter1.writeHeader(new VCFHeader(hInfo, samples)); + vcfWriter2 = VariantContextWriterFactory.create(file2, getMasterSequenceDictionary()); + vcfWriter2.writeHeader(new VCFHeader(hInfo, samples)); + } + + /** + * Subset VC record if necessary and emit the modified record (provided it satisfies criteria for printing) + * + * @param tracker the ROD tracker + * @param ref reference information + * @param context alignment info + * @return 1 if the record was printed to the output file, 0 if otherwise + */ + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if ( tracker == null ) + return 0; + + Collection vcs = tracker.getValues(variantCollection.variants, context.getLocation()); + for ( VariantContext vc : vcs ) { + double random = GenomeAnalysisEngine.getRandomGenerator().nextDouble(); + if ( random < fraction ) + vcfWriter1.add(vc); + else + vcfWriter2.add(vc); + } + + return 1; + } + + public Integer reduceInit() { return 0; } + + public Integer reduce(Integer value, Integer sum) { return value + sum; } + + public void onTraversalDone(Integer result) { + logger.info(result + " records processed."); + vcfWriter2.close(); + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java new file mode 100644 index 000000000..e4d182d13 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java @@ -0,0 +1,277 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; + +import org.apache.commons.io.FilenameUtils; +import org.broad.tribble.Feature; +import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; +import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.gatk.walkers.TreeReducible; +import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.interval.IntervalMergingRule; +import org.broadinstitute.sting.utils.interval.IntervalSetRule; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.*; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.sting.utils.text.ListFileUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.io.File; +import java.util.*; + +/** + * Selects headers from a VCF source. + *

+ *

+ * Often, a VCF containing many headers will need to be subset in order to facilitate certain formatting guidelines. + * SelectHeaders can be used for this purpose. Given a single VCF file, one or more headers can be extracted from the + * file (based on a complete header name or a pattern match). + *

+ *

Input

+ *

+ * A set of VCFs. + *

+ *

+ *

Output

+ *

+ * A header selected VCF. + *

+ *

+ *

Examples

+ * 
+ * Select only the FILTER, FORMAT, and INFO headers:
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T SelectHeaders \
+ *   --variant input.vcf \
+ *   -o output.vcf \
+ *   -hn FILTER \
+ *   -hn FORMAT \
+ *   -hn INFO
+ *
+ * Select only the FILTER, FORMAT, and INFO headers and add in the reference file names:
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T SelectHeaders \
+ *   --variant input.vcf \
+ *   -o output.vcf \
+ *   -hn FILTER \
+ *   -hn FORMAT \
+ *   -hn INFO \
+ *   -irn \
+ *   -iln
+ *
+ * Select only the FILTER, FORMAT, and INFO headers, plus any headers with SnpEff:
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T SelectHeaders \
+ *   --variant input.vcf \
+ *   -o output.vcf \
+ *   -hn FILTER \
+ *   -hn FORMAT \
+ *   -hn INFO \
+ *   -he '.*SnpEff.*'
+ *
+ */ +@SuppressWarnings("unused") +@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} ) +public class SelectHeaders extends RodWalker implements TreeReducible { + @ArgumentCollection + protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + + @Output(doc = "File to which variants should be written", required = true) + protected VariantContextWriter vcfWriter; + + @Argument(fullName = "header_name", shortName = "hn", doc = "Include header. Can be specified multiple times", required = false) + public Set headerNames; + + @Argument(fullName = "header_expression", shortName = "he", doc = "Regular expression to select many headers from the tracks provided. Can be specified multiple times", required = false) + public Set headerExpressions; + + /** + * Note that header exclusion takes precedence over inclusion, so that if a header is in both lists it will be excluded. + */ + @Argument(fullName = "exclude_header_name", shortName = "xl_hn", doc = "Exclude header. Can be specified multiple times", required = false) + public Set XLheaderNames; + + /** + * Note that interval name inclusion takes precedence over other header matching. If set other interval lines may be excluded but the intervals will still be added. + */ + @Argument(fullName = "include_interval_names", shortName = "iln", doc = "If set the interval file name minus the file extension, or the command line intervals, will be added to the headers", required = false) + public boolean includeIntervals; + + /** + * Note that engine header inclusion takes precedence over other header matching. If set other engine lines may be excluded but the intervals will still be added. + */ + @Hidden // TODO: Determine if others find this valuable and either remove @Hidden or remove -ieh. + @Argument(fullName = "include_engine_headers", shortName = "ieh", doc = "If set the headers normally output by the engine will be added to the headers", required = false) + public boolean includeEngineHeaders; + + private static final ListFileUtils.StringConverter headerKey = new ListFileUtils.StringConverter() { + @Override + public String convert(VCFHeaderLine value) { + return value.getKey(); + } + }; + + /** + * Set up the VCF writer, the header expressions and regexps + */ + @Override + public void initialize() { + // Get list of samples to include in the output + List rodNames = Arrays.asList(variantCollection.variants.getName()); + + Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); + Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); + + headerLines.add(new VCFHeaderLine(VCFHeader.SOURCE_KEY, "SelectHeaders")); + + // Select only the headers requested by name or expression. + headerLines = new LinkedHashSet(getSelectedHeaders(headerLines)); + + // Optionally add in the intervals. + if (includeIntervals) { + IntervalArgumentCollection intervalArguments = getToolkit().getArguments().intervalArguments; + if (intervalArguments.intervals != null) { + for (IntervalBinding intervalBinding : intervalArguments.intervals) { + String source = intervalBinding.getSource(); + if (source == null) + continue; + File file = new File(source); + if (file.exists()) { + headerLines.add(new VCFHeaderLine(VCFHeader.INTERVALS_KEY, FilenameUtils.getBaseName(file.getName()))); + } else { + headerLines.add(new VCFHeaderLine(VCFHeader.INTERVALS_KEY, source)); + } + } + } + + if (intervalArguments.excludeIntervals != null) { + for (IntervalBinding intervalBinding : intervalArguments.excludeIntervals) { + String source = intervalBinding.getSource(); + if (source == null) + continue; + File file = new File(source); + if (file.exists()) { + headerLines.add(new VCFHeaderLine(VCFHeader.EXCLUDE_INTERVALS_KEY, FilenameUtils.getBaseName(file.getName()))); + } else { + headerLines.add(new VCFHeaderLine(VCFHeader.EXCLUDE_INTERVALS_KEY, source)); + } + } + } + + if (intervalArguments.intervalMerging != IntervalMergingRule.ALL) { + headerLines.add(new VCFHeaderLine(VCFHeader.INTERVAL_MERGING_KEY, String.valueOf(intervalArguments.intervalMerging))); + } + + if (intervalArguments.intervalSetRule != IntervalSetRule.UNION) { + headerLines.add(new VCFHeaderLine(VCFHeader.INTERVAL_SET_RULE_KEY, String.valueOf(intervalArguments.intervalSetRule))); + } + + if (intervalArguments.intervalPadding != 0) { + headerLines.add(new VCFHeaderLine(VCFHeader.INTERVAL_PADDING_KEY, String.valueOf(intervalArguments.intervalPadding))); + } + } + + TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); + VCFHeader vcfHeader = new VCFHeader(headerLines, vcfSamples); + vcfHeader.setWriteEngineHeaders(includeEngineHeaders); + vcfWriter.writeHeader(vcfHeader); + } + + private Set getSelectedHeaders(Set headerLines) { + Set selectedHeaders = new TreeSet(); + if (headerNames == null && headerExpressions == null) { + // Include everything if nothing was explicitly included. + selectedHeaders.addAll(headerLines); + } else { + // Only include the selected headers. + if (headerNames != null) + selectedHeaders.addAll(ListFileUtils.includeMatching(headerLines, headerKey, headerNames, true)); + if (headerExpressions != null) + selectedHeaders.addAll(ListFileUtils.includeMatching(headerLines, headerKey, headerExpressions, false)); + } + + // Remove any excluded headers. + if (XLheaderNames != null) + selectedHeaders = ListFileUtils.excludeMatching(selectedHeaders, headerKey, XLheaderNames, true); + + // always include the contig lines + selectedHeaders = VCFUtils.withUpdatedContigsAsLines(selectedHeaders, getToolkit().getArguments().referenceFile, getToolkit().getMasterSequenceDictionary(), true); + return selectedHeaders; + } + + /** + * Pass through the VC record + * + * @param tracker the ROD tracker + * @param ref reference information + * @param context alignment info + * @return number of records processed + */ + @Override + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + int count = 0; + if (tracker != null) { + Collection vcs = tracker.getValues(variantCollection.variants, context.getLocation()); + if (vcs != null) { + for (VariantContext vc : vcs) { + vcfWriter.add(vc); + count++; + } + } + } + return count; + } + + @Override + public Integer reduceInit() { + return 0; + } + + @Override + public Integer reduce(Integer value, Integer sum) { + return value + sum; + } + + @Override + public Integer treeReduce(Integer lhs, Integer rhs) { + return lhs + rhs; + } + + @Override + public void onTraversalDone(Integer result) { + logger.info(result + " records processed."); + } +} diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java similarity index 73% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index ebad1e2ed..4d30408d8 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; 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LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM. -* -* 3. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; @@ -56,16 +35,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants; -import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; -import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; -import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper; -import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.utils.MendelianViolation; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; @@ -260,17 +234,6 @@ public class SelectVariants extends RodWalker implements TreeR @Argument(fullName="excludeFiltered", shortName="ef", doc="Don't include filtered loci in the analysis", required=false) protected boolean EXCLUDE_FILTERED = false; - /** - * This argument triggers re-genotyping of the selected samples through the Exact calculation model. Note that this is truly the - * mathematically correct way to select samples (especially when calls were generated from low coverage sequencing data); using the - * hard genotypes to select (i.e. the default mode of SelectVariants) can lead to false positives when errors are confused for variants - * in the original genotyping. We decided not to set the --regenotype option as the default though as the output can be unexpected if - * a user is strictly comparing against the original genotypes (GTs) in the file. - */ - @Argument(fullName="regenotype", shortName="regenotype", doc="re-genotype the selected samples based on their GLs (or PLs)", required=false) - protected Boolean REGENOTYPE = false; - private UnifiedGenotyperEngine UG_engine = null; - /** * When this argument is used, we can choose to include only multiallelic or biallelic sites, depending on how many alleles are listed in the ALT column of a vcf. * For example, a multiallelic record such as: @@ -375,7 +338,7 @@ public class SelectVariants extends RodWalker implements TreeR List rodNames = Arrays.asList(variantCollection.variants.getName()); vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); - TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); + TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); Collection samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles); Collection samplesFromExpressions = SampleUtils.matchSamplesExpressions(vcfSamples, sampleExpressions); @@ -438,7 +401,7 @@ public class SelectVariants extends RodWalker implements TreeR } // Initialize VCF header - Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger); + Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true); headerLines.add(new VCFHeaderLine("source", "SelectVariants")); if (KEEP_ORIGINAL_CHR_COUNTS) { @@ -471,15 +434,6 @@ public class SelectVariants extends RodWalker implements TreeR SELECT_RANDOM_FRACTION = fractionRandom > 0; if (SELECT_RANDOM_FRACTION) logger.info("Selecting approximately " + 100.0*fractionRandom + "% of the variants at random from the variant track"); - if ( REGENOTYPE ) { - final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection(); - UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH; - UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES; - UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES; - UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY); - headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null)); - } - /** load in the IDs file to a hashset for matching */ if ( rsIDFile != null ) { IDsToKeep = new HashSet(); @@ -557,14 +511,6 @@ public class SelectVariants extends RodWalker implements TreeR VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS); - if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) { - synchronized (UG_engine) { - final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(sub)).filters(sub.getFiltersMaybeNull()); - addAnnotations(builder, sub); - sub = builder.make(); - } - } - if ( (!EXCLUDE_NON_VARIANTS || sub.isPolymorphicInSamples()) && (!EXCLUDE_FILTERED || !sub.isFiltered()) ) { boolean failedJexlMatch = false; for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) { @@ -596,19 +542,11 @@ public class SelectVariants extends RodWalker implements TreeR return false; } - private boolean hasPLs(final VariantContext vc) { - for ( Genotype g : vc.getGenotypes() ) { - if ( g.hasLikelihoods() ) - return true; - } - return false; - } - /** * Checks if vc has a variant call for (at least one of) the samples. * @param vc the variant rod VariantContext. Here, the variant is the dataset you're looking for discordances to (e.g. HapMap) * @param compVCs the comparison VariantContext (discordance - * @return + * @return true if is discordant */ private boolean isDiscordant (VariantContext vc, Collection compVCs) { if (vc == null) @@ -724,7 +662,7 @@ public class SelectVariants extends RodWalker implements TreeR // if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs and AD (because they are no longer accurate) if ( vc.getAlleles().size() != sub.getAlleles().size() ) - newGC = VariantContextUtils.stripPLsAndAD(sub.getGenotypes()); + newGC = GATKVariantContextUtils.stripPLsAndAD(sub.getGenotypes()); // if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags if ( vc.getNSamples() != sub.getNSamples() ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java new file mode 100644 index 000000000..4b9f2c6c1 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -0,0 +1,184 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; + +import org.broad.tribble.TribbleException; +import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.CommandLineGATK; +import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; +import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; + +import java.io.File; +import java.util.Arrays; +import java.util.Collection; +import java.util.HashSet; +import java.util.Set; + + +/** + * Validates a VCF file with an extra strict set of criteria. + * + *

+ * ValidateVariants is a GATK tool that takes a VCF file and validates much of the information inside it. + * In addition to standard adherence to the VCF specification, this tool performs extra checks to make ensure + * the information contained within the file is correct. Checks include the correctness of the reference base(s), + * accuracy of AC & AN values, tests against rsIDs when a dbSNP file is provided, and that all alternate alleles + * are present in at least one sample. + * + * If you are looking simply to test the adherence to the VCF specification, use --validationType NONE. + * + *

Input

+ *

+ * A variant set to validate. + *

+ * + *

Examples

+ * 
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T ValidateVariants \
+ *   --variant input.vcf \
+ *   --dbsnp dbsnp.vcf
+ *
+ * + */ +@DocumentedGATKFeature( groupName = "Validation Utilities", extraDocs = {CommandLineGATK.class} ) +@Reference(window=@Window(start=0,stop=100)) +public class ValidateVariants extends RodWalker { + + @ArgumentCollection + protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); + + @ArgumentCollection + protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection(); + + public enum ValidationType { + ALL, REF, IDS, ALLELES, CHR_COUNTS, NONE + } + + @Argument(fullName = "validationType", shortName = "type", doc = "which validation type to run", required = false) + protected ValidationType type = ValidationType.ALL; + + /** + * By default, even filtered records are validated. + */ + @Argument(fullName = "doNotValidateFilteredRecords", shortName = "doNotValidateFilteredRecords", doc = "skip validation on filtered records", required = false) + 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; + + private long numErrors = 0; + + private File file = null; + + public void initialize() { + file = new File(variantCollection.variants.getSource()); + } + + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + if ( tracker == null ) + return 0; + + Collection VCs = tracker.getValues(variantCollection.variants, context.getLocation()); + for ( VariantContext vc : VCs ) + validate(vc, tracker, ref); + + return VCs.size(); + } + + public Integer reduceInit() { return 0; } + + public Integer reduce(Integer value, Integer sum) { return sum+value; } + + public void onTraversalDone(Integer result) { + if ( numErrors == 0 ) + System.out.println("Successfully validated the input file. Checked " + result + " records with no failures."); + else + System.out.println("Found " + numErrors + " records with failures."); + } + + private void validate(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref) { + if ( DO_NOT_VALIDATE_FILTERED && vc.isFiltered() ) + return; + + // get the true reference allele + final Allele reportedRefAllele = vc.getReference(); + final int refLength = reportedRefAllele.length(); + if ( refLength > 100 ) { + logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", refLength, vc.getChr(), vc.getStart())); + return; + } + + final byte[] observedRefBases = new byte[refLength]; + System.arraycopy(ref.getBases(), 0, observedRefBases, 0, refLength); + final Allele observedRefAllele = Allele.create(observedRefBases); + + // get the RS IDs + Set rsIDs = null; + if ( tracker.hasValues(dbsnp.dbsnp) ) { + rsIDs = new HashSet(); + for ( VariantContext rsID : tracker.getValues(dbsnp.dbsnp, ref.getLocus()) ) + rsIDs.addAll(Arrays.asList(rsID.getID().split(VCFConstants.ID_FIELD_SEPARATOR))); + } + + try { + switch( type ) { + case ALL: + vc.extraStrictValidation(reportedRefAllele, observedRefAllele, rsIDs); + break; + case REF: + vc.validateReferenceBases(reportedRefAllele, observedRefAllele); + break; + case IDS: + vc.validateRSIDs(rsIDs); + break; + case ALLELES: + vc.validateAlternateAlleles(); + break; + case CHR_COUNTS: + vc.validateChromosomeCounts(); + break; + } + } catch (TribbleException e) { + if ( WARN_ON_ERROR ) { + numErrors++; + logger.warn("***** " + e.getMessage() + " *****"); + } else { + throw new UserException.FailsStrictValidation(file, e.getMessage()); + } + } + } +} \ No newline at end of file diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java similarity index 61% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index 5ac70a8c3..5bf5b96e3 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; @@ -56,13 +35,13 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.util.*; @@ -277,7 +256,7 @@ public class VariantValidationAssessor extends RodWalker //if ( popFile != null ) { // throw new StingException("We still need to implement this!"); //} else { - return VariantContextUtils.computeHardyWeinbergPvalue(vc); + return GATKVariantContextUtils.computeHardyWeinbergPvalue(vc); //} } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java similarity index 72% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index e3cc27570..3bd95d9ec 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java similarity index 71% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 46bb4a48b..f6c02592d 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; @@ -50,6 +29,7 @@ import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; @@ -61,7 +41,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.io.PrintStream; import java.lang.reflect.Array; @@ -201,7 +180,7 @@ public class VariantsToTable extends RodWalker { if ( !genotypeFieldsToTake.isEmpty() ) { Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), variants); - TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); + TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); samples.addAll(vcfSamples); // optimization: if there are no samples, we don't have to worry about any genotype fields @@ -452,7 +431,7 @@ public class VariantsToTable extends RodWalker { getters.put("QUAL", new Getter() { public String get(VariantContext vc) { return Double.toString(vc.getPhredScaledQual()); } }); getters.put("TRANSITION", new Getter() { public String get(VariantContext vc) { if ( vc.isSNP() && vc.isBiallelic() ) - return VariantContextUtils.isTransition(vc) ? "1" : "0"; + return GATKVariantContextUtils.isTransition(vc) ? "1" : "0"; else return "-1"; }}); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java similarity index 54% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index 9f2aa68e3..a51014114 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -1,47 +1,26 @@ /* -* 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 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE). -* -* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 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 GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/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. -* 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. OWNERSHIP OF INTELLECTUAL PROPERTY -* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. -* Copyright 2012 Broad Institute, Inc. -* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc. -* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes. -* -* 4. 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. -* -* 5. 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. -* -* 6. 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. -* -* 7. MISCELLANEOUS -* 7.1 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. -* 7.2 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. -* 7.3 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. -* 7.4 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. -* 7.5 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. -* 7.6 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. -* 7.7 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. +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.walkers.variantutils; @@ -60,11 +39,12 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; @@ -140,7 +120,7 @@ public class VariantsToVCF extends RodWalker { if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) ) return 0; - String rsID = dbsnp == null ? null : VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP); + String rsID = dbsnp == null ? null : GATKVCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP); Collection contexts = getVariantContexts(tracker, ref); @@ -267,7 +247,7 @@ public class VariantsToVCF extends RodWalker { vcfwriter.writeHeader(new VCFHeader(hInfo, samples)); } - vc = VariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings); + vc = GATKVariantContextUtils.purgeUnallowedGenotypeAttributes(vc, allowedGenotypeFormatStrings); vcfwriter.add(vc); } diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java index 1bf4c69fc..51cc576aa 100644 --- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java +++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java @@ -158,12 +158,18 @@ public abstract class ArgumentDefinitionField extends ArgumentField { List fields = new ArrayList(); String gatherClass; + + // one can set the specific gatherer to use by adding @Gather before any output argument. + // For example (used to be part of UG): + // @Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer") + // @Output(doc="File to which variants should be written",required=true) + // protected VariantContextWriter writer = null; if (gatherer != null) gatherClass = gatherer; else if (SAMFileWriter.class.isAssignableFrom(argumentDefinition.argumentType)) gatherClass = "BamGatherFunction"; else if (VariantContextWriter.class.isAssignableFrom(argumentDefinition.argumentType)) - gatherClass = "VcfGatherFunction"; + gatherClass = "CatVariantsGatherer"; // used to be "VcfGatherFunction"; else gatherClass = "org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction"; diff --git a/public/java/src/org/broadinstitute/sting/tools/CatVariants.java b/public/java/src/org/broadinstitute/sting/tools/CatVariants.java index 1feb4e009..10fb606f9 100644 --- a/public/java/src/org/broadinstitute/sting/tools/CatVariants.java +++ b/public/java/src/org/broadinstitute/sting/tools/CatVariants.java @@ -36,9 +36,9 @@ import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.variant.bcf2.BCF2Codec; +import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.variant.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.writer.Options; @@ -51,7 +51,7 @@ import java.util.*; /** * - * Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.AppendVariants [sorted (optional)]"); + * Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants [sorted (optional)]"); * The input files can be of type: VCF (ends in .vcf or .VCF)"); * BCF2 (ends in .bcf or .BCF)"); * Output file must be vcf or bcf file (.vcf or .bcf)"); diff --git a/public/java/src/org/broadinstitute/variant/utils/BaseUtils.java b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java similarity index 68% rename from public/java/src/org/broadinstitute/variant/utils/BaseUtils.java rename to public/java/src/org/broadinstitute/sting/utils/BaseUtils.java index 819041a3e..46f8f2a84 100644 --- a/public/java/src/org/broadinstitute/variant/utils/BaseUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java @@ -1,78 +1,101 @@ /* -* Copyright (c) 2012 The Broad Institute -* -* 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. -*/ + * Copyright (c) 2012 The Broad Institute + * + * 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.variant.utils; +package org.broadinstitute.sting.utils; import net.sf.samtools.util.StringUtil; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.Arrays; -import java.util.Random; /** * BaseUtils contains some basic utilities for manipulating nucleotides. */ public class BaseUtils { - public final static byte A = (byte) 'A'; - public final static byte C = (byte) 'C'; - public final static byte G = (byte) 'G'; - public final static byte T = (byte) 'T'; - public final static byte N = (byte) 'N'; - public final static byte D = (byte) 'D'; + public enum Base { + A ('A'), + C ('C'), + G ('G'), + T ('T'), + N ('N'), + D ('D'); - // - // todo -- we need a generalized base abstraction using the Base enum. - // + public byte base; + + private Base(final char base) { + this.base = (byte)base; + } + } + + // todo -- add this to the generalized base abstraction using the Base enum. public final static byte[] BASES = {'A', 'C', 'G', 'T'}; public final static byte[] EXTENDED_BASES = {'A', 'C', 'G', 'T', 'N', 'D'}; static private final int[] baseIndexMap = new int[256]; static { Arrays.fill(baseIndexMap, -1); - baseIndexMap['A'] = 0; - baseIndexMap['a'] = 0; - baseIndexMap['*'] = 0; // the wildcard character counts as an A - baseIndexMap['C'] = 1; - baseIndexMap['c'] = 1; - baseIndexMap['G'] = 2; - baseIndexMap['g'] = 2; - baseIndexMap['T'] = 3; - baseIndexMap['t'] = 3; + baseIndexMap['A'] = Base.A.ordinal(); + baseIndexMap['a'] = Base.A.ordinal(); + baseIndexMap['*'] = Base.A.ordinal(); // the wildcard character counts as an A + baseIndexMap['C'] = Base.C.ordinal(); + baseIndexMap['c'] = Base.C.ordinal(); + baseIndexMap['G'] = Base.G.ordinal(); + baseIndexMap['g'] = Base.G.ordinal(); + baseIndexMap['T'] = Base.T.ordinal(); + baseIndexMap['t'] = Base.T.ordinal(); } - // todo -- fix me (enums?) - public static final byte DELETION_INDEX = 4; - public static final byte NO_CALL_INDEX = 5; // (this is 'N') - - public static final int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A'); - public static final int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C'); - public static final int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G'); - public static final int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T'); - - // Use a fixed random seed to allow for deterministic results when using random bases - private static final Random randomNumberGen = new Random(47382911L); + static private final int[] baseIndexWithIupacMap = baseIndexMap.clone(); + static { + baseIndexWithIupacMap['*'] = -1; // the wildcard character is bad + baseIndexWithIupacMap['N'] = Base.N.ordinal(); + baseIndexWithIupacMap['n'] = Base.N.ordinal(); + baseIndexWithIupacMap['R'] = Base.N.ordinal(); + baseIndexWithIupacMap['r'] = Base.N.ordinal(); + baseIndexWithIupacMap['Y'] = Base.N.ordinal(); + baseIndexWithIupacMap['y'] = Base.N.ordinal(); + baseIndexWithIupacMap['M'] = Base.N.ordinal(); + baseIndexWithIupacMap['m'] = Base.N.ordinal(); + baseIndexWithIupacMap['K'] = Base.N.ordinal(); + baseIndexWithIupacMap['k'] = Base.N.ordinal(); + baseIndexWithIupacMap['W'] = Base.N.ordinal(); + baseIndexWithIupacMap['w'] = Base.N.ordinal(); + baseIndexWithIupacMap['S'] = Base.N.ordinal(); + baseIndexWithIupacMap['s'] = Base.N.ordinal(); + baseIndexWithIupacMap['B'] = Base.N.ordinal(); + baseIndexWithIupacMap['b'] = Base.N.ordinal(); + baseIndexWithIupacMap['D'] = Base.N.ordinal(); + baseIndexWithIupacMap['d'] = Base.N.ordinal(); + baseIndexWithIupacMap['H'] = Base.N.ordinal(); + baseIndexWithIupacMap['h'] = Base.N.ordinal(); + baseIndexWithIupacMap['V'] = Base.N.ordinal(); + baseIndexWithIupacMap['v'] = Base.N.ordinal(); + } /// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or // a pyrimidine to another pyrimidine nucleotide (C <-> T). @@ -96,10 +119,10 @@ public class BaseUtils { } public static boolean isTransition(byte base1, byte base2) { - int b1 = simpleBaseToBaseIndex(base1); - int b2 = simpleBaseToBaseIndex(base2); - return b1 == 0 && b2 == 2 || b1 == 2 && b2 == 0 || - b1 == 1 && b2 == 3 || b1 == 3 && b2 == 1; + final int b1 = simpleBaseToBaseIndex(base1); + final int b2 = simpleBaseToBaseIndex(base2); + return b1 == Base.A.ordinal() && b2 == Base.G.ordinal() || b1 == Base.G.ordinal() && b2 == Base.A.ordinal() || + b1 == Base.C.ordinal() && b2 == Base.T.ordinal() || b1 == Base.T.ordinal() && b2 == Base.C.ordinal(); } public static boolean isTransversion(byte base1, byte base2) { @@ -141,6 +164,21 @@ public class BaseUtils { return base >= 'A' && base <= 'Z'; } + public static byte[] convertIUPACtoN(final byte[] bases, final boolean errorOnBadReferenceBase, final boolean ignoreConversionOfFirstByte) { + final int length = bases.length; + final int start = ignoreConversionOfFirstByte ? 1 : 0; + + for ( int i = start; i < length; i++ ) { + final int baseIndex = baseIndexWithIupacMap[bases[i]]; + if ( baseIndex == Base.N.ordinal() ) { + bases[i] = 'N'; + } else if ( errorOnBadReferenceBase && baseIndex == -1 ) { + throw new UserException.BadInput("We encountered a non-standard non-IUPAC base in the provided reference: '" + bases[i] + "'"); + } + } + return bases; + } + /** * Converts a IUPAC nucleotide code to a pair of bases * @@ -212,7 +250,7 @@ public class BaseUtils { */ static public int simpleBaseToBaseIndex(final byte base) { if ( base < 0 || base >= 256 ) - throw new IllegalArgumentException("Non-standard bases were encountered in either the input reference or BAM file(s)"); + throw new UserException.BadInput("Non-standard bases were encountered in either the input reference or BAM file(s)"); return baseIndexMap[base]; } @@ -231,10 +269,10 @@ public class BaseUtils { switch (base) { case 'd': case 'D': - return DELETION_INDEX; + return Base.D.ordinal(); case 'n': case 'N': - return NO_CALL_INDEX; + return Base.N.ordinal(); default: return simpleBaseToBaseIndex(base); @@ -452,9 +490,31 @@ public class BaseUtils { int randomBaseIndex = excludeBaseIndex; while (randomBaseIndex == excludeBaseIndex) { - randomBaseIndex = randomNumberGen.nextInt(4); + randomBaseIndex = GenomeAnalysisEngine.getRandomGenerator().nextInt(4); } return randomBaseIndex; } + + public static byte getComplement(byte base) { + switch(base) { + case 'a': + case 'A': + return 'T'; + case 'c': + case 'C': + return 'G'; + case 'g': + case 'G': + return 'C'; + case 't': + case 'T': + return 'A'; + case 'n': + case 'N': + return 'N'; + default: + throw new ReviewedStingException("base must be A, C, G or T. " + (char) base + " is not a valid base."); + } + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index c81e8e853..0a271b64c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -30,10 +30,7 @@ import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.Serializable; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; +import java.util.*; /** * Created by IntelliJ IDEA. @@ -530,4 +527,100 @@ public class GenomeLoc implements Comparable, Serializable, HasGenome final int cmp = this.compareTo(other); return cmp == -1 ? other : this; } + + /** + * create a new genome loc from an existing loc, with a new start position + * Note that this function will NOT explicitly check the ending offset, in case someone wants to + * set the start of a new GenomeLoc pertaining to a read that goes off the end of the contig. + * + * @param loc the old location + * @param start a new start position + * + * @return a newly allocated GenomeLoc as loc but with start == start + */ + public GenomeLoc setStart(GenomeLoc loc, int start) { + return new GenomeLoc(loc.getContig(), loc.getContigIndex(), start, loc.getStop()); + } + + /** + * create a new genome loc from an existing loc, with a new stop position + * Note that this function will NOT explicitly check the ending offset, in case someone wants to + * set the stop of a new GenomeLoc pertaining to a read that goes off the end of the contig. + * + * @param loc the old location + * @param stop a new stop position + * + * @return a newly allocated GenomeLoc as loc but with stop == stop + */ + public GenomeLoc setStop(GenomeLoc loc, int stop) { + return new GenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start, stop); + } + + /** + * return a new genome loc, with an incremented position + * + * @param loc the old location + * + * @return a newly allocated GenomeLoc as loc but with start == loc.getStart() + 1 + */ + public GenomeLoc incPos(GenomeLoc loc) { + return incPos(loc, 1); + } + + /** + * return a new genome loc, with an incremented position + * + * @param loc the old location + * @param by how much to move the start and stop by + * + * @return a newly allocated GenomeLoc as loc but with start == loc.getStart() + by + */ + public GenomeLoc incPos(GenomeLoc loc, int by) { + return new GenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start + by, loc.stop + by); + } + + /** + * Merges 2 *contiguous* locs into 1 + * + * @param a GenomeLoc #1 + * @param b GenomeLoc #2 + * @return one merged loc + */ + @Requires("a != null && b != null") + public static GenomeLoc merge(final T a, final T b) { + if ( isUnmapped(a) || isUnmapped(b) ) { + throw new ReviewedStingException("Tried to merge unmapped genome locs"); + } + + if ( !(a.contiguousP(b)) ) { + throw new ReviewedStingException("The two genome locs need to be contiguous"); + } + + return new GenomeLoc(a.getContig(), a.contigIndex, Math.min(a.getStart(), b.getStart()), Math.max(a.getStop(), b.getStop())); + } + + /** + * Merges a list of *sorted* *contiguous* locs into 1 + * + * @param sortedLocs a sorted list of contiguous locs + * @return one merged loc + */ + @Requires("sortedLocs != null") + public static GenomeLoc merge(final SortedSet sortedLocs) { + GenomeLoc result = null; + + for ( GenomeLoc loc : sortedLocs ) { + if ( loc.isUnmapped() ) + throw new ReviewedStingException("Tried to merge unmapped genome locs"); + + if ( result == null ) + result = loc; + else if ( !result.contiguousP(loc) ) + throw new ReviewedStingException("The genome locs need to be contiguous"); + else + result = merge(result, loc); + } + + return result; + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocComparator.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocComparator.java deleted file mode 100644 index c8380ee7b..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocComparator.java +++ /dev/null @@ -1,81 +0,0 @@ -/* -* Copyright (c) 2012 The Broad Institute -* -* 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.sting.utils; - -import com.google.java.contract.Ensures; -import com.google.java.contract.Requires; - -import java.util.Comparator; - -/** - * - * @author Mauricio Carneiro - * @since 9/28/11 - */ -public class GenomeLocComparator implements Comparator { - /** - * compares genomeLoc's contigs - * - * @param gl1 the genome loc to compare contigs - * @param gl2 the genome loc to compare contigs - * @return 0 if equal, -1 if gl2.contig is greater, 1 if gl1.contig is greater - */ - @Requires("gl2 != null") - @Ensures("result == 0 || result == 1 || result == -1") - public final int compareContigs( GenomeLoc gl1, GenomeLoc gl2 ) { - if (gl1.contigIndex == gl2.contigIndex) - return 0; - else if (gl1.contigIndex > gl2.contigIndex) - return 1; - return -1; - } - - @Requires("gl2 != null") - @Ensures("result == 0 || result == 1 || result == -1") - public int compare ( GenomeLoc gl1, GenomeLoc gl2 ) { - int result = 0; - - if ( gl1 == gl2 ) { - result = 0; - } - else if(GenomeLoc.isUnmapped(gl1)) - result = 1; - else if(GenomeLoc.isUnmapped(gl2)) - result = -1; - else { - final int cmpContig = compareContigs(gl1, gl2); - - if ( cmpContig != 0 ) { - result = cmpContig; - } else { - if ( gl1.getStart() < gl2.getStart() ) result = -1; - if ( gl1.getStart() > gl2.getStart() ) result = 1; - } - } - - return result; - } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index e70182acf..61478744d 100644 --- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -34,10 +34,8 @@ import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import org.broad.tribble.Feature; -import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; /** * Factory class for creating GenomeLocs @@ -45,6 +43,16 @@ import org.broadinstitute.variant.variantcontext.VariantContext; public final class GenomeLocParser { private static Logger logger = Logger.getLogger(GenomeLocParser.class); + /** + * How much validation should we do at runtime with this parser? + */ + public enum ValidationLevel { + /** Do the standard amount of validation */ + STANDARD, + /** Don't do any real checking at all */ + NONE + } + // -------------------------------------------------------------------------------------------------------------- // // Ugly global variable defining the optional ordering of contig elements @@ -58,120 +66,28 @@ public final class GenomeLocParser { final private SAMSequenceDictionary SINGLE_MASTER_SEQUENCE_DICTIONARY; /** - * A thread-local caching contig info + * A thread-local CachingSequenceDictionary */ - private final ThreadLocal contigInfoPerThread = - new ThreadLocal(); + private final ThreadLocal contigInfoPerThread = + new ThreadLocal() { + @Override + protected MRUCachingSAMSequenceDictionary initialValue() { + return new MRUCachingSAMSequenceDictionary(SINGLE_MASTER_SEQUENCE_DICTIONARY); + } + }; + + /** + * How much validation are we doing at runtime with this GenomeLocParser? + */ + private final ValidationLevel validationLevel; /** * @return a caching sequence dictionary appropriate for this thread */ - private CachingSequenceDictionary getContigInfo() { - if ( contigInfoPerThread.get() == null ) { - // initialize for this thread - contigInfoPerThread.set(new CachingSequenceDictionary(SINGLE_MASTER_SEQUENCE_DICTIONARY)); - } - - assert contigInfoPerThread.get() != null; - + private MRUCachingSAMSequenceDictionary getContigInfo() { return contigInfoPerThread.get(); } - /** - * A wrapper class that provides efficient last used caching for the global - * SAMSequenceDictionary underlying all of the GATK engine capabilities. - */ - private final class CachingSequenceDictionary { - final private SAMSequenceDictionary dict; - - // cache - SAMSequenceRecord lastSSR = null; - String lastContig = ""; - int lastIndex = -1; - - @Requires({"dict != null", "dict.size() > 0"}) - public CachingSequenceDictionary(SAMSequenceDictionary dict) { - this.dict = dict; - } - - @Ensures("result > 0") - public final int getNSequences() { - return dict.size(); - } - - @Requires("contig != null") - public final synchronized boolean hasContig(final String contig) { - return contig.equals(lastContig) || dict.getSequence(contig) != null; - } - - @Requires("index >= 0") - public final synchronized boolean hasContig(final int index) { - return lastIndex == index || dict.getSequence(index) != null; - } - - @Requires("contig != null") - @Ensures("result != null") - public synchronized final SAMSequenceRecord getSequence(final String contig) { - if ( isCached(contig) ) - return lastSSR; - else - return updateCache(contig, -1); - } - - @Requires("index >= 0") - @Ensures("result != null") - public synchronized final SAMSequenceRecord getSequence(final int index) { - if ( isCached(index) ) - return lastSSR; - else - return updateCache(null, index); - } - - @Requires("contig != null") - @Ensures("result >= 0") - public synchronized final int getSequenceIndex(final String contig) { - if ( ! isCached(contig) ) { - updateCache(contig, -1); - } - - return lastIndex; - } - - @Requires({"contig != null", "lastContig != null"}) - private synchronized boolean isCached(final String contig) { - return lastContig.equals(contig); - } - - @Requires({"lastIndex != -1", "index >= 0"}) - private synchronized boolean isCached(final int index) { - return lastIndex == index; - } - - /** - * The key algorithm. Given a new record, update the last used record, contig - * name, and index. - * - * @param contig - * @param index - * @return - */ - @Requires("contig != null || index >= 0") - @Ensures("result != null") - private synchronized SAMSequenceRecord updateCache(final String contig, int index ) { - SAMSequenceRecord rec = contig == null ? dict.getSequence(index) : dict.getSequence(contig); - if ( rec == null ) { - throw new ReviewedStingException("BUG: requested unknown contig=" + contig + " index=" + index); - } else { - lastSSR = rec; - lastContig = rec.getSequenceName(); - lastIndex = rec.getSequenceIndex(); - return rec; - } - } - - - } - /** * set our internal reference contig order * @param refFile the reference file @@ -181,16 +97,34 @@ public final class GenomeLocParser { this(refFile.getSequenceDictionary()); } + /** + * Create a new GenomeLocParser based on seqDictionary with the standard validation level + * @param seqDict a non-null sequence dictionary + */ public GenomeLocParser(SAMSequenceDictionary seqDict) { + this(seqDict, ValidationLevel.STANDARD); + } + + /** + * 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 + * @param validationLevel how much validation should we do of the genome locs at runtime? Purely for testing purposes + */ + protected GenomeLocParser(SAMSequenceDictionary seqDict, final ValidationLevel validationLevel) { + if (validationLevel == null) + throw new IllegalArgumentException("validation level cannot be null"); if (seqDict == null) { // we couldn't load the reference dictionary //logger.info("Failed to load reference dictionary, falling back to lexicographic order for contigs"); throw new UserException.CommandLineException("Failed to load reference dictionary"); } - SINGLE_MASTER_SEQUENCE_DICTIONARY = seqDict; - logger.debug(String.format("Prepared reference sequence contig dictionary")); - for (SAMSequenceRecord contig : seqDict.getSequences()) { - logger.debug(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength())); + this.validationLevel = validationLevel; + this.SINGLE_MASTER_SEQUENCE_DICTIONARY = seqDict; + if ( logger.isDebugEnabled() ) { + logger.debug(String.format("Prepared reference sequence contig dictionary")); + for (SAMSequenceRecord contig : seqDict.getSequences()) { + logger.debug(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength())); + } } } @@ -198,17 +132,13 @@ public final class GenomeLocParser { * Determines whether the given contig is valid with respect to the sequence dictionary * already installed in the GenomeLoc. * + * @param contig a potentially null string name for the contig * @return True if the contig is valid. False otherwise. */ - public final boolean contigIsInDictionary(String contig) { + public final boolean contigIsInDictionary(final String contig) { return contig != null && getContigInfo().hasContig(contig); } - public final boolean indexIsInDictionary(final int index) { - return index >= 0 && getContigInfo().hasContig(index); - } - - /** * get the contig's SAMSequenceRecord * @@ -249,7 +179,7 @@ public final class GenomeLocParser { * @return */ public final SAMSequenceDictionary getContigs() { - return getContigInfo().dict; + return getContigInfo().getDictionary(); } // -------------------------------------------------------------------------------------------------------------- @@ -257,14 +187,13 @@ public final class GenomeLocParser { // Low-level creation functions // // -------------------------------------------------------------------------------------------------------------- + /** - * create a genome loc, given the contig name, start, and stop + * @see #createGenomeLoc(String, int, int, int, boolean) for exact details of the creation. * - * @param contig the contig name - * @param start the starting position - * @param stop the stop position - * - * @return a new genome loc + * Note that because this function doesn't take the contig index as an argument for contig, it + * has a slight performance penalty over the version that does take the contig index. Does not + * require the created genome loc on the reference genome */ @Ensures("result != null") @ThrowEnsures({"UserException.MalformedGenomeLoc", "!isValidGenomeLoc(contig, start, stop)"}) @@ -272,24 +201,61 @@ public final class GenomeLocParser { return createGenomeLoc(contig, getContigIndex(contig), start, stop); } - public GenomeLoc createGenomeLoc(String contig, final int start, final int stop, boolean mustBeOnReference) { + /** + * @see #createGenomeLoc(String, int, int, int, boolean) for exact details of the creation. + * + * Note that because this function doesn't take the contig index as an argument for contig, it + * has a slight performance penalty over the version that does take the contig index. + */ + public GenomeLoc createGenomeLoc(final String contig, final int start, final int stop, boolean mustBeOnReference) { return createGenomeLoc(contig, getContigIndex(contig), start, stop, mustBeOnReference); } + /** + * @see #createGenomeLoc(String, int, int, int, boolean) for exact details of the creation. + * + * Doesn't require the start and stop to be on the genome + */ @ThrowEnsures({"UserException.MalformedGenomeLoc", "!isValidGenomeLoc(contig, start, stop, false)"}) public GenomeLoc createGenomeLoc(String contig, int index, final int start, final int stop) { return createGenomeLoc(contig, index, start, stop, false); } + /** + * Create a GenomeLoc on contig, starting at start and ending (inclusive) at stop. + * + * @param contig the contig name + * @param index the index into the GATK's SAMSequencingDictionary of contig (passed for efficiency to avoid the lookup) + * @param start the starting position + * @param stop the stop position of this loc, inclusive + * @param mustBeOnReference if true, this factory will throw a UserException.MalformedGenomeLoc if start or stop isn't on the contig + * + * @return a non-null GenomeLoc + */ @ThrowEnsures({"UserException.MalformedGenomeLoc", "!isValidGenomeLoc(contig, start, stop,mustBeOnReference)"}) - public GenomeLoc createGenomeLoc(String contig, int index, final int start, final int stop, boolean mustBeOnReference) { - validateGenomeLoc(contig, index, start, stop, mustBeOnReference, true); - return new GenomeLoc(contig, index, start, stop); + @Ensures("result != null") + public GenomeLoc createGenomeLoc(final String contig, int index, final int start, final int stop, boolean mustBeOnReference) { + // optimization: by interning the string we ensure that future comparisons use == not the full string comp + final String interned = validateGenomeLoc(contig, index, start, stop, mustBeOnReference); + return new GenomeLoc(interned, index, start, stop); } - public GenomeLoc createGenomeLocOnContig(final String contig, final int start, final int stop) { - GenomeLoc contigLoc = createOverEntireContig(contig); - return new GenomeLoc(contig, getContigIndex(contig), start, stop).intersect(contigLoc); + /** + * Create a new GenomeLoc, on contig, including the single position pos. + * + * Pos is not required to be on the reference + * + * @see #createGenomeLoc(String, int, int, int, boolean) for exact details of the creation. + * + * @param contig the contig name + * @param pos the start and stop of the created genome loc + * + * @return a genome loc representing a single base at the specified postion on the contig + */ + @Ensures("result != null") + @ThrowEnsures({"UserException.MalformedGenomeLoc", "!isValidGenomeLoc(contig, pos, pos, true)"}) + public GenomeLoc createGenomeLoc(final String contig, final int pos) { + return createGenomeLoc(contig, getContigIndex(contig), pos, pos); } /** @@ -306,50 +272,62 @@ public final class GenomeLocParser { * @param start the start position * @param stop the stop position * - * @return true if it's valid, false otherwise. If exceptOnError, then throws a UserException if invalid + * @return the interned contig name, an optimization that ensures that contig == the string in the sequence dictionary */ - private boolean validateGenomeLoc(String contig, int contigIndex, int start, int stop, boolean mustBeOnReference, boolean exceptOnError) { - if ( ! getContigInfo().hasContig(contig) ) - return vglHelper(exceptOnError, String.format("Unknown contig %s", contig)); + protected String validateGenomeLoc(final String contig, final int contigIndex, final int start, final int stop, final boolean mustBeOnReference) { + if ( validationLevel == ValidationLevel.NONE ) + return contig; + else { + if (stop < start) + vglHelper(String.format("The stop position %d is less than start %d in contig %s", stop, start, contig)); - if (stop < start) - return vglHelper(exceptOnError, String.format("The stop position %d is less than start %d in contig %s", stop, start, contig)); + final SAMSequenceRecord contigInfo = getContigInfo().getSequence(contig); + if ( contigInfo.getSequenceIndex() != contigIndex ) + vglHelper(String.format("The contig index %d is bad, doesn't equal the contig index %d of the contig from a string %s", + contigIndex, contigInfo.getSequenceIndex(), contig)); - if (contigIndex < 0) - return vglHelper(exceptOnError, String.format("The contig index %d is less than 0", contigIndex)); + if ( mustBeOnReference ) { + if (start < 1) + vglHelper(String.format("The start position %d is less than 1", start)); - if (contigIndex >= getContigInfo().getNSequences()) - return vglHelper(exceptOnError, String.format("The contig index %d is greater than the stored sequence count (%d)", contigIndex, getContigInfo().getNSequences())); + if (stop < 1) + vglHelper(String.format("The stop position %d is less than 1", stop)); - if ( mustBeOnReference ) { - if (start < 1) - return vglHelper(exceptOnError, String.format("The start position %d is less than 1", start)); + final int contigSize = contigInfo.getSequenceLength(); + if (start > contigSize || stop > contigSize) + vglHelper(String.format("The genome loc coordinates %d-%d exceed the contig size (%d)", start, stop, contigSize)); + } - if (stop < 1) - return vglHelper(exceptOnError, String.format("The stop position %d is less than 1", stop)); - - int contigSize = getContigInfo().getSequence(contigIndex).getSequenceLength(); - if (start > contigSize || stop > contigSize) - return vglHelper(exceptOnError, String.format("The genome loc coordinates %d-%d exceed the contig size (%d)", start, stop, contigSize)); + return contigInfo.getSequenceName(); } - - // we passed - return true; } + /** + * Would a genome loc created with the given parameters be valid w.r.t. the master sequence dictionary? + * @param contig the contig we'd use + * @param start the start position + * @param stop the stop + * @param mustBeOnReference should we require the resulting genome loc to be completely on the reference genome? + * @return true if this would produce a valid genome loc, false otherwise + */ public boolean isValidGenomeLoc(String contig, int start, int stop, boolean mustBeOnReference ) { - return validateGenomeLoc(contig, getContigIndexWithoutException(contig), start, stop, mustBeOnReference, false); - } - - public boolean isValidGenomeLoc(String contig, int start, int stop ) { - return validateGenomeLoc(contig, getContigIndexWithoutException(contig), start, stop, true, false); - } - - private boolean vglHelper(boolean exceptOnError, String msg) { - if ( exceptOnError ) - throw new UserException.MalformedGenomeLoc("Parameters to GenomeLocParser are incorrect:" + msg); - else + try { + validateGenomeLoc(contig, getContigIndexWithoutException(contig), start, stop, mustBeOnReference); + return true; + } catch ( ReviewedStingException e) { return false; + } + } + + /** + * @see #isValidGenomeLoc(String, int, int) with mustBeOnReference == true + */ + public boolean isValidGenomeLoc(String contig, int start, int stop ) { + return isValidGenomeLoc(contig, start, stop, true); + } + + private void vglHelper(final String msg) { + throw new UserException.MalformedGenomeLoc("Parameters to GenomeLocParser are incorrect:" + msg); } // -------------------------------------------------------------------------------------------------------------- @@ -421,7 +399,7 @@ public final class GenomeLocParser { */ @Requires("pos != null") @Ensures("result >= 0") - private int parsePosition(final String pos) { + protected int parsePosition(final String pos) { if(pos.indexOf('-') != -1) { throw new NumberFormatException("Position: '" + pos + "' can't contain '-'." ); } @@ -482,89 +460,34 @@ public final class GenomeLocParser { } /** - * Creates a GenomeLoc corresponding to the variant context vc. If includeSymbolicEndIfPossible - * is true, and VC is a symbolic allele the end of the created genome loc will be the value - * of the END info field key, if it exists, or vc.getEnd() if not. - * - * @param vc - * @param includeSymbolicEndIfPossible - * @return + * @see GenomeLoc.setStart */ - public GenomeLoc createGenomeLoc(final VariantContext vc, boolean includeSymbolicEndIfPossible) { - if ( includeSymbolicEndIfPossible && vc.isSymbolic() ) { - int end = vc.getAttributeAsInt(VCFConstants.END_KEY, vc.getEnd()); - return createGenomeLoc(vc.getChr(), vc.getStart(), end); - } - else - return createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd()); - } - - public GenomeLoc createGenomeLoc(final VariantContext vc) { - return createGenomeLoc(vc, false); - } - - /** - * create a new genome loc, given the contig name, and a single position. Must be on the reference - * - * @param contig the contig name - * @param pos the postion - * - * @return a genome loc representing a single base at the specified postion on the contig - */ - @Ensures("result != null") - @ThrowEnsures({"UserException.MalformedGenomeLoc", "!isValidGenomeLoc(contig, pos, pos, true)"}) - public GenomeLoc createGenomeLoc(final String contig, final int pos) { - return createGenomeLoc(contig, getContigIndex(contig), pos, pos); - } - - /** - * create a new genome loc from an existing loc, with a new start position - * Note that this function will NOT explicitly check the ending offset, in case someone wants to - * set the start of a new GenomeLoc pertaining to a read that goes off the end of the contig. - * - * @param loc the old location - * @param start a new start position - * - * @return the newly created genome loc - */ - public GenomeLoc setStart(GenomeLoc loc, int start) { + @Deprecated + public GenomeLoc setStart(final GenomeLoc loc, final int start) { return createGenomeLoc(loc.getContig(), loc.getContigIndex(), start, loc.getStop()); } /** - * create a new genome loc from an existing loc, with a new stop position - * Note that this function will NOT explicitly check the ending offset, in case someone wants to - * set the stop of a new GenomeLoc pertaining to a read that goes off the end of the contig. - * - * @param loc the old location - * @param stop a new stop position - * - * @return + * @see GenomeLoc.setStop */ - public GenomeLoc setStop(GenomeLoc loc, int stop) { + @Deprecated + public GenomeLoc setStop(final GenomeLoc loc, final int stop) { return createGenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start, stop); } /** - * return a new genome loc, with an incremented position - * - * @param loc the old location - * - * @return a new genome loc + * @see GenomeLoc.incPos */ - public GenomeLoc incPos(GenomeLoc loc) { + @Deprecated + public GenomeLoc incPos(final GenomeLoc loc) { return incPos(loc, 1); } /** - * return a new genome loc, with an incremented position - * - * @param loc the old location - * @param by how much to move the start and stop by - * - * @return a new genome loc + * @see GenomeLoc.incPos */ - public GenomeLoc incPos(GenomeLoc loc, int by) { + @Deprecated + public GenomeLoc incPos(final GenomeLoc loc, final int by) { return createGenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start + by, loc.stop + by); } @@ -575,7 +498,7 @@ public final class GenomeLocParser { */ @Requires("contigName != null") @Ensures("result != null") - public GenomeLoc createOverEntireContig(String contigName) { + public GenomeLoc createOverEntireContig(final String contigName) { SAMSequenceRecord contig = getContigInfo().getSequence(contigName); return createGenomeLoc(contigName,contig.getSequenceIndex(),1,contig.getSequenceLength(), true); } @@ -587,12 +510,12 @@ public final class GenomeLocParser { * @return The contiguous loc of up to maxBasePairs length or null if the loc is already at the start of the contig. */ @Requires({"loc != null", "maxBasePairs > 0"}) - public GenomeLoc createGenomeLocAtStart(GenomeLoc loc, int maxBasePairs) { + public GenomeLoc createGenomeLocAtStart(final GenomeLoc loc, final int maxBasePairs) { if (GenomeLoc.isUnmapped(loc)) return null; - String contigName = loc.getContig(); - SAMSequenceRecord contig = getContigInfo().getSequence(contigName); - int contigIndex = contig.getSequenceIndex(); + final String contigName = loc.getContig(); + final SAMSequenceRecord contig = getContigInfo().getSequence(contigName); + final int contigIndex = contig.getSequenceIndex(); int start = loc.getStart() - maxBasePairs; int stop = loc.getStart() - 1; @@ -611,19 +534,12 @@ public final class GenomeLocParser { * @param padding The number of base pairs to pad on either end * @return The contiguous loc of length up to the original length + 2*padding (depending on the start/end of the contig). */ - @Requires({"loc != null", "padding > 0"}) + @Requires({"loc != null", "padding >= 0"}) public GenomeLoc createPaddedGenomeLoc(final GenomeLoc loc, final int padding) { - if (GenomeLoc.isUnmapped(loc)) + if (GenomeLoc.isUnmapped(loc) || padding == 0) return loc; - final String contigName = loc.getContig(); - final SAMSequenceRecord contig = getContigInfo().getSequence(contigName); - final int contigIndex = contig.getSequenceIndex(); - final int contigLength = contig.getSequenceLength(); - - final int start = Math.max(1, loc.getStart() - padding); - final int stop = Math.min(contigLength, loc.getStop() + padding); - - return createGenomeLoc(contigName, contigIndex, start, stop, true); + else + return createGenomeLocOnContig(loc.getContig(), loc.getContigIndex(), loc.getStart() - padding, loc.getStop() + padding); } /** @@ -633,7 +549,7 @@ public final class GenomeLocParser { * @return The contiguous loc of up to maxBasePairs length or null if the loc is already at the end of the contig. */ @Requires({"loc != null", "maxBasePairs > 0"}) - public GenomeLoc createGenomeLocAtStop(GenomeLoc loc, int maxBasePairs) { + public GenomeLoc createGenomeLocAtStop(final GenomeLoc loc, final int maxBasePairs) { if (GenomeLoc.isUnmapped(loc)) return null; String contigName = loc.getContig(); @@ -651,4 +567,35 @@ public final class GenomeLocParser { return createGenomeLoc(contigName, contigIndex, start, stop, true); } + + /** + * @see #createGenomeLocOnContig(String, int, int, int) with the contig index looked up from contig + */ + public GenomeLoc createGenomeLocOnContig(final String contig, final int start, final int stop) { + return createGenomeLocOnContig(contig, getContigIndex(contig), start, stop); + } + + /** + * Create a new genome loc, bounding start and stop by the start and end of contig + * + * This function will return null if start and stop cannot be adjusted in any reasonable way + * to be on the contig. For example, if start and stop are both past the end of the contig, + * there's no way to fix this, and null will be returned. + * + * @param contig our contig + * @param start our start as an arbitrary integer (may be negative, etc) + * @param stop our stop as an arbitrary integer (may be negative, etc) + * @return a valid genome loc over contig, or null if a meaningful genome loc cannot be created + */ + public GenomeLoc createGenomeLocOnContig(final String contig, final int contigIndex, final int start, final int stop) { + final int contigLength = getContigInfo().getSequence(contigIndex).getSequenceLength(); + final int boundedStart = Math.max(1, start); + final int boundedStop = Math.min(contigLength, stop); + + if ( boundedStart > contigLength || boundedStop < 1 ) + // there's no meaningful way to create this genome loc, as the start and stop are off the contig + return null; + else + return createGenomeLoc(contig, contigIndex, boundedStart, boundedStop); + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java index efe9460cb..6e8a412c3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java @@ -37,12 +37,10 @@ import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.Serializable; import java.util.*; -public class Haplotype { - protected final byte[] bases; - protected final double[] quals; +public class Haplotype extends Allele { + private GenomeLoc genomeLocation = null; - private HashMap eventMap = null; - private boolean isRef = false; + private Map eventMap = null; private Cigar cigar; private int alignmentStartHapwrtRef; public int leftBreakPoint = 0; @@ -50,80 +48,54 @@ public class Haplotype { private Event artificialEvent = null; /** - * Create a simple consensus sequence with provided bases and a uniform quality over all bases of qual + * Main constructor * * @param bases bases - * @param qual qual + * @param isRef is reference allele? */ - public Haplotype( final byte[] bases, final int qual ) { - this.bases = bases.clone(); - quals = new double[bases.length]; - Arrays.fill(quals, (double)qual); - } - - public Haplotype( final byte[] bases, final double[] quals ) { - this.bases = bases.clone(); - this.quals = quals.clone(); + public Haplotype( final byte[] bases, final boolean isRef ) { + super(bases.clone(), isRef); } public Haplotype( final byte[] bases ) { - this(bases, 0); + this(bases, false); } protected Haplotype( final byte[] bases, final Event artificialEvent ) { - this(bases, 0); + this(bases, false); this.artificialEvent = artificialEvent; } public Haplotype( final byte[] bases, final GenomeLoc loc ) { - this(bases); + this(bases, false); this.genomeLocation = loc; } @Override public boolean equals( Object h ) { - return h instanceof Haplotype && Arrays.equals(bases, ((Haplotype) h).bases); - } - - @Override - public int hashCode() { - return Arrays.hashCode(bases); + return h instanceof Haplotype && Arrays.equals(getBases(), ((Haplotype) h).getBases()); } - public HashMap getEventMap() { + @Override + public int hashCode() { + return Arrays.hashCode(getBases()); + } + + public Map getEventMap() { return eventMap; } - public void setEventMap( final HashMap eventMap ) { + public void setEventMap( final Map eventMap ) { this.eventMap = eventMap; } - public boolean isReference() { - return isRef; - } - - public void setIsReference( boolean isRef ) { - this.isRef = isRef; - } - - public double getQualitySum() { - double s = 0; - for (int k=0; k < bases.length; k++) { - s += quals[k]; - } - return s; - } - @Override public String toString() { - return new String(bases); + return getDisplayString(); } - public double[] getQuals() { - return quals.clone(); - } public byte[] getBases() { - return bases.clone(); + return super.getBases().clone(); } public long getStartPosition() { @@ -178,19 +150,23 @@ public class Haplotype { public Haplotype insertAllele( final Allele refAllele, final Allele altAllele, final int refInsertLocation, final int genomicInsertLocation ) { // refInsertLocation is in ref haplotype offset coordinates NOT genomic coordinates final int haplotypeInsertLocation = ReadUtils.getReadCoordinateForReferenceCoordinate(alignmentStartHapwrtRef, cigar, refInsertLocation, ReadUtils.ClippingTail.RIGHT_TAIL, true); - if( haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= bases.length ) { // desired change falls inside deletion so don't bother creating a new haplotype + if( haplotypeInsertLocation == -1 || haplotypeInsertLocation + refAllele.length() >= getBases().length ) { // desired change falls inside deletion so don't bother creating a new haplotype return null; } byte[] newHaplotypeBases = new byte[]{}; - newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(bases, 0, haplotypeInsertLocation)); // bases before the variant + newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(getBases(), 0, haplotypeInsertLocation)); // bases before the variant newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, altAllele.getBases()); // the alt allele of the variant - newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(bases, haplotypeInsertLocation + refAllele.length(), bases.length)); // bases after the variant + newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(getBases(), haplotypeInsertLocation + refAllele.length(), getBases().length)); // bases after the variant return new Haplotype(newHaplotypeBases, new Event(refAllele, altAllele, genomicInsertLocation)); } public static class HaplotypeBaseComparator implements Comparator, Serializable { @Override public int compare( final Haplotype hap1, final Haplotype hap2 ) { + return compareHaplotypeBases(hap1, hap2); + } + + public static int compareHaplotypeBases(final Haplotype hap1, final Haplotype hap2) { final byte[] arr1 = hap1.getBases(); final byte[] arr2 = hap2.getBases(); // compares byte arrays using lexical ordering diff --git a/public/java/src/org/broadinstitute/sting/utils/LegacyReservoirDownsampler.java b/public/java/src/org/broadinstitute/sting/utils/LegacyReservoirDownsampler.java deleted file mode 100644 index 2d590dd80..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/LegacyReservoirDownsampler.java +++ /dev/null @@ -1,153 +0,0 @@ -/* -* Copyright (c) 2012 The Broad Institute -* -* 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.sting.utils; - -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.util.ArrayList; -import java.util.Collection; -import java.util.Iterator; - -/** - * THIS IMPLEMENTATION IS BROKEN AND WILL BE REMOVED ONCE THE DOWNSAMPLING ENGINE FORK COLLAPSES - * - * Randomly downsample from a stream of elements. This algorithm is a direct, - * naive implementation of reservoir downsampling as described in "Random Downsampling - * with a Reservoir" (Vitter 1985). At time of writing, this paper is located here: - * http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.138.784&rep=rep1&type=pdf - - * @author mhanna - * @version 0.1 - */ -public class LegacyReservoirDownsampler { - /** - * The reservoir of elements tracked by this downsampler. - */ - private final ArrayList reservoir; - - /** - * What is the maximum number of reads that can be returned in a single batch. - */ - private final int maxElements; - - /** - * Create a new downsampler with the given source iterator and given comparator. - * @param maxElements What is the maximum number of reads that can be returned in any call of this - */ - public LegacyReservoirDownsampler(final int maxElements) { - if(maxElements < 0) - throw new ReviewedStingException("Unable to work with an negative size collection of elements"); - this.reservoir = new ArrayList(maxElements); - this.maxElements = maxElements; - } - - /** - * Returns the eliminated element. - * @param element Eliminated element; null if no element has been eliminated. - * @return - */ - public T add(T element) { - if(maxElements <= 0) - return element; - else if(reservoir.size() < maxElements) { - reservoir.add(element); - return null; - } - else { - // Get a uniformly distributed int. If the chosen slot lives within the partition, replace the entry in that slot with the newest entry. - int slot = GenomeAnalysisEngine.getRandomGenerator().nextInt(maxElements); - if(slot >= 0 && slot < maxElements) { - T displaced = reservoir.get(slot); - reservoir.set(slot,element); - return displaced; - } - else - return element; - } - } - - public boolean addAll(Collection elements) { - boolean added = false; - for(T element: elements) - added |= (add(element) != null); - return added; - } - - /** - * Returns the contents of this reservoir, downsampled to the given value. Note that the return value - * @return The downsampled contents of this reservoir. - */ - public Collection getDownsampledContents() { - return reservoir; - } - - public void clear() { - reservoir.clear(); - } - - public boolean isEmpty() { - return reservoir.isEmpty(); - } - - public int size() { - return reservoir.size(); - } - - public Iterator iterator() { - return reservoir.iterator(); - } - - public boolean contains(Object o) { - return reservoir.contains(o); - } - - public boolean containsAll(Collection elements) { - return reservoir.containsAll(elements); - } - - public boolean retainAll(Collection elements) { - return reservoir.retainAll(elements); - } - - public boolean remove(Object o) { - return reservoir.remove(o); - } - - public boolean removeAll(Collection elements) { - return reservoir.removeAll(elements); - } - - public Object[] toArray() { - Object[] contents = new Object[reservoir.size()]; - reservoir.toArray(contents); - return contents; - } - - public T[] toArray(T[] array) { - return reservoir.toArray(array); - } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/MRUCachingSAMSequenceDictionary.java b/public/java/src/org/broadinstitute/sting/utils/MRUCachingSAMSequenceDictionary.java new file mode 100644 index 000000000..c11aeb730 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/MRUCachingSAMSequenceDictionary.java @@ -0,0 +1,186 @@ +/* + * Copyright (c) 2012 The Broad Institute + * + * 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.sting.utils; + +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; +import net.sf.samtools.SAMSequenceDictionary; +import net.sf.samtools.SAMSequenceRecord; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; + +/** + * A wrapper class that provides efficient most recently used caching for the global + * SAMSequenceDictionary underlying all of the GATK engine capabilities. It is essential + * that these class be as efficient as possible. It doesn't need to be thread-safe, as + * GenomeLocParser uses a thread-local variable to ensure that each thread gets its own MRU + * cache. + * + * The MRU elements are the SAMSequenceRecord, the lastContig, and the lastIndex. The + * cached value is the actual SAMSequenceRecord of the most recently accessed value from + * getSequence, along with local variables for the contig index and contig string. + */ +final class MRUCachingSAMSequenceDictionary { + /** + * Our sequence dictionary + */ + private final SAMSequenceDictionary dict; + + SAMSequenceRecord lastSSR = null; + String lastContig = ""; + int lastIndex = -1; + + /** + * Create a new MRUCachingSAMSequenceDictionary that provides information about sequences in dict + * @param dict a non-null, non-empty sequencing dictionary + */ + @Ensures("lastSSR == null") + public MRUCachingSAMSequenceDictionary(final SAMSequenceDictionary dict) { + if ( dict == null ) throw new IllegalArgumentException("Dictionary cannot be null"); + if ( dict.size() == 0 ) throw new IllegalArgumentException("Dictionary cannot have size zero"); + + this.dict = dict; + } + + /** + * Get our sequence dictionary + * @return a non-null SAMSequenceDictionary + */ + @Ensures("result != null") + public SAMSequenceDictionary getDictionary() { + return dict; + } + + /** + * Is contig present in the dictionary? Efficiently caching. + * @param contig a non-null contig we want to test + * @return true if contig is in dictionary, false otherwise + */ + @Requires("contig != null") + public final boolean hasContig(final String contig) { + return contig.equals(lastContig) || dict.getSequence(contig) != null; + } + + /** + * Is contig index present in the dictionary? Efficiently caching. + * @param contigIndex an integer offset that might map to a contig in this dictionary + * @return true if contigIndex is in dictionary, false otherwise + */ + @Requires("contigIndex >= 0") + public final boolean hasContigIndex(final int contigIndex) { + return lastIndex == contigIndex || dict.getSequence(contigIndex) != null; + } + + /** + * Same as SAMSequenceDictionary.getSequence but uses a MRU cache for efficiency + * + * @param contig the contig name we want to get the sequence record of + * @throws ReviewedStingException if contig isn't present in the dictionary + * @return the sequence record for contig + */ + @Requires("contig != null") + @Ensures("result != null") + public final SAMSequenceRecord getSequence(final String contig) { + if ( isCached(contig) ) + return lastSSR; + else + return updateCache(contig, -1); + } + + /** + * Same as SAMSequenceDictionary.getSequence but uses a MRU cache for efficiency + * + * @param index the contig index we want to get the sequence record of + * @throws ReviewedStingException if contig isn't present in the dictionary + * @return the sequence record for contig + */ + @Requires("index >= 0") + @Ensures("result != null") + public final SAMSequenceRecord getSequence(final int index) { + if ( isCached(index) ) + return lastSSR; + else + return updateCache(null, index); + } + + /** + * Same as SAMSequenceDictionary.getSequenceIndex but uses a MRU cache for efficiency + * + * @param contig the contig we want to get the sequence record of + * @throws ReviewedStingException if index isn't present in the dictionary + * @return the sequence record index for contig + */ + @Requires("contig != null") + @Ensures("result >= 0") + public final int getSequenceIndex(final String contig) { + if ( ! isCached(contig) ) { + updateCache(contig, -1); + } + + return lastIndex; + } + + /** + * Is contig the MRU cached contig? + * @param contig the contig to test + * @return true if contig is the currently cached contig, false otherwise + */ + @Requires({"contig != null"}) + protected boolean isCached(final String contig) { + return contig.equals(lastContig); + } + + /** + * Is the contig index index the MRU cached index? + * @param index the contig index to test + * @return true if contig index is the currently cached contig index, false otherwise + */ + protected boolean isCached(final int index) { + return lastIndex == index; + } + + /** + * The key algorithm. Given a new record, update the last used record, contig + * name, and index. + * + * @param contig the contig we want to look up. If null, index is used instead + * @param index the contig index we want to look up. Only used if contig is null + * @throws ReviewedStingException if index isn't present in the dictionary + * @return the SAMSequenceRecord for contig / index + */ + @Requires("contig != null || index >= 0") + @Ensures("result != null") + private SAMSequenceRecord updateCache(final String contig, int index ) { + SAMSequenceRecord rec = contig == null ? dict.getSequence(index) : dict.getSequence(contig); + if ( rec == null ) { + throw new ReviewedStingException("BUG: requested unknown contig=" + contig + " index=" + index); + } else { + lastSSR = rec; + lastContig = rec.getSequenceName(); + lastIndex = rec.getSequenceIndex(); + return rec; + } + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java index 7462416bc..0c3ed87c0 100644 --- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java @@ -634,6 +634,30 @@ public class MathUtils { return normalizeFromLog10(array, false); } + /** + * normalizes the real-space probability array. + * + * Does not assume anything about the values in the array, beyond that no elements are below 0. It's ok + * to have values in the array of > 1, or have the sum go above 0. + * + * @param array the array to be normalized + * @return a newly allocated array corresponding the normalized values in array + */ + @Requires("array != null") + @Ensures({"result != null"}) + public static double[] normalizeFromRealSpace(final double[] array) { + if ( array.length == 0 ) + return array; + + final double sum = sum(array); + final double[] normalized = new double[array.length]; + if ( sum < 0.0 ) throw new IllegalArgumentException("Values in probability array sum to a negative number " + sum); + for ( int i = 0; i < array.length; i++ ) { + normalized[i] = array[i] / sum; + } + return normalized; + } + public static int maxElementIndex(final double[] array) { return maxElementIndex(array, array.length); } diff --git a/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java b/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java index 0d6450c8f..04205350f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java +++ b/public/java/src/org/broadinstitute/sting/utils/R/RScriptExecutor.java @@ -110,15 +110,17 @@ public class RScriptExecutor { List tempFiles = new ArrayList(); try { - File tempLibDir = IOUtils.tempDir("Rlib.", ""); - tempFiles.add(tempLibDir); + File tempLibSourceDir = IOUtils.tempDir("RlibSources.", ""); + File tempLibInstallationDir = IOUtils.tempDir("Rlib.", ""); + tempFiles.add(tempLibSourceDir); + tempFiles.add(tempLibInstallationDir); - StringBuilder expression = new StringBuilder("tempLibDir = '").append(tempLibDir).append("';"); + StringBuilder expression = new StringBuilder("tempLibDir = '").append(tempLibInstallationDir).append("';"); if (this.libraries.size() > 0) { List tempLibraryPaths = new ArrayList(); for (RScriptLibrary library: this.libraries) { - File tempLibrary = library.writeTemp(); + File tempLibrary = library.writeLibrary(tempLibSourceDir); tempFiles.add(tempLibrary); tempLibraryPaths.add(tempLibrary.getAbsolutePath()); } diff --git a/public/java/src/org/broadinstitute/sting/utils/R/RScriptLibrary.java b/public/java/src/org/broadinstitute/sting/utils/R/RScriptLibrary.java index 685979d83..93110ccdc 100644 --- a/public/java/src/org/broadinstitute/sting/utils/R/RScriptLibrary.java +++ b/public/java/src/org/broadinstitute/sting/utils/R/RScriptLibrary.java @@ -57,4 +57,10 @@ public enum RScriptLibrary { public File writeTemp() { return IOUtils.writeTempResource(new Resource(getResourcePath(), RScriptLibrary.class)); } + + public File writeLibrary(File tempDir) { + File libraryFile = new File(tempDir, getLibraryName()); + IOUtils.writeResource(new Resource(getResourcePath(), RScriptLibrary.class), libraryFile); + return libraryFile; + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java index 94e073ca3..b1de89dd8 100644 --- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java @@ -29,11 +29,11 @@ import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.text.ListFileUtils; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.io.File; import java.io.FileNotFoundException; @@ -117,21 +117,43 @@ public class SampleUtils { } public static Set getSampleList(Map headers) { - return getSampleList(headers, VariantContextUtils.GenotypeMergeType.PRIORITIZE); + return getSampleList(headers, GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE); } - public static Set getSampleList(Map headers, VariantContextUtils.GenotypeMergeType mergeOption) { + public static Set getSampleList(Map headers, GATKVariantContextUtils.GenotypeMergeType mergeOption) { Set samples = new TreeSet(); for ( Map.Entry val : headers.entrySet() ) { VCFHeader header = val.getValue(); for ( String sample : header.getGenotypeSamples() ) { - samples.add(VariantContextUtils.mergedSampleName(val.getKey(), sample, mergeOption == VariantContextUtils.GenotypeMergeType.UNIQUIFY)); + samples.add(GATKVariantContextUtils.mergedSampleName(val.getKey(), sample, mergeOption == GATKVariantContextUtils.GenotypeMergeType.UNIQUIFY)); } } return samples; } + + /** + * + * @param VCF_Headers + * @return false if there are names duplication between the samples names in the VCF headers + */ + public static boolean verifyUniqueSamplesNames(Map VCF_Headers) { + Set samples = new HashSet(); + for ( Map.Entry val : VCF_Headers.entrySet() ) { + VCFHeader header = val.getValue(); + for ( String sample : header.getGenotypeSamples() ) { + if (samples.contains(sample)){ + + return false; + } + samples.add(sample); + } + } + + return true; + } + /** * Gets the sample names from all VCF rods input by the user and uniquifies them if there is overlap * (e.g. sampleX.1, sampleX.2, ...) diff --git a/public/java/src/org/broadinstitute/sting/utils/UnvalidatingGenomeLoc.java b/public/java/src/org/broadinstitute/sting/utils/UnvalidatingGenomeLoc.java new file mode 100644 index 000000000..5a611c21e --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/UnvalidatingGenomeLoc.java @@ -0,0 +1,50 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils; + +import com.google.java.contract.Requires; + +/** + * GenomeLocs are very useful objects to keep track of genomic locations and perform set operations + * with them. + * + * However, GenomeLocs are bound to strict validation through the GenomeLocParser and cannot + * be created easily for small tasks that do not require the rigors of the GenomeLocParser validation + * + * UnvalidatingGenomeLoc is a simple utility to create GenomeLocs without going through the parser. + * + * WARNING: SHOULD BE USED ONLY BY EXPERT USERS WHO KNOW WHAT THEY ARE DOING! + * + * User: carneiro + * Date: 10/16/12 + * Time: 2:07 PM + */ +public class UnvalidatingGenomeLoc extends GenomeLoc { + + public UnvalidatingGenomeLoc(String contigName, int contigIndex, int start, int stop) { + super(contigName, contigIndex, start, stop); + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java index 3f5dffa68..77f3a84c3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.utils; +import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMProgramRecord; @@ -34,7 +35,10 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.utils.text.TextFormattingUtils; +import java.math.BigInteger; import java.net.InetAddress; +import java.security.MessageDigest; +import java.security.NoSuchAlgorithmException; import java.util.*; /** @@ -236,6 +240,13 @@ public class Utils { } } + /** + * Create a new list that contains the elements of left along with elements elts + * @param left a non-null list of elements + * @param elts a varargs vector for elts to append in order to left + * @param + * @return A newly allocated linked list containing left followed by elts + */ public static List append(final List left, T ... elts) { final List l = new LinkedList(left); l.addAll(Arrays.asList(elts)); @@ -325,15 +336,6 @@ public class Utils { return str.substring(start, end+1); } - public static byte listMaxByte(List quals) { - if (quals.size() == 0) return 0; - byte m = quals.get(0); - for (byte b : quals) { - m = b > m ? b : m; - } - return m; - } - /** * Splits expressions in command args by spaces and returns the array of expressions. * Expressions may use single or double quotes to group any individual expression, but not both. @@ -396,173 +398,6 @@ public class Utils { return concatArrays(A, B); } - /** - * Returns indices of all occurrences of the specified symbol in the string - * @param s Search string - * @param ch Character to search for - * @return Indices of all occurrences of the specified symbol - */ - public static int[] indexOfAll(String s, int ch) { - int[] pos = new int[64]; - int z = 0; - - for (int i = 0; i < s.length(); i++) { - if (s.charAt(i) == ch) pos[z++] = i; - } - return reallocate(pos, z); - } - - public static int countSetBits(boolean[] array) { - int counter = 0; - for ( int i = 0; i < array.length; i++ ) { - if ( array[i] ) - counter++; - } - return counter; - } - - /** - * Returns new (reallocated) integer array of the specified size, with content - * of the original array orig copied into it. If newSize is - * less than the size of the original array, only first newSize elements will be copied. - * If new size is greater than the size of the original array, the content of the original array will be padded - * with zeros up to the new size. Finally, if new size is the same as original size, no memory reallocation - * will be performed and the original array will be returned instead. - * - * @param orig Original size. - * @param newSize New Size. - * - * @return New array with length equal to newSize. - */ - public static int[] reallocate(int[] orig, int newSize) { - if (orig.length == newSize) return orig; - int[] new_array = new int[newSize]; - int L = (newSize > orig.length ? orig.length : newSize); - for (int i = 0; i < L; i++) new_array[i] = orig[i]; - return new_array; - } - - - /** - * Returns a copy of array a, extended with additional n elements to the right (if n > 0 ) or -n elements to the - * left (if n<0), copying the values form the original array. Newly added elements are filled with value v. Note that - * if array a is being padded to the left, first (-n) elements of the returned array are v's, followed by the content of - * array a. - * @param a original array - * @param n number of (v-filled) elements to append to a on the right (n>0) or on the left (n<0) - * @param v element value - * @return the extended copy of array a with additional n elements - */ - public static byte [] extend(final byte[] a, int n, byte v) { - - byte [] newA; - - if ( n > 0 ) { - newA = Arrays.copyOf(a, a.length+n); - if ( v != 0) { // java pads with 0's for us, so there is nothing to do if v==0 - for ( int i = a.length; i < newA.length ; i++ ) newA[i] = v; - } - return newA; - } - - // we are here only if n < 0: - n = (-n); - newA = new byte[ a.length + n ]; - int i; - if ( v!= 0 ) { - i = 0; - for( ; i < n; i++ ) newA[i] = v; - } else { - i = n; - } - for ( int j = 0 ; j < a.length ; i++, j++) newA[i]=a[j]; - return newA; - } - - - /** - * Returns a copy of array a, extended with additional n elements to the right (if n > 0 ) or -n elements to the - * left (if n<0), copying the values form the original array. Newly added elements are filled with value v. Note that - * if array a is padded to the left, first (-n) elements of the returned array are v's, followed by the content of - * array a. - * @param a original array - * @param n number of (v-filled) elements to append to a on the right (n>0) or on the left (n<0) - * @param v element value - * @return the extended copy of array a with additional n elements - */ - public static short [] extend(final short[] a, int n, short v) { - - short [] newA; - - if ( n > 0 ) { - newA = Arrays.copyOf(a, a.length+n); - if ( v != 0) { // java pads with 0's for us, so there is nothing to do if v==0 - for ( int i = a.length; i < newA.length ; i++ ) newA[i] = v; - } - return newA; - } - - // we are here only if n < 0: - n = (-n); - newA = new short[ a.length + n ]; - int i; - if ( v!= 0 ) { - i = 0; - for( ; i < n; i++ ) newA[i] = v; - } else { - i = n; - } - for ( int j = 0 ; j < a.length ; i++, j++) newA[i]=a[j]; - return newA; - } - - /* TEST ME - public static void main(String[] argv) { - List l1 = new LinkedList(); - List l2 = new ArrayList(); - - l1.add(1); - l1.add(5); - l1.add(3); - l1.add(10); - l1.add(4); - l1.add(2); - l2.add(1); - l2.add(5); - l2.add(3); - l2.add(10); - l2.add(4); - l2.add(2); - - Predicate p = new Predicate() { - public boolean apply(Integer i) { - return i > 2; - } - }; - filterInPlace(p, l1); - filterInPlace(p, l2); - - for ( int i = 0 ; i < l1.size(); i++ ) System.out.print(" "+l1.get(i)); - System.out.println(); - for ( int i = 0 ; i < l2.size(); i++ ) System.out.print(" " + l2.get(i)); - System.out.println(); - - } - - */ - - /** - * a helper method. Turns a single character string into a char. - * - * @param str the string - * - * @return a char - */ - public static char stringToChar(String str) { - if (str.length() != 1) throw new IllegalArgumentException("String length must be one"); - return str.charAt(0); - } - public static > List sorted(Collection c) { return sorted(c, false); } @@ -590,18 +425,6 @@ public class Utils { return l; } - public static , V> String sortedString(Map c) { - List t = new ArrayList(c.keySet()); - Collections.sort(t); - - List pairs = new ArrayList(); - for ( T k : t ) { - pairs.add(k + "=" + c.get(k)); - } - - return "{" + join(", ", pairs) + "}"; - } - /** * Reverse a byte array of bases * @@ -650,14 +473,6 @@ public class Utils { return new String( reverse( bases.getBytes() )) ; } - public static byte[] charSeq2byteSeq(char[] seqIn) { - byte[] seqOut = new byte[seqIn.length]; - for ( int i = 0; i < seqIn.length; i++ ) { - seqOut[i] = (byte)seqIn[i]; - } - return seqOut; - } - public static boolean isFlagSet(int value, int flag) { return ((value & flag) == flag); } @@ -911,4 +726,28 @@ public class Utils { return subLists; } + /** + * @see #calcMD5(byte[]) + */ + public static String calcMD5(final String s) throws NoSuchAlgorithmException { + return calcMD5(s.getBytes()); + } + + /** + * Calculate the md5 for bytes, and return the result as a 32 character string + * + * @param bytes the bytes to calculate the md5 of + * @return the md5 of bytes, as a 32-character long string + * @throws NoSuchAlgorithmException + */ + @Ensures({"result != null", "result.length() == 32"}) + public static String calcMD5(final byte[] bytes) throws NoSuchAlgorithmException { + if ( bytes == null ) throw new IllegalArgumentException("bytes cannot be null"); + final byte[] thedigest = MessageDigest.getInstance("MD5").digest(bytes); + final BigInteger bigInt = new BigInteger(1, thedigest); + + String md5String = bigInt.toString(16); + while (md5String.length() < 32) md5String = "0" + md5String; // pad to length 32 + return md5String; + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java index 809d4867e..dd6735d89 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java @@ -25,102 +25,350 @@ package org.broadinstitute.sting.utils.activeregion; -import com.google.java.contract.Requires; +import com.google.java.contract.Ensures; +import com.google.java.contract.Invariant; +import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.HasGenomeLocation; import org.broadinstitute.sting.utils.clipping.ReadClipper; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.sam.ReadUtils; import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.List; /** - * Created by IntelliJ IDEA. + * Represents a single active region created by the Active Region Traversal for processing + * + * An active region is a single contiguous span of bases on the genome that should be operated + * on as a single unit for the active region traversal. The action may contains a list of + * reads that overlap the region (may because there may be no reads in the region). The region + * is tagged as being either active or inactive, depending on the probabilities provided by + * the isActiveProb results from the ART walker. Each region carries with it the + * exact span of the region (bases which are the core of the isActiveProbs from the walker) as + * well as an extended size, that includes the ART walker's extension size. Reads in the region + * provided by ART include all reads overlapping the extended span, not the raw span. + * * User: rpoplin * Date: 1/4/12 */ - +@Invariant({ + "extension >= 0", + "activeRegionLoc != null", + "genomeLocParser != null", + "spanIncludingReads != null", + "extendedLoc != null" +}) public class ActiveRegion implements HasGenomeLocation { + /** + * The reads included in this active region. May be empty upon creation, and expand / contract + * as reads are added or removed from this region. + */ + private final List reads = new ArrayList(); - private final ArrayList reads = new ArrayList(); + /** + * An ordered list (by genomic coordinate) of the ActivityProfileStates that went + * into this active region. May be empty, which says that no supporting states were + * provided when this region was created. + */ + private final List supportingStates; + + /** + * The raw span of this active region, not including the active region extension + */ private final GenomeLoc activeRegionLoc; - private final GenomeLoc extendedLoc; - private final int extension; - private GenomeLoc fullExtentReferenceLoc = null; - private final GenomeLocParser genomeLocParser; - public final boolean isActive; - public ActiveRegion( final GenomeLoc activeRegionLoc, final boolean isActive, final GenomeLocParser genomeLocParser, final int extension ) { + /** + * The span of this active region on the genome, including the active region extension + */ + private final GenomeLoc extendedLoc; + + /** + * The extension, in bp, of this active region. + */ + private final int extension; + + /** + * A genomeLocParser so we can create genomeLocs + */ + private final GenomeLocParser genomeLocParser; + + /** + * Does this region represent an active region (all isActiveProbs above threshold) or + * an inactive region (all isActiveProbs below threshold)? + */ + private final boolean isActive; + + /** + * The span of this active region, including the bp covered by all reads in this + * region. This union of extensionLoc and the loc of all reads in this region. + * + * Must be at least as large as extendedLoc, but may be larger when reads + * partially overlap this region. + */ + private GenomeLoc spanIncludingReads; + + /** + * Create a new ActiveRegion containing no reads + * + * @param activeRegionLoc the span of this active region + * @param supportingStates the states that went into creating this region, or null / empty if none are available. + * If not empty, must have exactly one state for each bp in activeRegionLoc + * @param isActive indicates whether this is an active region, or an inactve one + * @param genomeLocParser a non-null parser to let us create new genome locs + * @param extension the active region extension to use for this active region + */ + public ActiveRegion( final GenomeLoc activeRegionLoc, final List supportingStates, final boolean isActive, final GenomeLocParser genomeLocParser, final int extension ) { + if ( activeRegionLoc == null ) throw new IllegalArgumentException("activeRegionLoc cannot be null"); + if ( activeRegionLoc.size() == 0 ) throw new IllegalArgumentException("Active region cannot be of zero size, but got " + activeRegionLoc); + if ( genomeLocParser == null ) throw new IllegalArgumentException("genomeLocParser cannot be null"); + if ( extension < 0 ) throw new IllegalArgumentException("extension cannot be < 0 but got " + extension); + this.activeRegionLoc = activeRegionLoc; + this.supportingStates = supportingStates == null ? Collections.emptyList() : new ArrayList(supportingStates); this.isActive = isActive; this.genomeLocParser = genomeLocParser; this.extension = extension; - extendedLoc = genomeLocParser.createGenomeLocOnContig(activeRegionLoc.getContig(), activeRegionLoc.getStart() - extension, activeRegionLoc.getStop() + extension); - fullExtentReferenceLoc = extendedLoc; + this.extendedLoc = genomeLocParser.createGenomeLocOnContig(activeRegionLoc.getContig(), activeRegionLoc.getStart() - extension, activeRegionLoc.getStop() + extension); + this.spanIncludingReads = extendedLoc; + + if ( ! this.supportingStates.isEmpty() ) { + if ( this.supportingStates.size() != activeRegionLoc.size() ) + throw new IllegalArgumentException("Supporting states wasn't empty but it doesn't have exactly one state per bp in the active region: states " + this.supportingStates.size() + " vs. bp in region = " + activeRegionLoc.size()); + GenomeLoc lastStateLoc = null; + for ( final ActivityProfileState state : this.supportingStates ) { + if ( lastStateLoc != null ) { + if ( state.getLoc().getStart() != lastStateLoc.getStart() + 1 || state.getLoc().getContigIndex() != lastStateLoc.getContigIndex()) + throw new IllegalArgumentException("Supporting state has an invalid sequence: last state was " + lastStateLoc + " but next state was " + state); + } + lastStateLoc = state.getLoc(); + } + } } @Override public String toString() { - return "ActiveRegion " + activeRegionLoc.toString(); + return "ActiveRegion " + activeRegionLoc.toString() + " active?=" + isActive() + " nReads=" + reads.size() + " "; } - // add each read to the bin and extend the reference genome activeRegionLoc if needed - public void add( final GATKSAMRecord read ) { - fullExtentReferenceLoc = fullExtentReferenceLoc.union( genomeLocParser.createGenomeLoc( read ) ); - reads.add( read ); - } - - public void hardClipToActiveRegion() { - final ArrayList clippedReads = ReadClipper.hardClipToRegion( reads, extendedLoc.getStart(), extendedLoc.getStop() ); - reads.clear(); - reads.addAll(clippedReads); - } - - public ArrayList getReads() { return reads; } - - @Requires("referenceReader.isUppercasingBases()") - public byte[] getActiveRegionReference( final CachingIndexedFastaSequenceFile referenceReader ) { + /** + * See #getActiveRegionReference but with padding == 0 + */ + public byte[] getActiveRegionReference( final IndexedFastaSequenceFile referenceReader ) { return getActiveRegionReference(referenceReader, 0); } - @Requires("referenceReader.isUppercasingBases()") - public byte[] getActiveRegionReference( final CachingIndexedFastaSequenceFile referenceReader, final int padding ) { - return getReference( referenceReader, padding, extendedLoc ); + /** + * Get the reference bases from referenceReader spanned by the extended location of this active region, + * including additional padding bp on either side. If this expanded region would exceed the boundaries + * of the active region's contig, the returned result will be truncated to only include on-genome reference + * bases + * @param referenceReader the source of the reference genome bases + * @param padding the padding, in BP, we want to add to either side of this active region extended region + * @return a non-null array of bytes holding the reference bases in referenceReader + */ + @Ensures("result != null") + public byte[] getActiveRegionReference( final IndexedFastaSequenceFile referenceReader, final int padding ) { + return getReference(referenceReader, padding, extendedLoc); } - @Requires("referenceReader.isUppercasingBases()") - public byte[] getFullReference( final CachingIndexedFastaSequenceFile referenceReader ) { + /** + * See #getActiveRegionReference but using the span including regions not the extended span + */ + public byte[] getFullReference( final IndexedFastaSequenceFile referenceReader ) { return getFullReference(referenceReader, 0); } - @Requires("referenceReader.isUppercasingBases()") - public byte[] getFullReference( final CachingIndexedFastaSequenceFile referenceReader, final int padding ) { - return getReference( referenceReader, padding, fullExtentReferenceLoc ); + /** + * See #getActiveRegionReference but using the span including regions not the extended span + */ + public byte[] getFullReference( final IndexedFastaSequenceFile referenceReader, final int padding ) { + return getReference(referenceReader, padding, spanIncludingReads); } - @Requires("referenceReader.isUppercasingBases()") - private byte[] getReference( final CachingIndexedFastaSequenceFile referenceReader, final int padding, final GenomeLoc genomeLoc ) { + /** + * Get the reference bases from referenceReader spanned by the extended location of this active region, + * including additional padding bp on either side. If this expanded region would exceed the boundaries + * of the active region's contig, the returned result will be truncated to only include on-genome reference + * bases + * @param referenceReader the source of the reference genome bases + * @param padding the padding, in BP, we want to add to either side of this active region extended region + * @param genomeLoc a non-null genome loc indicating the base span of the bp we'd like to get the reference for + * @return a non-null array of bytes holding the reference bases in referenceReader + */ + @Ensures("result != null") + private byte[] getReference( final IndexedFastaSequenceFile referenceReader, final int padding, final GenomeLoc genomeLoc ) { + if ( referenceReader == null ) throw new IllegalArgumentException("referenceReader cannot be null"); + if ( padding < 0 ) throw new IllegalArgumentException("padding must be a positive integer but got " + padding); + if ( genomeLoc == null ) throw new IllegalArgumentException("genomeLoc cannot be null"); + if ( genomeLoc.size() == 0 ) throw new IllegalArgumentException("GenomeLoc must have size > 0 but got " + genomeLoc); + final byte[] reference = referenceReader.getSubsequenceAt( genomeLoc.getContig(), Math.max(1, genomeLoc.getStart() - padding), Math.min(referenceReader.getSequenceDictionary().getSequence(genomeLoc.getContig()).getSequenceLength(), genomeLoc.getStop() + padding) ).getBases(); + return reference; } + /** + * Get the raw span of this active region (excluding the extension) + * @return a non-null genome loc + */ @Override + @Ensures("result != null") public GenomeLoc getLocation() { return activeRegionLoc; } + + /** + * Get the span of this active region including the extension value + * @return a non-null GenomeLoc + */ + @Ensures("result != null") public GenomeLoc getExtendedLoc() { return extendedLoc; } - public GenomeLoc getReferenceLoc() { return fullExtentReferenceLoc; } + /** + * Get the span of this active region including the extension and the projects on the + * genome of all reads in this active region. That is, returns the bp covered by this + * region and all reads in the region. + * @return a non-null genome loc + */ + @Ensures("result != null") + public GenomeLoc getReadSpanLoc() { return spanIncludingReads; } + + /** + * Get the active profile states that went into creating this region, if possible + * @return an unmodifiable list of states that led to the creation of this region, or an empty + * list if none were provided + */ + @Ensures("result != null") + public List getSupportingStates() { + return Collections.unmodifiableList(supportingStates); + } + + /** + * Get the active region extension applied to this region + * + * The extension is >= 0 bp in size, and indicates how much padding this art walker wanted for its regions + * + * @return the size in bp of the region extension + */ + @Ensures("result >= 0") public int getExtension() { return extension; } - public int size() { return reads.size(); } - public void clearReads() { reads.clear(); } - public void remove( final GATKSAMRecord read ) { reads.remove( read ); } - public void removeAll( final ArrayList readsToRemove ) { reads.removeAll( readsToRemove ); } - public boolean equalExceptReads(final ActiveRegion other) { + /** + * Get an unmodifiable list of reads currently in this active region. + * + * The reads are sorted by their coordinate position + * + * @return an unmodifiable list of reads in this active region + */ + @Ensures("result != null") + public List getReads() { + return Collections.unmodifiableList(reads); + } + + /** + * Get the number of reads currently in this active region + * @return an integer >= 0 + */ + @Ensures("result >= 0") + public int size() { return reads.size(); } + + /** + * Add read to this active region + * + * Read must have alignment start >= than the last read currently in this active region. + * + * @throws IllegalArgumentException if read doesn't overlap the extended region of this active region + * + * @param read a non-null GATKSAMRecord + */ + @Ensures("reads.size() == old(reads.size()) + 1") + public void add( final GATKSAMRecord read ) { + if ( read == null ) throw new IllegalArgumentException("Read cannot be null"); + + final GenomeLoc readLoc = genomeLocParser.createGenomeLoc( read ); + if ( ! readOverlapsRegion(read) ) + throw new IllegalArgumentException("Read location " + readLoc + " doesn't overlap with active region extended span " + extendedLoc); + + spanIncludingReads = spanIncludingReads.union( readLoc ); + + if ( ! reads.isEmpty() ) { + final GATKSAMRecord lastRead = reads.get(size() - 1); + if ( ! lastRead.getReferenceIndex().equals(read.getReferenceIndex()) ) + throw new IllegalArgumentException("Attempting to add a read to ActiveRegion not on the same contig as other reads: lastRead " + lastRead + " attempting to add " + read); + + if ( read.getAlignmentStart() < lastRead.getAlignmentStart() ) + throw new IllegalArgumentException("Attempting to add a read to ActiveRegion out of order w.r.t. other reads: lastRead " + lastRead + " at " + lastRead.getAlignmentStart() + " attempting to add " + read + " at " + read.getAlignmentStart()); + } + + reads.add( read ); + } + + /** + * Returns true if read would overlap the extended extent of this region + * @param read the read we want to test + * @return true if read can be added to this region, false otherwise + */ + public boolean readOverlapsRegion(final GATKSAMRecord read) { + final GenomeLoc readLoc = genomeLocParser.createGenomeLoc( read ); + return readLoc.overlapsP(extendedLoc); + } + + /** + * Add all reads to this active region + * @param reads a collection of reads to add to this active region + */ + public void addAll(final Collection reads) { + if ( reads == null ) throw new IllegalArgumentException("reads cannot be null"); + for ( final GATKSAMRecord read : reads ) + add(read); + } + + /** + * Clear all of the reads currently in this active region + */ + @Ensures("size() == 0") + public void clearReads() { + spanIncludingReads = extendedLoc; + reads.clear(); + } + + /** + * Remove all of the reads in readsToRemove from this active region + * @param readsToRemove the collection of reads we want to remove + */ + public void removeAll( final Collection readsToRemove ) { + reads.removeAll(readsToRemove); + spanIncludingReads = extendedLoc; + for ( final GATKSAMRecord read : reads ) { + spanIncludingReads = spanIncludingReads.union( genomeLocParser.createGenomeLoc(read) ); + } + } + + /** + * Clips all of the reads in this active region so that none extend beyond the active region extended loc + * + * This function may change the getReadSpanLoc, as it updates the read span based on the new clipped + * read coordinates. + */ + public void hardClipToActiveRegion() { + final List clippedReads = ReadClipper.hardClipToRegion( reads, extendedLoc.getStart(), extendedLoc.getStop() ); + ReadUtils.sortReadsByCoordinate(clippedReads); + clearReads(); + addAll(clippedReads); + } + + /** + * Is this region equal to other, excluding any reads in either region in the comparison + * @param other the other active region we want to test + * @return true if this region is equal, excluding any reads and derived values, to other + */ + protected boolean equalExceptReads(final ActiveRegion other) { if ( activeRegionLoc.compareTo(other.activeRegionLoc) != 0 ) return false; - if ( isActive != other.isActive ) return false; + if ( isActive() != other.isActive()) return false; if ( genomeLocParser != other.genomeLocParser ) return false; if ( extension != other.extension ) return false; if ( extendedLoc.compareTo(other.extendedLoc) != 0 ) return false; @@ -128,17 +376,10 @@ public class ActiveRegion implements HasGenomeLocation { } /** - * A comparator class which is used to sort ActiveRegions by their start location + * Does this region represent an active region (all isActiveProbs above threshold) or + * an inactive region (all isActiveProbs below threshold)? */ - /* - public static class ActiveRegionStartLocationComparator implements Comparator { - - public ActiveRegionStartLocationComparator() {} - - @Override - public int compare(final ActiveRegion left, final ActiveRegion right) { - return left.getLocation().compareTo(right.getLocation()); - } + public boolean isActive() { + return isActive; } - */ } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegionReadState.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegionReadState.java index d9b458f51..5da88cb6d 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegionReadState.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegionReadState.java @@ -26,12 +26,11 @@ package org.broadinstitute.sting.utils.activeregion; /** - * Created with IntelliJ IDEA. + * Describes how a read relates to an assigned ActiveRegion + * * User: thibault * Date: 11/26/12 * Time: 2:35 PM - * - * Describes how a read relates to an assigned ActiveRegion */ public enum ActiveRegionReadState { PRIMARY, // This is the read's primary region diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java index 909d99424..ff4673717 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java @@ -25,15 +25,12 @@ package org.broadinstitute.sting.utils.activeregion; +import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; -import java.util.ArrayList; -import java.util.Collections; -import java.util.List; +import java.util.*; /** * Class holding information about per-base activity scores for the @@ -43,34 +40,30 @@ import java.util.List; * @since Date created */ public class ActivityProfile { - final GenomeLocParser parser; - final boolean presetRegions; - GenomeLoc regionStartLoc = null; - GenomeLoc regionStopLoc = null; - final List isActiveList; - private static final int FILTER_SIZE = 80; - private static final double[] GaussianKernel; + private final static int MAX_PROB_PROPOGATION_DISTANCE = 50; + protected final static double ACTIVE_PROB_THRESHOLD = 0.002; // TODO: needs to be set-able by the walker author - static { - GaussianKernel = new double[2*FILTER_SIZE + 1]; - for( int iii = 0; iii < 2*FILTER_SIZE + 1; iii++ ) { - GaussianKernel[iii] = MathUtils.NormalDistribution(FILTER_SIZE, 55.0, iii); - } - } + protected final List stateList; + protected final GenomeLocParser parser; - // todo -- add upfront the start and stop of the intervals - // todo -- check that no regions are unexpectedly missing - // todo -- add unit tests - // TODO -- own preset regions - public ActivityProfile(final GenomeLocParser parser, final boolean presetRegions) { - this(parser, presetRegions, new ArrayList(), null); - } + protected GenomeLoc regionStartLoc = null; + protected GenomeLoc regionStopLoc = null; + + /** + * A cached value of the regionStartLoc contig length, to make calls to + * getCurrentContigLength efficient + */ + protected int contigLength = -1; + + /** + * Create a new empty ActivityProfile + * @param parser the parser we can use to create genome locs, cannot be null + */ + public ActivityProfile(final GenomeLocParser parser) { + if ( parser == null ) throw new IllegalArgumentException("parser cannot be null"); - protected ActivityProfile(final GenomeLocParser parser, final boolean presetRegions, final List isActiveList, final GenomeLoc regionStartLoc) { this.parser = parser; - this.presetRegions = presetRegions; - this.isActiveList = isActiveList; - this.regionStartLoc = regionStartLoc; + this.stateList = new ArrayList(); } @Override @@ -82,149 +75,419 @@ public class ActivityProfile { } /** - * Add the next ActivityProfileResult to this profile. + * How far away can probability mass be moved around in this profile? + * + * This distance puts an upper limit on how far, in bp, we will ever propagate probability max around + * when adding a new ActivityProfileState. For example, if the value of this function is + * 10, and you are looking at a state at bp 5, and we know that no states beyond 5 + 10 will have + * their probability propagated back to that state. + * + * @return a positive integer distance in bp + */ + @Ensures("result >= 0") + public int getMaxProbPropagationDistance() { + return MAX_PROB_PROPOGATION_DISTANCE; + } + + /** + * How many profile results are in this profile? + * @return the number of profile results + */ + @Ensures("result >= 0") + public int size() { + return stateList.size(); + } + + /** + * Is this profile empty? + * @return true if the profile is empty + */ + @Ensures("isEmpty() == (size() == 0)") + public boolean isEmpty() { + return stateList.isEmpty(); + } + + /** + * Get the span of this activity profile, which is from the start of the first state to the stop of the last + * @return a potentially null GenomeLoc. Will be null if this profile is empty + */ + public GenomeLoc getSpan() { + return isEmpty() ? null : regionStartLoc.endpointSpan(regionStopLoc); + } + + @Requires("! isEmpty()") + public int getContigIndex() { + return regionStartLoc.getContigIndex(); + } + + @Requires("! isEmpty()") + public int getStop() { + return regionStopLoc.getStop(); + } + + /** + * Get the list of active profile results in this object + * @return a non-null, ordered list of active profile results + */ + @Ensures("result != null") + protected List getStateList() { + return stateList; + } + + /** + * Get the probabilities of the states as a single linear array of doubles + * @return a non-null array + */ + @Ensures("result != null") + protected double[] getProbabilitiesAsArray() { + final double[] probs = new double[getStateList().size()]; + int i = 0; + for ( final ActivityProfileState state : getStateList() ) + probs[i++] = state.isActiveProb; + return probs; + } + + /** + * Helper function that gets the genome loc for a site offset from relativeLoc, protecting ourselves from + * falling off the edge of the contig. + * + * @param relativeLoc the location offset is relative to + * @param offset the offset from relativeLoc where we'd like to create a GenomeLoc + * @return a genome loc with relativeLoc.start + offset, if this is on the contig, null otherwise + */ + @Requires("relativeLoc != null") + protected GenomeLoc getLocForOffset(final GenomeLoc relativeLoc, final int offset) { + final int start = relativeLoc.getStart() + offset; + if ( start < 0 || start > getCurrentContigLength() ) { + return null; + } else { + return parser.createGenomeLoc(regionStartLoc.getContig(), regionStartLoc.getContigIndex(), start, start); + } + } + + /** + * Get the length of the current contig + * @return the length in bp + */ + @Requires("regionStartLoc != null") + @Ensures("result > 0") + private int getCurrentContigLength() { + return contigLength; + } + + // -------------------------------------------------------------------------------- + // + // routines to add states to a profile + // + // -------------------------------------------------------------------------------- + + /** + * Add the next ActivityProfileState to this profile. * * Must be contiguous with the previously added result, or an IllegalArgumentException will be thrown * - * @param result a well-formed ActivityProfileResult result to incorporate into this profile + * @param state a well-formed ActivityProfileState result to incorporate into this profile */ - @Requires("result != null") - public void add(final ActivityProfileResult result) { - final GenomeLoc loc = result.getLoc(); + @Requires("state != null") + public void add(final ActivityProfileState state) { + final GenomeLoc loc = state.getLoc(); if ( regionStartLoc == null ) { regionStartLoc = loc; regionStopLoc = loc; + contigLength = parser.getContigInfo(regionStartLoc.getContig()).getSequenceLength(); } else { if ( regionStopLoc.getStart() != loc.getStart() - 1 ) throw new IllegalArgumentException("Bad add call to ActivityProfile: loc " + loc + " not immediate after last loc " + regionStopLoc ); regionStopLoc = loc; } - isActiveList.add(result); - } - - public int size() { - return isActiveList.size(); - } - - public boolean isEmpty() { - return isActiveList.isEmpty(); - } - - public boolean hasPresetRegions() { - return presetRegions; + final Collection processedStates = processState(state); + for ( final ActivityProfileState processedState : processedStates ) { + incorporateSingleState(processedState); + } } /** - * Band pass this ActivityProfile, producing a new profile that's band pass filtered - * @return a new ActivityProfile that's the band-pass filtered version of this profile + * Incorporate a single activity profile state into the current list of states + * + * If state's position occurs immediately after the last position in this profile, then + * the state is appended to the state list. If it's within the existing states list, + * the prob of stateToAdd is added to its corresponding state in the list. If the + * position would be before the start of this profile, stateToAdd is simply ignored. + * + * @param stateToAdd the state we want to add to the states list */ - public ActivityProfile bandPassFilter() { - final double[] activeProbArray = new double[isActiveList.size()]; - int iii = 0; - for( final ActivityProfileResult result : isActiveList ) { - activeProbArray[iii++] = result.isActiveProb; - } - iii = 0; - for( final ActivityProfileResult result : isActiveList ) { - if( result.resultState.equals(ActivityProfileResult.ActivityProfileResultState.HIGH_QUALITY_SOFT_CLIPS) ) { // special code to deal with the problem that high quality soft clipped bases aren't added to pileups - final int numHQClips = result.resultValue.intValue(); - for( int jjj = Math.max(0, iii - numHQClips); jjj < Math.min(activeProbArray.length, iii+numHQClips); jjj++ ) { - activeProbArray[jjj] = Math.max(activeProbArray[jjj], activeProbArray[iii]); - } - } - iii++; - } + @Requires("stateToAdd != null") + private void incorporateSingleState(final ActivityProfileState stateToAdd) { + final int position = stateToAdd.getOffset(regionStartLoc); - final double[] filteredProbArray; - if( !presetRegions ) { - // if we aren't using preset regions, actually apply the band pass filter for activeProbArray into filteredProbArray - filteredProbArray = new double[activeProbArray.length]; - for( iii = 0; iii < activeProbArray.length; iii++ ) { - final double[] kernel = ArrayUtils.subarray(GaussianKernel, Math.max(FILTER_SIZE-iii, 0), Math.min(GaussianKernel.length,FILTER_SIZE + activeProbArray.length - iii)); - final double[] activeProbSubArray = ArrayUtils.subarray(activeProbArray, Math.max(0,iii - FILTER_SIZE), Math.min(activeProbArray.length,iii + FILTER_SIZE + 1)); - filteredProbArray[iii] = MathUtils.dotProduct(activeProbSubArray, kernel); + if ( position > size() ) + // should we allow this? probably not + throw new IllegalArgumentException("Must add state contiguous to existing states"); + + if ( position >= 0 ) { + // ignore states starting before this regions start + if ( position < size() ) { + stateList.get(position).isActiveProb += stateToAdd.isActiveProb; + } else { + if ( position != size() ) throw new IllegalStateException("position == size but it wasn't"); + stateList.add(stateToAdd); } + } + } + + /** + * Process justAddedState, returning a collection of derived states that actually be added to the stateList + * + * The purpose of this function is to transform justAddedStates, if needed, into a series of atomic states + * that we actually want to track. For example, if state is for soft clips, we transform that single + * state into a list of states that surround the state up to the distance of the soft clip. + * + * Can be overridden by subclasses to transform states in any way + * + * There's no particular contract for the output states, except that they can never refer to states + * beyond the current end of the stateList unless the explictly include preceding states before + * the reference. So for example if the current state list is [1, 2, 3] this function could return + * [1,2,3,4,5] but not [1,2,3,5]. + * + * @param justAddedState the state our client provided to use to add to the list + * @return a list of derived states that should actually be added to this profile's state list + */ + protected Collection processState(final ActivityProfileState justAddedState) { + if ( justAddedState.resultState.equals(ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS) ) { + // special code to deal with the problem that high quality soft clipped bases aren't added to pileups + final List states = new LinkedList(); + // add no more than the max prob propagation distance num HQ clips + final int numHQClips = Math.min(justAddedState.resultValue.intValue(), getMaxProbPropagationDistance()); + for( int jjj = - numHQClips; jjj <= numHQClips; jjj++ ) { + final GenomeLoc loc = getLocForOffset(justAddedState.getLoc(), jjj); + if ( loc != null ) + states.add(new ActivityProfileState(loc, justAddedState.isActiveProb)); + } + + return states; } else { - // otherwise we simply use the activeProbArray directly - filteredProbArray = activeProbArray; + return Collections.singletonList(justAddedState); } - - iii = 0; - for( final double prob : filteredProbArray ) { - final ActivityProfileResult result = isActiveList.get(iii++); - result.isActiveProb = prob; - result.resultState = ActivityProfileResult.ActivityProfileResultState.NONE; - result.resultValue = null; - } - - return new ActivityProfile(parser, presetRegions, isActiveList, regionStartLoc); } - /** - * Partition this profile into active regions - * @param activeRegionExtension the amount of margin overlap in the active region - * @return the list of active regions - */ - public List createActiveRegions( final int activeRegionExtension, final int maxRegionSize ) { - final double ACTIVE_PROB_THRESHOLD = 0.002; // TODO: needs to be set-able by the walker author - final ArrayList returnList = new ArrayList(); + // -------------------------------------------------------------------------------- + // + // routines to get active regions from the profile + // + // -------------------------------------------------------------------------------- - if( isActiveList.size() == 0 ) { - // no elements in the active list, just return an empty one - return Collections.emptyList(); - } else if( isActiveList.size() == 1 ) { - // there's a single element, it's either active or inactive - boolean isActive = isActiveList.get(0).isActiveProb > ACTIVE_PROB_THRESHOLD; - returnList.addAll(createActiveRegion(isActive, 0, 0, activeRegionExtension, maxRegionSize)); - } else { - // there are 2+ elements, divide these up into regions - boolean isActive = isActiveList.get(0).isActiveProb > ACTIVE_PROB_THRESHOLD; - int curStart = 0; - for(int iii = 1; iii < isActiveList.size(); iii++ ) { - final boolean thisStatus = isActiveList.get(iii).isActiveProb > ACTIVE_PROB_THRESHOLD; - if( isActive != thisStatus ) { - returnList.addAll(createActiveRegion(isActive, curStart, iii - 1, activeRegionExtension, maxRegionSize)); - isActive = thisStatus; - curStart = iii; - } + /** + * Get the next completed active regions from this profile, and remove all states supporting them from this profile + * + * Takes the current profile and finds all of the active / inactive from the start of the profile that are + * ready. By ready we mean unable to have their probability modified any longer by future additions to the + * profile. The regions that are popped off the profile take their states with them, so the start of this + * profile will always be after the end of the last region returned here. + * + * The regions are returned sorted by genomic position. + * + * This function may not return anything in the list, if no regions are ready + * + * No returned region will be larger than maxRegionSize. + * + * @param activeRegionExtension the extension value to provide to the constructed regions + * @param minRegionSize the minimum region size, in the case where we have to cut up regions that are too large + * @param maxRegionSize the maximize size of the returned region + * @param forceConversion if true, we'll return a region whose end isn't sufficiently far from the end of the + * stateList. Used to close out the active region when we've hit some kind of end (such + * as the end of the contig) + * @return a non-null list of active regions + */ + @Ensures("result != null") + public List popReadyActiveRegions(final int activeRegionExtension, final int minRegionSize, final int maxRegionSize, final boolean forceConversion) { + if ( activeRegionExtension < 0 ) throw new IllegalArgumentException("activeRegionExtension must be >= 0 but got " + activeRegionExtension); + if ( minRegionSize < 1 ) throw new IllegalArgumentException("minRegionSize must be >= 1 but got " + minRegionSize); + if ( maxRegionSize < 1 ) throw new IllegalArgumentException("maxRegionSize must be >= 1 but got " + maxRegionSize); + + final LinkedList regions = new LinkedList(); + + while ( true ) { + final ActiveRegion nextRegion = popNextReadyActiveRegion(activeRegionExtension, minRegionSize, maxRegionSize, forceConversion); + if ( nextRegion == null ) + return regions; + else { + regions.add(nextRegion); } - returnList.addAll(createActiveRegion(isActive, curStart, isActiveList.size() - 1, activeRegionExtension, maxRegionSize)); // close out the current active region } - return returnList; } /** - * Helper routine to create an active region based on our current start and end offsets - * @param isActive should the region be active? - * @param curStart offset (0-based) from the start of this region - * @param curEnd offset (0-based) from the start of this region - * @param activeRegionExtension the amount of margin overlap in the active region - * @return a fully initialized ActiveRegion with the above properties + * Helper function for popReadyActiveRegions that pops the first ready region off the front of this profile + * + * If a region is returned, modifies the state of this profile so that states used to make the region are + * no longer part of the profile. Associated information (like the region start position) of this profile + * are also updated. + * + * @param activeRegionExtension the extension value to provide to the constructed regions + * @param minRegionSize the minimum region size, in the case where we have to cut up regions that are too large + * @param maxRegionSize the maximize size of the returned region + * @param forceConversion if true, we'll return a region whose end isn't sufficiently far from the end of the + * stateList. Used to close out the active region when we've hit some kind of end (such + * as the end of the contig) + * @return a fully formed active region, or null if none can be made */ - private final List createActiveRegion(final boolean isActive, final int curStart, final int curEnd, final int activeRegionExtension, final int maxRegionSize) { - return createActiveRegion(isActive, curStart, curEnd, activeRegionExtension, maxRegionSize, new ArrayList()); + private ActiveRegion popNextReadyActiveRegion(final int activeRegionExtension, final int minRegionSize, final int maxRegionSize, final boolean forceConversion) { + if ( stateList.isEmpty() ) + return null; + + final ActivityProfileState first = stateList.get(0); + final boolean isActiveRegion = first.isActiveProb > ACTIVE_PROB_THRESHOLD; + final int offsetOfNextRegionEnd = findEndOfRegion(isActiveRegion, minRegionSize, maxRegionSize, forceConversion); + if ( offsetOfNextRegionEnd == -1 ) + // couldn't find a valid ending offset, so we return null + return null; + + // we need to create the active region, and clip out the states we're extracting from this profile + final List sub = stateList.subList(0, offsetOfNextRegionEnd + 1); + final List supportingStates = new ArrayList(sub); + sub.clear(); + + // update the start and stop locations as necessary + if ( stateList.isEmpty() ) { + regionStartLoc = regionStopLoc = null; + } else { + regionStartLoc = stateList.get(0).getLoc(); + } + final GenomeLoc regionLoc = parser.createGenomeLoc(first.getLoc().getContig(), first.getLoc().getStart(), first.getLoc().getStart() + offsetOfNextRegionEnd); + return new ActiveRegion(regionLoc, supportingStates, isActiveRegion, parser, activeRegionExtension); } - private final List createActiveRegion(final boolean isActive, final int curStart, final int curEnd, final int activeRegionExtension, final int maxRegionSize, final List returnList) { - if( !isActive || curEnd - curStart < maxRegionSize ) { - final GenomeLoc loc = parser.createGenomeLoc(regionStartLoc.getContig(), regionStartLoc.getStart() + curStart, regionStartLoc.getStart() + curEnd); - returnList.add(new ActiveRegion(loc, isActive, parser, activeRegionExtension)); - return returnList; + /** + * Find the end of the current region, returning the index into the element isActive element, or -1 if the region isn't done + * + * The current region is defined from the start of the stateList, looking for elements that have the same isActiveRegion + * flag (i.e., if isActiveRegion is true we are looking for states with isActiveProb > threshold, or alternatively + * for states < threshold). The maximize size of the returned region is maxRegionSize. If forceConversion is + * true, then we'll return the region end even if this isn't safely beyond the max prob propagation distance. + * + * Note that if isActiveRegion is true, and we can construct a active region > maxRegionSize in bp, we + * find the further local minimum within that max region, and cut the region there, under the constraint + * that the resulting region must be at least minRegionSize in bp. + * + * @param isActiveRegion is the region we're looking for an active region or inactive region? + * @param minRegionSize the minimum region size, in the case where we have to cut up regions that are too large + * @param maxRegionSize the maximize size of the returned region + * @param forceConversion if true, we'll return a region whose end isn't sufficiently far from the end of the + * stateList. Used to close out the active region when we've hit some kind of end (such + * as the end of the contig) + * @return the index into stateList of the last element of this region, or -1 if it cannot be found + */ + @Ensures({ + "result >= -1", + "result == -1 || result < maxRegionSize", + "! (result == -1 && forceConversion)"}) + private int findEndOfRegion(final boolean isActiveRegion, final int minRegionSize, final int maxRegionSize, final boolean forceConversion) { + if ( ! forceConversion && stateList.size() < maxRegionSize + getMaxProbPropagationDistance() ) { + // we really haven't finalized at the probability mass that might affect our decision, so keep + // waiting until we do before we try to make any decisions + return -1; } - // find the best place to break up the large active region - Double minProb = Double.MAX_VALUE; - int cutPoint = -1; - final int size = curEnd - curStart + 1; - for( int iii = curStart + (int)(size*0.15); iii < curEnd - (int)(size*0.15); iii++ ) { - if( isActiveList.get(iii).isActiveProb < minProb ) { minProb = isActiveList.get(iii).isActiveProb; cutPoint = iii; } + int endOfActiveRegion = findFirstActivityBoundary(isActiveRegion, maxRegionSize); + + if ( isActiveRegion && endOfActiveRegion == maxRegionSize ) + // we've run to the end of the region, let's find a good place to cut + endOfActiveRegion = findBestCutSite(endOfActiveRegion, minRegionSize); + + // we're one past the end, so i must be decremented + return endOfActiveRegion - 1; + } + + /** + * Find the the local minimum within 0 - endOfActiveRegion where we should divide region + * + * This algorithm finds the global minimum probability state within the region [minRegionSize, endOfActiveRegion) + * (exclusive of endOfActiveRegion), and returns the state index of that state. + * that it + * + * @param endOfActiveRegion the last state of the current active region (exclusive) + * @param minRegionSize the minimum of the left-most region, after cutting + * @return the index of state after the cut site (just like endOfActiveRegion) + */ + @Requires({"endOfActiveRegion >= minRegionSize", "minRegionSize >= 0"}) + @Ensures({"result >= minRegionSize", "result <= endOfActiveRegion"}) + private int findBestCutSite(final int endOfActiveRegion, final int minRegionSize) { + int minI = endOfActiveRegion - 1; + double minP = Double.MAX_VALUE; + + for ( int i = minI; i >= minRegionSize - 1; i-- ) { + double cur = getProb(i); + if ( cur < minP && isMinimum(i) ) { + minP = cur; + minI = i; + } + } + + return minI + 1; + } + + /** + * Find the first index into the state list where the state is considered ! isActiveRegion + * + * Note that each state has a probability of being active, and this function thresholds that + * value on ACTIVE_PROB_THRESHOLD, coloring each state as active or inactive. Finds the + * largest contiguous stretch of states starting at the first state (index 0) with the same isActive + * state as isActiveRegion. If the entire state list has the same isActive value, then returns + * maxRegionSize + * + * @param isActiveRegion are we looking for a stretch of active states, or inactive ones? + * @param maxRegionSize don't look for a boundary that would yield a region of size > maxRegionSize + * @return the index of the first state in the state list with isActive value != isActiveRegion, or maxRegionSize + * if no such element exists + */ + @Requires({"maxRegionSize > 0"}) + @Ensures({"result >= 0", "result <= stateList.size()"}) + private int findFirstActivityBoundary(final boolean isActiveRegion, final int maxRegionSize) { + final int nStates = stateList.size(); + int endOfActiveRegion = 0; + + while ( endOfActiveRegion < nStates && endOfActiveRegion < maxRegionSize ) { + if ( getProb(endOfActiveRegion) > ACTIVE_PROB_THRESHOLD != isActiveRegion ) { + break; + } + endOfActiveRegion++; + } + + return endOfActiveRegion; + } + + /** + * Helper function to get the probability of the state at offset index + * @param index a valid offset into the state list + * @return the isActiveProb of the state at index + */ + @Requires({"index >= 0", "index < stateList.size()"}) + private double getProb(final int index) { + return stateList.get(index).isActiveProb; + } + + /** + * Is the probability at index in a local minimum? + * + * Checks that the probability at index is <= both the probabilities to either side. + * Returns false if index is at the end or the start of the state list. + * + * @param index the index of the state we want to test + * @return true if prob at state is a minimum, false otherwise + */ + @Requires({"index >= 0", "index < stateList.size()"}) + private boolean isMinimum(final int index) { + if ( index == stateList.size() - 1 ) + // we cannot be at a minimum if the current position is the last in the state list + return false; + else if ( index < 1 ) + // we cannot be at a minimum if the current position is the first or second + return false; + else { + final double indexP = getProb(index); + return indexP <= getProb(index+1) && indexP < getProb(index-1); } - final List leftList = createActiveRegion(isActive, curStart, cutPoint, activeRegionExtension, maxRegionSize, new ArrayList()); - final List rightList = createActiveRegion(isActive, cutPoint+1, curEnd, activeRegionExtension, maxRegionSize, new ArrayList()); - returnList.addAll( leftList ); - returnList.addAll( rightList ); - return returnList; } } diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileResult.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileState.java similarity index 62% rename from public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileResult.java rename to public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileState.java index bf2636465..309405be0 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileResult.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfileState.java @@ -30,44 +30,50 @@ import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.GenomeLoc; /** - * Created with IntelliJ IDEA. + * The state of an active region walker's isActive call at a specific locus in the genome + * * User: rpoplin * Date: 7/27/12 */ -public class ActivityProfileResult { - private GenomeLoc loc; +public class ActivityProfileState { + final private GenomeLoc loc; public double isActiveProb; - public ActivityProfileResultState resultState; + public Type resultState; public Number resultValue; - public enum ActivityProfileResultState { + public enum Type { NONE, HIGH_QUALITY_SOFT_CLIPS } /** - * Create a new ActivityProfileResult at loc with probability of being active of isActiveProb + * Create a new ActivityProfileState at loc with probability of being active of isActiveProb * * @param loc the position of the result profile (for debugging purposes) * @param isActiveProb the probability of being active (between 0 and 1) */ @Requires({"loc != null", "isActiveProb >= 0.0 && isActiveProb <= 1.0"}) - public ActivityProfileResult( final GenomeLoc loc, final double isActiveProb ) { - this(loc, isActiveProb, ActivityProfileResultState.NONE, null); + public ActivityProfileState(final GenomeLoc loc, final double isActiveProb) { + this(loc, isActiveProb, Type.NONE, null); } /** - * Create a new ActivityProfileResult at loc with probability of being active of isActiveProb that maintains some - * information about the result state and value (TODO RYAN -- what do these mean?) + * Create a new ActivityProfileState at loc with probability of being active of isActiveProb that maintains some + * information about the result state and value + * + * The only state value in use is HIGH_QUALITY_SOFT_CLIPS, and here the value is interpreted as the number + * of bp affected by the soft clips. * * @param loc the position of the result profile (for debugging purposes) * @param isActiveProb the probability of being active (between 0 and 1) */ @Requires({"loc != null", "isActiveProb >= 0.0 && isActiveProb <= 1.0"}) - public ActivityProfileResult( final GenomeLoc loc, final double isActiveProb, final ActivityProfileResultState resultState, final Number resultValue ) { + public ActivityProfileState(final GenomeLoc loc, final double isActiveProb, final Type resultState, final Number resultValue) { // make sure the location of that activity profile is 1 if ( loc.size() != 1 ) - throw new IllegalArgumentException("Location for an ActivityProfileResult must have to size 1 bp but saw " + loc); + throw new IllegalArgumentException("Location for an ActivityProfileState must have to size 1 bp but saw " + loc); + if ( resultValue != null && resultValue.doubleValue() < 0 ) + throw new IllegalArgumentException("Result value isn't null and its < 0, which is illegal: " + resultValue); this.loc = loc; this.isActiveProb = isActiveProb; @@ -76,7 +82,17 @@ public class ActivityProfileResult { } /** - * Get the genome loc associated with the ActivityProfileResult + * The offset of state w.r.t. our current region's start location + * @param regionStartLoc the start of the region, as a genome loc + * @return the position of this profile relative to the start of this region + */ + public int getOffset(final GenomeLoc regionStartLoc) { + return getLoc().getStart() - regionStartLoc.getStart(); + } + + + /** + * Get the genome loc associated with the ActivityProfileState * @return the location of this result */ @Ensures("result != null") @@ -86,7 +102,7 @@ public class ActivityProfileResult { @Override public String toString() { - return "ActivityProfileResult{" + + return "ActivityProfileState{" + "loc=" + loc + ", isActiveProb=" + isActiveProb + ", resultState=" + resultState + diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java new file mode 100644 index 000000000..abbc74df4 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfile.java @@ -0,0 +1,179 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.activeregion; + +import com.google.java.contract.Ensures; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.MathUtils; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.LinkedList; + +/** + * A band pass filtering version of the activity profile + * + * Applies a band pass filter with a Gaussian kernel to the input state probabilities to smooth + * them out of an interval + * + * @author Mark DePristo + * @since 2011 + */ +public class BandPassActivityProfile extends ActivityProfile { + public static final int MAX_FILTER_SIZE = 50; + private final static double MIN_PROB_TO_KEEP_IN_FILTER = 1e-5; + public static final double DEFAULT_SIGMA = 17.0; + + private final int filterSize; + private final double sigma; + private final double[] GaussianKernel; + + /** + * Create a new BandPassActivityProfile with default sigma and file sizes + * @param parser our genome loc parser + */ + public BandPassActivityProfile(final GenomeLocParser parser) { + this(parser, MAX_FILTER_SIZE, DEFAULT_SIGMA, true); + } + + /** + * Create an activity profile that implements a band pass filter on the states + * @param parser our genome loc parser + * @param maxFilterSize the maximum size of the band pass filter we are allowed to create, regardless of sigma + * @param sigma the variance of the Gaussian kernel for this band pass filter + */ + public BandPassActivityProfile(final GenomeLocParser parser, final int maxFilterSize, final double sigma) { + this(parser, maxFilterSize, sigma, true); + } + + public BandPassActivityProfile(final GenomeLocParser parser, final int maxFilterSize, final double sigma, final boolean adaptiveFilterSize) { + super(parser); + + if ( sigma < 0 ) throw new IllegalArgumentException("Sigma must be greater than or equal to 0 but got " + sigma); + + // setup the Gaussian kernel for the band pass filter + this.sigma = sigma; + final double[] fullKernel = makeKernel(maxFilterSize, sigma); + this.filterSize = adaptiveFilterSize ? determineFilterSize(fullKernel, MIN_PROB_TO_KEEP_IN_FILTER) : maxFilterSize; + this.GaussianKernel = makeKernel(this.filterSize, sigma); + } + + protected static int determineFilterSize(final double[] kernel, final double minProbToKeepInFilter) { + final int middle = (kernel.length - 1) / 2; + int filterEnd = middle; + while ( filterEnd > 0 ) { + if ( kernel[filterEnd - 1] < minProbToKeepInFilter ) { + break; + } + filterEnd--; + } + return middle - filterEnd; + } + + protected static double[] makeKernel(final int filterSize, final double sigma) { + final int bandSize = 2 * filterSize + 1; + final double[] kernel = new double[bandSize]; + for( int iii = 0; iii < bandSize; iii++ ) { + kernel[iii] = MathUtils.NormalDistribution(filterSize, sigma, iii); + } + return MathUtils.normalizeFromRealSpace(kernel); + } + + /** + * Our maximize propagation distance is whatever our parent's is, plus our filter size + * + * Stops the profile from interpreting sites that aren't yet fully determined due to + * propagation of the probabilities. + * + * @return the distance in bp we might move our probabilities around for some site i + */ + @Override + public int getMaxProbPropagationDistance() { + return super.getMaxProbPropagationDistance() + filterSize; + } + + /** + * Get the size (in bp) of the band pass filter + * @return a positive integer + */ + @Ensures("result >= 1") + public int getBandSize() { + return 2 * filterSize + 1; + } + + /** + * Get the filter size (which is the size of each wing of the band, minus the center point) + * @return a positive integer + */ + @Ensures("result >= 0") + public int getFilteredSize() { + return filterSize; + } + + /** + * Get the Gaussian kernel sigma value + * @return a positive double + */ + @Ensures("result >= 0") + public double getSigma() { + return sigma; + } + + /** + * Get the kernel of this band pass filter. Do not modify returned result + * @return the kernel used in this band pass filter + */ + @Ensures({"result != null", "result.length == getBandSize()"}) + protected double[] getKernel() { + return GaussianKernel; + } + + /** + * Band pass the probabilities in the ActivityProfile, producing a new profile that's band pass filtered + * @return a new double[] that's the band-pass filtered version of this profile + */ + @Override + protected Collection processState(final ActivityProfileState justAddedState) { + final Collection states = new LinkedList(); + + for ( final ActivityProfileState superState : super.processState(justAddedState) ) { + if ( superState.isActiveProb > 0.0 ) { + for( int jjj = -filterSize; jjj <= filterSize; jjj++ ) { + final GenomeLoc loc = getLocForOffset(justAddedState.getLoc(), jjj); + if ( loc != null ) { + final double newProb = superState.isActiveProb * GaussianKernel[jjj + filterSize]; + states.add(new ActivityProfileState(loc, newProb)); + } + } + } else { + states.add(justAddedState); + } + } + + return states; + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java index 8c7bce6ac..73e129105 100644 --- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java +++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java @@ -673,7 +673,9 @@ public class BAQ { } else if ( excludeReadFromBAQ(read) ) { ; // just fall through } else { - if ( calculationType == CalculationMode.RECALCULATE || ! hasBAQTag(read) ) { + final boolean readHasBAQTag = hasBAQTag(read); + + if ( calculationType == CalculationMode.RECALCULATE || ! readHasBAQTag ) { if ( DEBUG ) System.out.printf(" Calculating BAQ on the fly%n"); BAQCalculationResult hmmResult = calcBAQFromHMM(read, refReader); if ( hmmResult != null ) { @@ -683,6 +685,9 @@ public class BAQ { case DONT_MODIFY: BAQQuals = hmmResult.bq; break; default: throw new ReviewedStingException("BUG: unexpected qmode " + qmode); } + } else if ( readHasBAQTag ) { + // remove the BAQ tag if it's there because we cannot trust it + read.setAttribute(BAQ_TAG, null); } } else if ( qmode == QualityMode.OVERWRITE_QUALS ) { // only makes sense if we are overwriting quals if ( DEBUG ) System.out.printf(" Taking BAQ from tag%n"); diff --git a/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java index 524c29d64..45dd55af7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java @@ -362,8 +362,8 @@ public class ReadClipper { return GATKSAMRecord.emptyRead(read); } - public static ArrayList hardClipToRegion( final ArrayList reads, final int refStart, final int refStop ) { - final ArrayList returnList = new ArrayList( reads.size() ); + public static List hardClipToRegion( final List reads, final int refStart, final int refStop ) { + final List returnList = new ArrayList( reads.size() ); for( final GATKSAMRecord read : reads ) { final GATKSAMRecord clippedRead = hardClipToRegion( read, refStart, refStop ); if( !clippedRead.isEmpty() ) { @@ -381,9 +381,9 @@ public class ReadClipper { * @return a new read without adaptor sequence */ private GATKSAMRecord hardClipAdaptorSequence () { - final Integer adaptorBoundary = ReadUtils.getAdaptorBoundary(read); + final int adaptorBoundary = ReadUtils.getAdaptorBoundary(read); - if (adaptorBoundary == null || !ReadUtils.isInsideRead(read, adaptorBoundary)) + if (adaptorBoundary == ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY || !ReadUtils.isInsideRead(read, adaptorBoundary)) return read; return read.getReadNegativeStrandFlag() ? hardClipByReferenceCoordinatesLeftTail(adaptorBoundary) : hardClipByReferenceCoordinatesRightTail(adaptorBoundary); diff --git a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java index 39f5b06c6..c78294505 100644 --- a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.duplicates; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index 268ac6ca1..08d5882b1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -28,7 +28,6 @@ package org.broadinstitute.sting.utils.exceptions; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMSequenceDictionary; -import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; @@ -50,6 +49,11 @@ import java.io.File; groupName = "User exceptions", summary = "Exceptions caused by incorrect user behavior, such as bad files, bad arguments, etc." ) public class UserException extends ReviewedStingException { + /** + * 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 UserException(String msg) { super(msg); } public UserException(String msg, Throwable e) { super(msg, e); } private UserException(Throwable e) { super("", e); } // cannot be called, private access @@ -407,7 +411,7 @@ public class UserException extends ReviewedStingException { public UnreadableKeyException ( File f, Exception e ) { super(String.format("Key file %s cannot be read (possibly the key file is corrupt?). Error was: %s. " + "Please see %s for help.", - f.getAbsolutePath(), getMessage(e), GATKRunReport.PHONE_HOME_DOCS_URL)); + f.getAbsolutePath(), getMessage(e), PHONE_HOME_DOCS_URL)); } public UnreadableKeyException ( String message, Exception e ) { @@ -417,7 +421,7 @@ public class UserException extends ReviewedStingException { public UnreadableKeyException ( String message ) { super(String.format("Key file cannot be read (possibly the key file is corrupt?): %s. " + "Please see %s for help.", - message, GATKRunReport.PHONE_HOME_DOCS_URL)); + message, PHONE_HOME_DOCS_URL)); } } @@ -426,7 +430,7 @@ public class UserException extends ReviewedStingException { super(String.format("The signature in key file %s failed cryptographic verification. " + "If this key was valid in the past, it's likely been revoked. " + "Please see %s for help.", - f.getAbsolutePath(), GATKRunReport.PHONE_HOME_DOCS_URL)); + f.getAbsolutePath(), PHONE_HOME_DOCS_URL)); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java index 3d43d5d4d..c30ac4f7f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java +++ b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java @@ -33,6 +33,7 @@ import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.util.StringUtil; import org.apache.log4j.Priority; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.BaseUtils; import java.io.File; import java.io.FileNotFoundException; @@ -41,9 +42,10 @@ import java.util.Arrays; /** * A caching version of the IndexedFastaSequenceFile that avoids going to disk as often as the raw indexer. * - * Thread-safe! Uses a thread-local cache + * Thread-safe! Uses a thread-local cache. * - * Automatically upper-cases the bases coming in, unless they the flag preserveCase is explicitly set + * Automatically upper-cases the bases coming in, unless the flag preserveCase is explicitly set. + * Automatically converts IUPAC bases to Ns, unless the flag preserveIUPAC is explicitly set. */ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { protected static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(CachingIndexedFastaSequenceFile.class); @@ -64,10 +66,15 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { private final long cacheMissBackup; /** - * If true, we will preserve the case of the original base in the genome, not + * If true, we will preserve the case of the original base in the genome */ private final boolean preserveCase; + /** + * If true, we will preserve the IUPAC bases in the genome + */ + private final boolean preserveIUPAC; + // information about checking efficiency long cacheHits = 0; long cacheMisses = 0; @@ -97,13 +104,15 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { * @param index the index of the fasta file, used for efficient random access * @param cacheSize the size in bp of the cache we will use for this reader * @param preserveCase If true, we will keep the case of the underlying bases in the FASTA, otherwise everything is converted to upper case + * @param preserveIUPAC If true, we will keep the IUPAC bases in the FASTA, otherwise they are converted to Ns */ - public CachingIndexedFastaSequenceFile(final File fasta, final FastaSequenceIndex index, final long cacheSize, final boolean preserveCase) { + public CachingIndexedFastaSequenceFile(final File fasta, final FastaSequenceIndex index, final long cacheSize, final boolean preserveCase, final boolean preserveIUPAC) { super(fasta, index); if ( cacheSize < 0 ) throw new IllegalArgumentException("cacheSize must be > 0"); this.cacheSize = cacheSize; this.cacheMissBackup = Math.max(cacheSize / 1000, 1); this.preserveCase = preserveCase; + this.preserveIUPAC = preserveIUPAC; } /** @@ -116,25 +125,15 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { * @param cacheSize the size of the cache to use in this CachingIndexedFastaReader, must be >= 0 * @param preserveCase If true, we will keep the case of the underlying bases in the FASTA, otherwise everything is converted to upper case */ - public CachingIndexedFastaSequenceFile(final File fasta, final long cacheSize, final boolean preserveCase ) throws FileNotFoundException { + public CachingIndexedFastaSequenceFile(final File fasta, final long cacheSize, final boolean preserveCase, final boolean preserveIUPAC) throws FileNotFoundException { super(fasta); if ( cacheSize < 0 ) throw new IllegalArgumentException("cacheSize must be > 0"); this.cacheSize = cacheSize; this.cacheMissBackup = Math.max(cacheSize / 1000, 1); this.preserveCase = preserveCase; + this.preserveIUPAC = preserveIUPAC; } -// /** -// * Open the given indexed fasta sequence file. Throw an exception if the file cannot be opened. -// * -// * @param fasta The file to open. -// * @param index Pre-built FastaSequenceIndex, for the case in which one does not exist on disk. -// * @throws java.io.FileNotFoundException If the fasta or any of its supporting files cannot be found. -// */ -// public CachingIndexedFastaSequenceFile(final File fasta, final FastaSequenceIndex index) { -// this(fasta, index, DEFAULT_CACHE_SIZE); -// } - /** * Same as general constructor but allows one to override the default cacheSize * @@ -145,7 +144,7 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { * @param cacheSize the size in bp of the cache we will use for this reader */ public CachingIndexedFastaSequenceFile(final File fasta, final FastaSequenceIndex index, final long cacheSize) { - this(fasta, index, cacheSize, false); + this(fasta, index, cacheSize, false, false); } /** @@ -169,7 +168,7 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { * @param preserveCase If true, we will keep the case of the underlying bases in the FASTA, otherwise everything is converted to upper case */ public CachingIndexedFastaSequenceFile(final File fasta, final boolean preserveCase) throws FileNotFoundException { - this(fasta, DEFAULT_CACHE_SIZE, preserveCase); + this(fasta, DEFAULT_CACHE_SIZE, preserveCase, false); } /** @@ -182,7 +181,7 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { * @param cacheSize the size of the cache to use in this CachingIndexedFastaReader, must be >= 0 */ public CachingIndexedFastaSequenceFile(final File fasta, final long cacheSize ) throws FileNotFoundException { - this(fasta, cacheSize, false); + this(fasta, cacheSize, false, false); } /** @@ -240,6 +239,15 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { return ! isPreservingCase(); } + /** + * Is this CachingIndexedFastaReader keeping the IUPAC bases in the fasta, or is it turning them into Ns? + * + * @return true if the IUPAC bases coming from this reader are not modified + */ + public boolean isPreservingIUPAC() { + return preserveIUPAC; + } + /** * Gets the subsequence of the contig in the range [start,stop] * @@ -253,7 +261,7 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { * all of the bases in the ReferenceSequence returned by this method will be upper cased. */ @Override - public ReferenceSequence getSubsequenceAt( final String contig, final long start, final long stop ) { + public ReferenceSequence getSubsequenceAt( final String contig, long start, final long stop ) { final ReferenceSequence result; final Cache myCache = cache.get(); @@ -261,8 +269,9 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { cacheMisses++; result = super.getSubsequenceAt(contig, start, stop); if ( ! preserveCase ) StringUtil.toUpperCase(result.getBases()); + if ( ! preserveIUPAC ) BaseUtils.convertIUPACtoN(result.getBases(), true, start < 1); } else { - // todo -- potential optimization is to check if contig.name == contig, as this in generally will be true + // todo -- potential optimization is to check if contig.name == contig, as this in general will be true SAMSequenceRecord contigInfo = super.getSequenceDictionary().getSequence(contig); if (stop > contigInfo.getSequenceLength()) @@ -276,6 +285,7 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { // convert all of the bases in the sequence to upper case if we aren't preserving cases if ( ! preserveCase ) StringUtil.toUpperCase(myCache.seq.getBases()); + if ( ! preserveIUPAC ) BaseUtils.convertIUPACtoN(myCache.seq.getBases(), true, myCache.start == 0); } else { cacheHits++; } diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java index febc62716..ceae4bb47 100644 --- a/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.genotyper; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; public enum DiploidGenotype { AA ('A', 'A'), diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java new file mode 100644 index 000000000..9cfa20b8f --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java @@ -0,0 +1,198 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.genotyper; + + +import com.google.java.contract.Ensures; +import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.variant.variantcontext.Allele; + +import java.io.PrintStream; +import java.util.*; + +/** + * Wrapper class that holds a set of maps of the form (Read -> Map(Allele->Double)) + * For each read, this holds underlying alleles represented by an aligned read, and corresponding relative likelihood. + */ +public class PerReadAlleleLikelihoodMap { + + + public static final double INFORMATIVE_LIKELIHOOD_THRESHOLD = 0.2; + + protected List alleles; + protected Map> likelihoodReadMap; + + public PerReadAlleleLikelihoodMap() { + likelihoodReadMap = new LinkedHashMap>(); + alleles = new ArrayList(); + } + + /** + * Adds a read, allele and corresponding likelihood to map + * @param read SAM record to add + * @param a corresponding allele + * @param likelihood corresponding likelihood + */ + public void add(GATKSAMRecord read, Allele a, Double likelihood) { + Map likelihoodMap; + if (likelihoodReadMap.containsKey(read)){ + // seen pileup element before + likelihoodMap = likelihoodReadMap.get(read); + } + else { + likelihoodMap = new HashMap(); + likelihoodReadMap.put(read,likelihoodMap); + } + likelihoodMap.put(a,likelihood); + + if (!alleles.contains(a)) + alleles.add(a); + + } + + public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { + return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log); + } + + public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) { + // special case removal of all or no reads + if ( downsamplingFraction <= 0.0 ) + return; + if ( downsamplingFraction >= 1.0 ) { + likelihoodReadMap.clear(); + return; + } + + // start by stratifying the reads by the alleles they represent at this position + final Map> alleleReadMap = new HashMap>(alleles.size()); + for ( Allele allele : alleles ) + alleleReadMap.put(allele, new ArrayList()); + + for ( Map.Entry> entry : likelihoodReadMap.entrySet() ) { + // do not remove reduced reads! + if ( !entry.getKey().isReducedRead() ) { + final Allele bestAllele = getMostLikelyAllele(entry.getValue()); + if ( bestAllele != Allele.NO_CALL ) + alleleReadMap.get(bestAllele).add(entry.getKey()); + } + } + + // compute the reads to remove and actually remove them + final List readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log); + for ( final GATKSAMRecord read : readsToRemove ) + likelihoodReadMap.remove(read); + } + + @Ensures("result >=0") + public int size() { + return likelihoodReadMap.size(); + } + + /** + * Helper function to add the read underneath a pileup element to the map + * @param p Pileup element + * @param a Corresponding allele + * @param likelihood Allele likelihood + */ + public void add(PileupElement p, Allele a, Double likelihood) { + if (p==null || p.getRead()==null || a == null ) + throw new IllegalArgumentException("Invalid parameters passed to PerReadAlleleLikelihoodMap.add"); + add(p.getRead(), a, likelihood); + } + + /** + * Does the current map contain the key associated with a particular SAM record in pileup? + * @param p Pileup element + * @return + */ + public boolean containsPileupElement(PileupElement p) { + if (p==null ) + throw new IllegalArgumentException("Invalid pileup element"); + + return likelihoodReadMap.containsKey(p.getRead()); + } + + public boolean isEmpty() { + return likelihoodReadMap.isEmpty(); + } + + public Map> getLikelihoodReadMap() { + return likelihoodReadMap; + } + public void clear() { + alleles.clear(); + likelihoodReadMap.clear(); + } + + public Set getStoredElements() { + return likelihoodReadMap.keySet(); + } + + public Collection> getLikelihoodMapValues() { + return likelihoodReadMap.values(); + } + + public int getNumberOfStoredElements() { + return likelihoodReadMap.size(); + } + + public Map getLikelihoodsAssociatedWithPileupElement(PileupElement p) { + if (!likelihoodReadMap.containsKey(p.getRead())) + return null; + + return likelihoodReadMap.get(p.getRead()); + } + + + /** + * For a given alleleMap, return most likely allele, i.e. the one with highest associated likelihood + * @param alleleMap Underlying allele map + * @return Most likely allele. If all alleles are equally likely, returns a no-call allele. + */ + @Ensures("result != null") + public static Allele getMostLikelyAllele( final Map alleleMap ) { + double maxLike = Double.NEGATIVE_INFINITY; + double prevMaxLike = Double.NEGATIVE_INFINITY; + Allele mostLikelyAllele = Allele.NO_CALL; + + if (alleleMap==null) + throw new IllegalArgumentException("alleleMap in getMostLikelyAllele() method can't be null"); + + for (final Map.Entry el : alleleMap.entrySet()) { + if (el.getValue() > maxLike) { + prevMaxLike = maxLike; + maxLike = el.getValue(); + mostLikelyAllele = el.getKey(); + } else if( el.getValue() > prevMaxLike ) { + prevMaxLike = el.getValue(); + } + } + return (maxLike - prevMaxLike > INFORMATIVE_LIKELIHOOD_THRESHOLD ? mostLikelyAllele : Allele.NO_CALL ); + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java index c647a7b80..7374dda14 100644 --- a/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java @@ -32,6 +32,7 @@ import net.sf.picard.util.IntervalList; import net.sf.samtools.SAMFileHeader; import org.apache.log4j.Logger; import org.broad.tribble.Feature; +import org.broadinstitute.sting.commandline.IntervalArgumentCollection; import org.broadinstitute.sting.commandline.IntervalBinding; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; import org.broadinstitute.sting.utils.GenomeLoc; @@ -534,6 +535,47 @@ public class IntervalUtils { } } + public static GenomeLocSortedSet parseIntervalArguments(final ReferenceDataSource referenceDataSource, IntervalArgumentCollection argCollection) { + GenomeLocSortedSet intervals = null; + + // return if no interval arguments at all + if ( argCollection.intervals == null && argCollection.excludeIntervals == null ) + return intervals; + + // Note that the use of '-L all' is no longer supported. + + // if include argument isn't given, create new set of all possible intervals + + final Pair includeExcludePair = IntervalUtils.parseIntervalBindingsPair( + referenceDataSource, + argCollection.intervals, + argCollection.intervalSetRule, argCollection.intervalMerging, argCollection.intervalPadding, + argCollection.excludeIntervals); + + final GenomeLocSortedSet includeSortedSet = includeExcludePair.getFirst(); + final GenomeLocSortedSet excludeSortedSet = includeExcludePair.getSecond(); + + // if no exclude arguments, can return parseIntervalArguments directly + if ( excludeSortedSet == null ) + intervals = includeSortedSet; + + // otherwise there are exclude arguments => must merge include and exclude GenomeLocSortedSets + else { + intervals = includeSortedSet.subtractRegions(excludeSortedSet); + + // logging messages only printed when exclude (-XL) arguments are given + final long toPruneSize = includeSortedSet.coveredSize(); + final long toExcludeSize = excludeSortedSet.coveredSize(); + final long intervalSize = intervals.coveredSize(); + logger.info(String.format("Initial include intervals span %d loci; exclude intervals span %d loci", toPruneSize, toExcludeSize)); + logger.info(String.format("Excluding %d loci from original intervals (%.2f%% reduction)", + toPruneSize - intervalSize, (toPruneSize - intervalSize) / (0.01 * toPruneSize))); + } + + logger.info(String.format("Processing %d bp from intervals", intervals.coveredSize())); + return intervals; + } + public static Pair parseIntervalBindingsPair( final ReferenceDataSource referenceDataSource, final List> intervals, diff --git a/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java b/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java index c25ecb49b..59466dad3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/io/IOUtils.java @@ -359,19 +359,9 @@ public class IOUtils { */ public static void writeResource(Resource resource, File file) { String path = resource.getPath(); - Class clazz = resource.getRelativeClass(); - InputStream inputStream = null; + InputStream inputStream = resource.getResourceContentsAsStream(); OutputStream outputStream = null; try { - if (clazz == null) { - inputStream = ClassLoader.getSystemResourceAsStream(path); - if (inputStream == null) - throw new IllegalArgumentException("Resource not found: " + path); - } else { - inputStream = clazz.getResourceAsStream(path); - if (inputStream == null) - throw new IllegalArgumentException("Resource not found relative to " + clazz + ": " + path); - } outputStream = FileUtils.openOutputStream(file); org.apache.commons.io.IOUtils.copy(inputStream, outputStream); } catch (IOException e) { diff --git a/public/java/src/org/broadinstitute/sting/utils/io/Resource.java b/public/java/src/org/broadinstitute/sting/utils/io/Resource.java index 1f181a826..85ca5ce1c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/io/Resource.java +++ b/public/java/src/org/broadinstitute/sting/utils/io/Resource.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.utils.io; import java.io.File; +import java.io.InputStream; /** * Stores a resource by path and a relative class. @@ -64,4 +65,27 @@ public class Resource { File.separator, path); } + + /** + * Get the contents of this resource as an InputStream + * @throws IllegalArgumentException if resource cannot be read + * @return an input stream that will read the contents of this resource + */ + public InputStream getResourceContentsAsStream() { + final Class clazz = getRelativeClass(); + + final InputStream inputStream; + if (clazz == null) { + inputStream = ClassLoader.getSystemResourceAsStream(path); + if (inputStream == null) + throw new IllegalArgumentException("Resource not found: " + path); + } else { + inputStream = clazz.getResourceAsStream(path); + if (inputStream == null) + throw new IllegalArgumentException("Resource not found relative to " + clazz + ": " + path); + + } + + return inputStream; + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java index 32e56866b..c4b566582 100644 --- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java +++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; @@ -113,6 +113,16 @@ public class AlignmentStateMachine { return read; } + /** + * Get the reference index of the underlying read + * + * @return the reference index of the read + */ + @Ensures("result == getRead().getReferenceIndex()") + public int getReferenceIndex() { + return getRead().getReferenceIndex(); + } + /** * Is this the left edge state? I.e., one that is before or after the current read? * @return true if this state is an edge state, false otherwise diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSDownsamplingInfo.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSDownsamplingInfo.java index fc282163e..c7875354f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSDownsamplingInfo.java +++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSDownsamplingInfo.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java index 0985ed196..8069ea29f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java +++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; @@ -63,6 +63,8 @@ public class LIBSPerformance extends CommandLineProgram { @Argument(fullName = "L", shortName = "L", doc = "Query location", required = false) public String location = null; + @Argument(fullName = "dt", shortName = "dt", doc = "Enable downsampling", required = false) + public boolean downsample = false; @Override public int execute() throws IOException { @@ -86,7 +88,7 @@ public class LIBSPerformance extends CommandLineProgram { for ( final SAMReadGroupRecord rg : reader.getFileHeader().getReadGroups() ) samples.add(rg.getSample()); - final LIBSDownsamplingInfo ds = new LIBSDownsamplingInfo(false, -1); + final LIBSDownsamplingInfo ds = new LIBSDownsamplingInfo(downsample, 250); final LocusIteratorByState libs = new LocusIteratorByState( diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java index f830dcb30..1243b2893 100644 --- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java @@ -1,3 +1,28 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; import net.sf.samtools.util.CloseableIterator; @@ -9,11 +34,6 @@ import java.util.Iterator; * Iterator that traverses a SAM File, accumulating information on a per-locus basis */ public abstract class LocusIterator implements Iterable, CloseableIterator { - // ----------------------------------------------------------------------------------------------------------------- - // - // constructors and other basic operations - // - // ----------------------------------------------------------------------------------------------------------------- public Iterator iterator() { return this; } @@ -25,9 +45,15 @@ public abstract class LocusIterator implements Iterable, Close public abstract boolean hasNext(); public abstract AlignmentContext next(); - // TODO -- remove me when ART testing is done + /** + * Get, if possible, the underlying LocusIteratorByState from this LocusIterator. + * + * @throws UnsupportedOperationException if we don't support this operation + * + * @return a non-null locus iterator by state + */ public LocusIteratorByState getLIBS() { - return null; + throw new UnsupportedOperationException("This locus iterator does not support getting the underlying LocusIteratorByState"); } public void remove() { diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java index 01c9e564e..435f9901a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java +++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java @@ -34,8 +34,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.downsampling.DownsampleType; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; @@ -66,7 +65,7 @@ import java.util.*; * occurs, if requested. This allows users of LIBS to see both a ReadBackedPileup view of the data as well as * a stream of unique, sorted reads */ -public class LocusIteratorByState extends LocusIterator { +public final class LocusIteratorByState extends LocusIterator { /** * our log, which we want to capture anything from this class */ @@ -234,17 +233,16 @@ public class LocusIteratorByState extends LocusIterator { final GenomeLoc location = getLocation(); final Map fullPileup = new HashMap(); - // TODO: How can you determine here whether the current pileup has been downsampled? - boolean hasBeenSampled = false; - - for (final String sample : samples) { - final Iterator iterator = readStates.iterator(sample); - final List pile = new ArrayList(readStates.size(sample)); + for (final Map.Entry sampleStatePair : readStates ) { + final String sample = sampleStatePair.getKey(); + final PerSampleReadStateManager readState = sampleStatePair.getValue(); + final Iterator iterator = readState.iterator(); + final List pile = new ArrayList(readState.size()); while (iterator.hasNext()) { // state object with the read/offset information final AlignmentStateMachine state = iterator.next(); - final GATKSAMRecord read = (GATKSAMRecord) state.getRead(); + final GATKSAMRecord read = state.getRead(); final CigarOperator op = state.getCigarOperator(); if (op == CigarOperator.N) // N's are never added to any pileup @@ -263,29 +261,9 @@ public class LocusIteratorByState extends LocusIterator { fullPileup.put(sample, new ReadBackedPileupImpl(location, pile)); } - updateReadStates(); // critical - must be called after we get the current state offsets and location + readStates.updateReadStates(); // critical - must be called after we get the current state offsets and location if (!fullPileup.isEmpty()) // if we got reads with non-D/N over the current position, we are done - nextAlignmentContext = new AlignmentContext(location, new ReadBackedPileupImpl(location, fullPileup), hasBeenSampled); - } - } - - /** - * Advances all fo the read states by one bp. After this call the read states are reflective - * of the next pileup. - */ - private void updateReadStates() { - for (final String sample : samples) { - Iterator it = readStates.iterator(sample); - while (it.hasNext()) { - AlignmentStateMachine state = it.next(); - CigarOperator op = state.stepForwardOnGenome(); - if (op == null) { - // we discard the read only when we are past its end AND indel at the end of the read (if any) was - // already processed. Keeping the read state that returned null upon stepForwardOnGenome() is safe - // as the next call to stepForwardOnGenome() will return null again AND will clear hadIndel() flag. - it.remove(); // we've stepped off the end of the object - } - } + nextAlignmentContext = new AlignmentContext(location, new ReadBackedPileupImpl(location, fullPileup), false); } } @@ -350,7 +328,7 @@ public class LocusIteratorByState extends LocusIterator { * @return true if the read should be excluded from the pileup, false otherwise */ @Requires({"rec != null", "pos > 0"}) - private boolean dontIncludeReadInPileup(GATKSAMRecord rec, long pos) { + private boolean dontIncludeReadInPileup(final GATKSAMRecord rec, final long pos) { return ReadUtils.isBaseInsideAdaptor(rec, pos); } diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManager.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManager.java new file mode 100644 index 000000000..2caaf9d27 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManager.java @@ -0,0 +1,261 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; + +import com.google.java.contract.Ensures; +import com.google.java.contract.Invariant; +import com.google.java.contract.Requires; +import net.sf.samtools.CigarOperator; +import org.apache.log4j.Logger; +import org.broadinstitute.sting.gatk.downsampling.Downsampler; +import org.broadinstitute.sting.gatk.downsampling.LevelingDownsampler; + +import java.util.Iterator; +import java.util.LinkedList; +import java.util.List; + +/** + * ReadStateManager for a single sample + * + * User: depristo + * Date: 1/13/13 + * Time: 12:28 PM + */ +@Invariant({ + "readStartsAreWellOrdered()", + "! isDownsampling() || downsamplingTarget > 0", + "nSites >= 0", + "nSitesNeedingDownsampling >= 0", + "nSitesNeedingDownsampling <= nSites" +}) +final class PerSampleReadStateManager implements Iterable { + private final static Logger logger = Logger.getLogger(ReadStateManager.class); + private final static boolean CAPTURE_DOWNSAMPLING_STATS = false; + + /** + * A list (potentially empty) of alignment state machines. + * + * The state machines must be ordered by the alignment start of their underlying reads, with the + * lowest alignment starts on the left, and the largest on the right + */ + private LinkedList readStatesByAlignmentStart = new LinkedList(); + + private final Downsampler> levelingDownsampler; + private final int downsamplingTarget; + + /** + * The number of sites where downsampling has been invoked + */ + private int nSitesNeedingDownsampling = 0; + + /** + * The number of sites we've visited + */ + private int nSites = 0; + + /** + * Create a new PerSampleReadStateManager with downsampling parameters as requested by LIBSDownsamplingInfo + * @param LIBSDownsamplingInfo the downsampling params we want to use + */ + public PerSampleReadStateManager(final LIBSDownsamplingInfo LIBSDownsamplingInfo) { + this.downsamplingTarget = LIBSDownsamplingInfo.isPerformDownsampling() ? LIBSDownsamplingInfo.getToCoverage() : -1; + this.levelingDownsampler = LIBSDownsamplingInfo.isPerformDownsampling() + ? new LevelingDownsampler, AlignmentStateMachine>(LIBSDownsamplingInfo.getToCoverage()) + : null; + } + + /** + * Group the underlying readStatesByAlignmentStart into a list of list of alignment state machines, + * where each list contains machines with a unique genome site. The outer list is ordered + * by alignment start. + * + * For example, if the flat list has alignment starts [10, 10, 11, 12, 12, 13] then + * the resulting grouping will be [[10, 10], [11], [12, 12], [13]]. + * + * @return a non-null list of lists + */ + @Ensures("result != null") + private List> groupByAlignmentStart() { + final LinkedList> grouped = new LinkedList>(); + + AlignmentStateMachine last = null; + for ( final AlignmentStateMachine stateMachine : readStatesByAlignmentStart ) { + if ( last == null || stateMachine.getGenomeOffset() != last.getGenomeOffset() ) { + // we've advanced to a place where the state machine has a different state, + // so start a new list + grouped.add(new LinkedList()); + last = stateMachine; + } + grouped.getLast().add(stateMachine); + } + + return grouped; + } + + /** + * Flattens the grouped list of list of alignment state machines into a single list in order + * @return a non-null list contains the state machines + */ + @Ensures("result != null") + private LinkedList flattenByAlignmentStart(final List> grouped) { + final LinkedList flat = new LinkedList(); + for ( final List l : grouped ) + flat.addAll(l); + return flat; + } + + /** + * Test that the reads are ordered by their alignment starts + * @return true if well ordered, false otherwise + */ + private boolean readStartsAreWellOrdered() { + int lastStart = -1; + for ( final AlignmentStateMachine machine : readStatesByAlignmentStart ) { + if ( lastStart > machine.getRead().getAlignmentStart() ) + return false; + lastStart = machine.getRead().getAlignmentStart(); + } + return true; + } + + /** + * Assumes it can just keep the states linked lists without making a copy + * @param states the new states to add to this manager + * @return The change in the number of states, after including states and potentially downsampling. Note + * that this return result might be negative, if downsampling is enabled, as we might drop + * more sites than have been added by the downsampler + */ + @Requires("states != null") + public int addStatesAtNextAlignmentStart(final LinkedList states) { + if ( states.isEmpty() ) { + return 0; + } + + readStatesByAlignmentStart.addAll(states); + int nStatesAdded = states.size(); + + if ( isDownsampling() && readStatesByAlignmentStart.size() > downsamplingTarget ) { + // only go into the downsampling branch if we are downsampling and the coverage > the target + captureDownsamplingStats(); + levelingDownsampler.submit(groupByAlignmentStart()); + levelingDownsampler.signalEndOfInput(); + + nStatesAdded -= levelingDownsampler.getNumberOfDiscardedItems(); + + // use returned List directly rather than make a copy, for efficiency's sake + readStatesByAlignmentStart = flattenByAlignmentStart(levelingDownsampler.consumeFinalizedItems()); + levelingDownsampler.reset(); + } + + return nStatesAdded; + } + + /** + * Is downsampling enabled for this manager? + * @return true if we are downsampling, false otherwise + */ + private boolean isDownsampling() { + return levelingDownsampler != null; + } + + /** + * Get the leftmost alignment state machine, or null if the read states is empty + * @return a potentially null AlignmentStateMachine + */ + public AlignmentStateMachine getFirst() { + return isEmpty() ? null : readStatesByAlignmentStart.getFirst(); + } + + /** + * Capture some statistics about the behavior of the downsampling, but only if CAPTURE_DOWNSAMPLING_STATS is true + */ + @Requires("isDownsampling()") + private void captureDownsamplingStats() { + if ( CAPTURE_DOWNSAMPLING_STATS ) { + nSites++; + final int loc = getFirst().getGenomePosition(); + String message = "Pass through"; + final boolean downsampling = size() > downsamplingTarget; + if ( downsampling ) { + nSitesNeedingDownsampling++; + message = "Downsampling"; + } + + if ( downsampling || nSites % 10000 == 0 ) + logger.info(String.format("%20s at %s: coverage=%d, max=%d, fraction of downsampled sites=%.2e", + message, loc, size(), downsamplingTarget, (1.0 * nSitesNeedingDownsampling / nSites))); + } + } + + /** + * Is there at least one alignment for this sample in this manager? + * @return true if there's at least one alignment, false otherwise + */ + public boolean isEmpty() { + return readStatesByAlignmentStart.isEmpty(); + } + + /** + * Get the number of read states currently in this manager + * @return the number of read states + */ + @Ensures("result >= 0") + public int size() { + return readStatesByAlignmentStart.size(); + } + + /** + * Advances all read states forward by one element, removing states that are + * no long aligned to the current position. + * @return the number of states we're removed after advancing + */ + public int updateReadStates() { + int nRemoved = 0; + final Iterator it = iterator(); + while (it.hasNext()) { + final AlignmentStateMachine state = it.next(); + final CigarOperator op = state.stepForwardOnGenome(); + if (op == null) { + // we discard the read only when we are past its end AND indel at the end of the read (if any) was + // already processed. Keeping the read state that returned null upon stepForwardOnGenome() is safe + // as the next call to stepForwardOnGenome() will return null again AND will clear hadIndel() flag. + it.remove(); // we've stepped off the end of the object + nRemoved++; + } + } + + return nRemoved; + } + + /** + * Iterate over the AlignmentStateMachine in this manager in alignment start order. + * @return a valid iterator + */ + @Ensures("result != null") + public Iterator iterator() { + return readStatesByAlignmentStart.iterator(); + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java index 2dcf01d72..8fbd302a8 100644 --- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java +++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java @@ -1,35 +1,34 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.picard.util.PeekableIterator; -import org.broadinstitute.sting.gatk.downsampling.Downsampler; -import org.broadinstitute.sting.gatk.downsampling.LevelingDownsampler; +import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.util.*; @@ -48,11 +47,18 @@ import java.util.*; * Date: 1/5/13 * Time: 2:02 PM */ -class ReadStateManager { +final class ReadStateManager implements Iterable> { private final List samples; private final PeekableIterator iterator; private final SamplePartitioner samplePartitioner; - private final Map readStatesBySample = new HashMap(); + + /** + * A mapping from sample name -> the per sample read state manager that manages + * + * IT IS CRITICAL THAT THIS BE A LINKED HASH MAP, SO THAT THE ITERATION OF THE MAP OCCURS IN THE SAME + * ORDER AS THE ORIGINL SAMPLES + */ + private final Map readStatesBySample = new LinkedHashMap(); private LinkedList submittedReads; private final boolean keepSubmittedReads; @@ -70,6 +76,7 @@ class ReadStateManager { this.submittedReads = new LinkedList(); for (final String sample : samples) { + // because this is a linked hash map the order of iteration will be in sample order readStatesBySample.put(sample, new PerSampleReadStateManager(LIBSDownsamplingInfo)); } @@ -77,29 +84,16 @@ class ReadStateManager { } /** - * Returns a iterator over all the reads associated with the given sample. Note that remove() is implemented - * for this iterator; if present, total read states will be decremented. + * Returns a iterator over all the sample -> per-sample read state managers with each sample in this read state manager. * - * @param sample The sample. - * @return Iterator over the reads associated with that sample. + * The order of iteration is the same as the order of the samples provided upon construction to this + * ReadStateManager. + * + * @return Iterator over sample + per sample read state manager pairs for this read state manager. */ - public Iterator iterator(final String sample) { - // TODO -- why is this wrapped? - return new Iterator() { - private Iterator wrappedIterator = readStatesBySample.get(sample).iterator(); - - public boolean hasNext() { - return wrappedIterator.hasNext(); - } - - public AlignmentStateMachine next() { - return wrappedIterator.next(); - } - - public void remove() { - wrappedIterator.remove(); - } - }; + @Override + public Iterator> iterator() { + return readStatesBySample.entrySet().iterator(); } public boolean isEmpty() { @@ -126,10 +120,9 @@ class ReadStateManager { } public AlignmentStateMachine getFirst() { - for (final String sample : samples) { - PerSampleReadStateManager reads = readStatesBySample.get(sample); - if (!reads.isEmpty()) - return reads.peek(); + for ( final PerSampleReadStateManager manager : readStatesBySample.values() ) { + if ( ! manager.isEmpty() ) + return manager.getFirst(); } return null; } @@ -138,55 +131,69 @@ class ReadStateManager { return totalReadStates > 0 || iterator.hasNext(); } - // fast testing of position - /** - * TODO -- this function needs to be optimized - * - * Notes: - * -- the only place where it's called is in a block where we know isEmpty is false - * -- getFirst() is quite expensive, and it seems that we could cache this value in the outer - * block, and then pass this in as an argument - * - * @param read - * @return + * Advances all fo the read states by one bp. After this call the read states are reflective + * of the next pileup. */ - private boolean readIsPastCurrentPosition(GATKSAMRecord read) { - if (isEmpty()) - return false; - else { - final AlignmentStateMachine state = getFirst(); - final GATKSAMRecord ourRead = state.getRead(); - return read.getReferenceIndex() > ourRead.getReferenceIndex() || read.getAlignmentStart() > state.getGenomePosition(); + public void updateReadStates() { + for (final PerSampleReadStateManager perSampleReadStateManager : readStatesBySample.values() ) { + totalReadStates -= perSampleReadStateManager.updateReadStates(); } } + /** + * Does read start at the same position as described by currentContextIndex and currentAlignmentStart? + * + * @param read the read we want to test + * @param currentContigIndex the contig index (from the read's getReferenceIndex) of the reads in this state manager + * @param currentAlignmentStart the alignment start of the of the left-most position on the + * genome of the reads in this read state manager + * @return true if read has contig index and start equal to the current ones + */ + private boolean readStartsAtCurrentPosition(final GATKSAMRecord read, final int currentContigIndex, final int currentAlignmentStart) { + return read.getAlignmentStart() == currentAlignmentStart && read.getReferenceIndex() == currentContigIndex; + } + + /** + * Pull all of the reads off the iterator that overlap the left-most position among all + * reads this ReadStateManager + */ public void collectPendingReads() { if (!iterator.hasNext()) return; - // the next record in the stream, peeked as to not remove it from the stream + // determine the left-most boundary that determines which reads to keep in this new pileup + final int firstContigIndex; + final int firstAlignmentStart; if ( isEmpty() ) { - final int firstContigIndex = iterator.peek().getReferenceIndex(); - final int firstAlignmentStart = iterator.peek().getAlignmentStart(); - while (iterator.hasNext() && iterator.peek().getReferenceIndex() == firstContigIndex && iterator.peek().getAlignmentStart() == firstAlignmentStart) { - submitRead(iterator.next()); - } + // there are no reads here, so our next state is the next read in the stream + firstContigIndex = iterator.peek().getReferenceIndex(); + firstAlignmentStart = iterator.peek().getAlignmentStart(); } else { - // Fast fail in the case that the read is past the current position. - if (readIsPastCurrentPosition(iterator.peek())) - return; + // there's a read in the system, so it's our targeted first read + final AlignmentStateMachine firstState = getFirst(); + firstContigIndex = firstState.getReferenceIndex(); + // note this isn't the alignment start of the read, but rather the alignment start position + firstAlignmentStart = firstState.getGenomePosition(); + } - while (iterator.hasNext() && !readIsPastCurrentPosition(iterator.peek())) { - submitRead(iterator.next()); - } + while ( iterator.hasNext() && readStartsAtCurrentPosition(iterator.peek(), firstContigIndex, firstAlignmentStart) ) { + submitRead(iterator.next()); } samplePartitioner.doneSubmittingReads(); for (final String sample : samples) { final Collection newReads = samplePartitioner.getReadsForSample(sample); - PerSampleReadStateManager statesBySample = readStatesBySample.get(sample); + + // if we're keeping reads, take the (potentially downsampled) list of new reads for this sample + // and add to the list of reads. Note this may reorder the list of reads someone (it groups them + // by sample, but it cannot change their absolute position on the genome as they all must + // start at the current location + if ( keepSubmittedReads ) + submittedReads.addAll(newReads); + + final PerSampleReadStateManager statesBySample = readStatesBySample.get(sample); addReadsToSample(statesBySample, newReads); } @@ -199,8 +206,6 @@ class ReadStateManager { */ @Requires("read != null") protected void submitRead(final GATKSAMRecord read) { - if ( keepSubmittedReads ) - submittedReads.add(read); samplePartitioner.submitRead(read); } @@ -271,94 +276,15 @@ class ReadStateManager { if (reads.isEmpty()) return; - Collection newReadStates = new LinkedList(); + final LinkedList newReadStates = new LinkedList(); - for (GATKSAMRecord read : reads) { - AlignmentStateMachine state = new AlignmentStateMachine(read); - if ( state.stepForwardOnGenome() != null ) + for (final GATKSAMRecord read : reads) { + final AlignmentStateMachine state = new AlignmentStateMachine(read); + if ( state.stepForwardOnGenome() != null ) // todo -- should be an assertion not a skip // explicitly filter out reads that are all insertions / soft clips newReadStates.add(state); } - readStates.addStatesAtNextAlignmentStart(newReadStates); - } - - protected class PerSampleReadStateManager implements Iterable { - private List> readStatesByAlignmentStart = new LinkedList>(); - private final Downsampler> levelingDownsampler; - - private int thisSampleReadStates = 0; - - public PerSampleReadStateManager(final LIBSDownsamplingInfo LIBSDownsamplingInfo) { - this.levelingDownsampler = LIBSDownsamplingInfo.isPerformDownsampling() - ? new LevelingDownsampler, AlignmentStateMachine>(LIBSDownsamplingInfo.getToCoverage()) - : null; - } - - public void addStatesAtNextAlignmentStart(Collection states) { - if ( states.isEmpty() ) { - return; - } - - readStatesByAlignmentStart.add(new LinkedList(states)); - thisSampleReadStates += states.size(); - totalReadStates += states.size(); - - if ( levelingDownsampler != null ) { - levelingDownsampler.submit(readStatesByAlignmentStart); - levelingDownsampler.signalEndOfInput(); - - thisSampleReadStates -= levelingDownsampler.getNumberOfDiscardedItems(); - totalReadStates -= levelingDownsampler.getNumberOfDiscardedItems(); - - // use returned List directly rather than make a copy, for efficiency's sake - readStatesByAlignmentStart = levelingDownsampler.consumeFinalizedItems(); - levelingDownsampler.reset(); - } - } - - public boolean isEmpty() { - return readStatesByAlignmentStart.isEmpty(); - } - - public AlignmentStateMachine peek() { - return isEmpty() ? null : readStatesByAlignmentStart.get(0).peek(); - } - - public int size() { - return thisSampleReadStates; - } - - public Iterator iterator() { - return new Iterator() { - private Iterator> alignmentStartIterator = readStatesByAlignmentStart.iterator(); - private LinkedList currentPositionReadStates = null; - private Iterator currentPositionReadStatesIterator = null; - - public boolean hasNext() { - return alignmentStartIterator.hasNext() || - (currentPositionReadStatesIterator != null && currentPositionReadStatesIterator.hasNext()); - } - - public AlignmentStateMachine next() { - if ( currentPositionReadStatesIterator == null || ! currentPositionReadStatesIterator.hasNext() ) { - currentPositionReadStates = alignmentStartIterator.next(); - currentPositionReadStatesIterator = currentPositionReadStates.iterator(); - } - - return currentPositionReadStatesIterator.next(); - } - - public void remove() { - currentPositionReadStatesIterator.remove(); - thisSampleReadStates--; - totalReadStates--; - - if ( currentPositionReadStates.isEmpty() ) { - alignmentStartIterator.remove(); - } - } - }; - } + totalReadStates += readStates.addStatesAtNextAlignmentStart(newReadStates); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java index 1653c6a92..49a8d10aa 100644 --- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java +++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java @@ -1,30 +1,32 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.downsampling.Downsampler; import org.broadinstitute.sting.gatk.downsampling.PassThroughDownsampler; @@ -33,49 +35,138 @@ import org.broadinstitute.sting.gatk.downsampling.ReservoirDownsampler; import java.util.*; /** - * Divides reads by sample and (if requested) does a preliminary downsampling pass with a ReservoirDownsampler. + * Divides reads by sample and (if requested) does a preliminary downsampling pass + * with a ReservoirDownsampler. * * Note: stores reads by sample ID string, not by sample object */ class SamplePartitioner { - private Map> readsBySample; + /** + * Map from sample name (as a string) to a downsampler of reads for that sample + */ + final private Map> readsBySample; + /** + * Are we in a state where we're done submitting reads and have semi-finalized the + * underlying per sample downsampler? + */ + boolean doneSubmittingReads = false; + + /** + * Create a new SamplePartitioner capable of splitting reads up into buckets of reads for + * each sample in samples, and perform a preliminary downsampling of these reads + * (separately for each sample) if downsampling is requested in LIBSDownsamplingInfo + * + * Note that samples must be comprehensive, in that all reads every submitted to this + * partitioner must come from one of the samples provided here. If not, submitRead + * will throw an exception. Duplicates in the list of samples will be ignored + * + * @param LIBSDownsamplingInfo do we want to downsample, and if so to what coverage? + * @param samples the complete list of samples we're going to partition reads into. Can be + * empty, but in that case this code cannot function properly if you + * attempt to add data to it. + */ + @Ensures({ + "readsBySample != null", + "readsBySample.size() == new HashSet(samples).size()" + }) public SamplePartitioner(final LIBSDownsamplingInfo LIBSDownsamplingInfo, final List samples) { - readsBySample = new HashMap>(samples.size()); - for ( String sample : samples ) { + if ( LIBSDownsamplingInfo == null ) throw new IllegalArgumentException("LIBSDownsamplingInfo cannot be null"); + if ( samples == null ) throw new IllegalArgumentException("samples must be a non-null list"); + + readsBySample = new LinkedHashMap>(samples.size()); + for ( final String sample : samples ) { readsBySample.put(sample, createDownsampler(LIBSDownsamplingInfo)); } } + /** + * Create a new, ready to use downsampler based on the parameters in LIBSDownsamplingInfo + * @param LIBSDownsamplingInfo the parameters to use in creating the downsampler + * @return a downsampler appropriate for LIBSDownsamplingInfo. If no downsampling is requested, + * uses the PassThroughDownsampler, which does nothing at all. + */ + @Requires("LIBSDownsamplingInfo != null") + @Ensures("result != null") private Downsampler createDownsampler(final LIBSDownsamplingInfo LIBSDownsamplingInfo) { return LIBSDownsamplingInfo.isPerformDownsampling() - ? new ReservoirDownsampler(LIBSDownsamplingInfo.getToCoverage()) + ? new ReservoirDownsampler(LIBSDownsamplingInfo.getToCoverage(), true) : new PassThroughDownsampler(); } - public void submitRead(T read) { - String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null; - if (readsBySample.containsKey(sampleName)) - readsBySample.get(sampleName).submit(read); + /** + * Offer this read to the partitioner, putting it into the bucket of reads for the sample + * of read (obtained via the read's read group). + * + * If the read group is missing, uses the special "null" read group + * + * @throws IllegalStateException if the sample of read wasn't present in the original + * set of samples provided to this SamplePartitioner at construction + * + * @param read the read to add to the sample's list of reads + */ + @Requires("read != null") + @Ensures("doneSubmittingReads == false") + public void submitRead(final T read) { + final String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null; + final Downsampler downsampler = readsBySample.get(sampleName); + if ( downsampler == null ) + throw new IllegalStateException("Offered read with sample name " + sampleName + " to SamplePartitioner " + + "but this sample wasn't provided as one of possible samples at construction"); + + downsampler.submit(read); + doneSubmittingReads = false; } + /** + * Tell this partitioner that all reads in this cycle have been submitted, so that we + * can finalize whatever downsampling is required by each sample. + * + * Note that we *must* call this function before getReadsForSample, or else that + * function will exception out. + */ + @Ensures("doneSubmittingReads == true") public void doneSubmittingReads() { - for ( Map.Entry> perSampleReads : readsBySample.entrySet() ) { - perSampleReads.getValue().signalEndOfInput(); + for ( final Downsampler downsampler : readsBySample.values() ) { + downsampler.signalEndOfInput(); } + doneSubmittingReads = true; } - public Collection getReadsForSample(String sampleName) { - if ( ! readsBySample.containsKey(sampleName) ) - throw new NoSuchElementException("Sample name not found"); + /** + * Get the final collection of reads for this sample for this cycle + * + * The cycle is defined as all of the reads that occur between + * the first call to submitRead until doneSubmittingReads is called. At that + * point additional downsampling may occur (depending on construction arguments) + * and that set of reads is returned here. + * + * Note that this function can only be called once per cycle, as underlying + * collection of reads is cleared. + * + * @param sampleName the sample we want reads for, must be present in the original samples + * @return a non-null collection of reads for sample in this cycle + */ + @Ensures("result != null") + public Collection getReadsForSample(final String sampleName) { + if ( ! doneSubmittingReads ) throw new IllegalStateException("getReadsForSample called before doneSubmittingReads was called"); - return readsBySample.get(sampleName).consumeFinalizedItems(); + final Downsampler downsampler = readsBySample.get(sampleName); + if ( downsampler == null ) throw new NoSuchElementException("Sample name not found"); + + return downsampler.consumeFinalizedItems(); } + /** + * Resets this SamplePartitioner, indicating that we're starting a new + * cycle of adding reads to each underlying downsampler. + */ + @Ensures("doneSubmittingReads == false") public void reset() { - for ( Map.Entry> perSampleReads : readsBySample.entrySet() ) { - perSampleReads.getValue().clear(); - perSampleReads.getValue().reset(); + for ( final Downsampler downsampler : readsBySample.values() ) { + downsampler.clear(); + downsampler.reset(); } + doneSubmittingReads = false; } } diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java index c0e18f227..51753ca5e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java @@ -29,9 +29,8 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -52,7 +51,7 @@ public class PileupElement implements Comparable { private final static EnumSet ON_GENOME_OPERATORS = EnumSet.of(CigarOperator.M, CigarOperator.EQ, CigarOperator.X, CigarOperator.D); - public static final byte DELETION_BASE = BaseUtils.D; + public static final byte DELETION_BASE = BaseUtils.Base.D.base; public static final byte DELETION_QUAL = (byte) 16; public static final byte A_FOLLOWED_BY_INSERTION_BASE = (byte) 87; public static final byte C_FOLLOWED_BY_INSERTION_BASE = (byte) 88; diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java index fe43f85bd..65c47c23b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java @@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.fragments.FragmentCollection; import org.broadinstitute.sting.utils.fragments.FragmentUtils; import org.broadinstitute.sting.utils.locusiterator.LocusIteratorByState; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.sting.utils.BaseUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java index dbf70f4ce..600700484 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java @@ -36,6 +36,7 @@ public class BQSRArgumentSet { private boolean disableIndelQuals; private boolean emitOriginalQuals; private int PRESERVE_QSCORES_LESS_THAN; + private double globalQScorePrior; public BQSRArgumentSet(final GATKArgumentCollection args) { this.BQSR_RECAL_FILE = args.BQSR_RECAL_FILE; @@ -43,6 +44,7 @@ public class BQSRArgumentSet { this.disableIndelQuals = args.disableIndelQuals; this.emitOriginalQuals = args.emitOriginalQuals; this.PRESERVE_QSCORES_LESS_THAN = args.PRESERVE_QSCORES_LESS_THAN; + this.globalQScorePrior = args.globalQScorePrior; } public File getRecalFile() { return BQSR_RECAL_FILE; } @@ -55,6 +57,8 @@ public class BQSRArgumentSet { public int getPreserveQscoresLessThan() { return PRESERVE_QSCORES_LESS_THAN; } + public double getGlobalQScorePrior() { return globalQScorePrior; } + public void setRecalFile(final File BQSR_RECAL_FILE) { this.BQSR_RECAL_FILE = BQSR_RECAL_FILE; } @@ -74,4 +78,8 @@ public class BQSRArgumentSet { public void setPreserveQscoresLessThan(final int PRESERVE_QSCORES_LESS_THAN) { this.PRESERVE_QSCORES_LESS_THAN = PRESERVE_QSCORES_LESS_THAN; } + + public void setGlobalQScorePrior(final double globalQScorePrior) { + this.globalQScorePrior = globalQScorePrior; + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 0907a0239..f29721a7e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -25,13 +25,14 @@ package org.broadinstitute.sting.utils.sam; +import com.google.java.contract.Ensures; +import com.google.java.contract.Requires; import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.variant.utils.BaseUtils; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -39,9 +40,16 @@ import org.broadinstitute.sting.utils.recalibration.EventType; import java.util.ArrayList; import java.util.Arrays; +import java.util.EnumSet; +import java.util.List; -public class AlignmentUtils { +public final class AlignmentUtils { + private final static EnumSet ALIGNED_TO_GENOME_OPERATORS = EnumSet.of(CigarOperator.M, CigarOperator.EQ, CigarOperator.X); + private final static EnumSet ALIGNED_TO_GENOME_PLUS_SOFTCLIPS = EnumSet.of(CigarOperator.M, CigarOperator.EQ, CigarOperator.X, CigarOperator.S); + + // cannot be instantiated + private AlignmentUtils() { } public static class MismatchCount { public int numMismatches = 0; @@ -117,103 +125,6 @@ public class AlignmentUtils { return mc; } - /** - * Returns the number of mismatches in the pileup within the given reference context. - * - * @param pileup the pileup with reads - * @param ref the reference context - * @param ignoreTargetSite if true, ignore mismatches at the target locus (i.e. the center of the window) - * @return the number of mismatches - */ - public static int mismatchesInRefWindow(ReadBackedPileup pileup, ReferenceContext ref, boolean ignoreTargetSite) { - int mismatches = 0; - for (PileupElement p : pileup) - mismatches += mismatchesInRefWindow(p, ref, ignoreTargetSite); - return mismatches; - } - - /** - * Returns the number of mismatches in the pileup element within the given reference context. - * - * @param p the pileup element - * @param ref the reference context - * @param ignoreTargetSite if true, ignore mismatches at the target locus (i.e. the center of the window) - * @return the number of mismatches - */ - public static int mismatchesInRefWindow(PileupElement p, ReferenceContext ref, boolean ignoreTargetSite) { - return mismatchesInRefWindow(p, ref, ignoreTargetSite, false); - } - - /** - * Returns the number of mismatches in the pileup element within the given reference context. - * - * @param p the pileup element - * @param ref the reference context - * @param ignoreTargetSite if true, ignore mismatches at the target locus (i.e. the center of the window) - * @param qualitySumInsteadOfMismatchCount - * if true, return the quality score sum of the mismatches rather than the count - * @return the number of mismatches - */ - public static int mismatchesInRefWindow(PileupElement p, ReferenceContext ref, boolean ignoreTargetSite, boolean qualitySumInsteadOfMismatchCount) { - int sum = 0; - - int windowStart = ref.getWindow().getStart(); - int windowStop = ref.getWindow().getStop(); - byte[] refBases = ref.getBases(); - byte[] readBases = p.getRead().getReadBases(); - byte[] readQualities = p.getRead().getBaseQualities(); - Cigar c = p.getRead().getCigar(); - - int readIndex = 0; - int currentPos = p.getRead().getAlignmentStart(); - int refIndex = Math.max(0, currentPos - windowStart); - - for (int i = 0; i < c.numCigarElements(); i++) { - CigarElement ce = c.getCigarElement(i); - int cigarElementLength = ce.getLength(); - switch (ce.getOperator()) { - case EQ: - case X: - case M: - for (int j = 0; j < cigarElementLength; j++, readIndex++, currentPos++) { - // are we past the ref window? - if (currentPos > windowStop) - break; - - // are we before the ref window? - if (currentPos < windowStart) - continue; - - byte refChr = refBases[refIndex++]; - - // do we need to skip the target site? - if (ignoreTargetSite && ref.getLocus().getStart() == currentPos) - continue; - - byte readChr = readBases[readIndex]; - if (readChr != refChr) - sum += (qualitySumInsteadOfMismatchCount) ? readQualities[readIndex] : 1; - } - break; - case I: - case S: - readIndex += cigarElementLength; - break; - case D: - case N: - currentPos += cigarElementLength; - if (currentPos > windowStart) - refIndex += Math.min(cigarElementLength, currentPos - windowStart); - break; - case H: - case P: - break; - } - } - - return sum; - } - /** * Returns number of alignment blocks (continuous stretches of aligned bases) in the specified alignment. * This method follows closely the SAMRecord::getAlignmentBlocks() implemented in samtools library, but @@ -224,31 +135,54 @@ public class AlignmentUtils { * @param r alignment * @return number of continuous alignment blocks (i.e. 'M' elements of the cigar; all indel and clipping elements are ignored). */ + @Ensures("result >= 0") public static int getNumAlignmentBlocks(final SAMRecord r) { - int n = 0; + if ( r == null ) throw new IllegalArgumentException("read cannot be null"); final Cigar cigar = r.getCigar(); if (cigar == null) return 0; + int n = 0; for (final CigarElement e : cigar.getCigarElements()) { - if (e.getOperator() == CigarOperator.M) n++; + if (ALIGNED_TO_GENOME_OPERATORS.contains(e.getOperator())) + n++; } return n; } - public static int getNumAlignedBasesCountingSoftClips(final SAMRecord r) { + + /** + * Get the number of bases aligned to the genome, including soft clips + * + * If read is not mapped (i.e., doesn't have a cigar) returns 0 + * + * @param r a non-null GATKSAMRecord + * @return the number of bases aligned to the genome in R, including soft clipped bases + */ + public static int getNumAlignedBasesCountingSoftClips(final GATKSAMRecord r) { int n = 0; final Cigar cigar = r.getCigar(); if (cigar == null) return 0; for (final CigarElement e : cigar.getCigarElements()) - if (e.getOperator() == CigarOperator.M || e.getOperator() == CigarOperator.S) + if (ALIGNED_TO_GENOME_PLUS_SOFTCLIPS.contains(e.getOperator())) n += e.getLength(); return n; } + /** + * Count the number of bases hard clipped from read + * + * If read's cigar is null, return 0 + * + * @param r a non-null read + * @return a positive integer + */ + @Ensures("result >= 0") public static int getNumHardClippedBases(final SAMRecord r) { + if ( r == null ) throw new IllegalArgumentException("Read cannot be null"); + int n = 0; final Cigar cigar = r.getCigar(); if (cigar == null) return 0; @@ -260,16 +194,28 @@ public class AlignmentUtils { return n; } + /** + * Calculate the number of bases that are soft clipped in read with quality score greater than threshold + * + * Handles the case where the cigar is null (i.e., the read is unmapped), returning 0 + * + * @param read a non-null GATKSAMRecord. + * @param qualThreshold consider bases with quals > this value as high quality. Must be >= 0 + * @return positive integer + */ + @Ensures("result >= 0") public static int calcNumHighQualitySoftClips( final GATKSAMRecord read, final byte qualThreshold ) { + if ( read == null ) throw new IllegalArgumentException("Read cannot be null"); + if ( qualThreshold < 0 ) throw new IllegalArgumentException("Expected qualThreshold to be a positive byte but saw " + qualThreshold); + + if ( read.getCigar() == null ) // the read is unmapped + return 0; + + final byte[] qual = read.getBaseQualities( EventType.BASE_SUBSTITUTION ); int numHQSoftClips = 0; int alignPos = 0; - final Cigar cigar = read.getCigar(); - final byte[] qual = read.getBaseQualities( EventType.BASE_SUBSTITUTION ); - - for( int iii = 0; iii < cigar.numCigarElements(); iii++ ) { - - final CigarElement ce = cigar.getCigarElement(iii); + for ( final CigarElement ce : read.getCigar().getCigarElements() ) { final int elementLength = ce.getLength(); switch( ce.getOperator() ) { @@ -278,35 +224,26 @@ public class AlignmentUtils { if( qual[alignPos++] > qualThreshold ) { numHQSoftClips++; } } break; - case M: - case I: - case EQ: - case X: + case M: case I: case EQ: case X: alignPos += elementLength; break; - case H: - case P: - case D: - case N: + case H: case P: case D: case N: break; default: - throw new ReviewedStingException("Unsupported cigar operator: " + ce.getOperator()); + throw new IllegalStateException("Unsupported cigar operator: " + ce.getOperator()); } } + return numHQSoftClips; } public static int calcAlignmentByteArrayOffset(final Cigar cigar, final PileupElement pileupElement, final int alignmentStart, final int refLocus) { - return calcAlignmentByteArrayOffset( cigar, pileupElement.getOffset(), false, pileupElement.isDeletion(), alignmentStart, refLocus ); + return calcAlignmentByteArrayOffset( cigar, pileupElement.getOffset(), pileupElement.isDeletion(), alignmentStart, refLocus ); } - public static int calcAlignmentByteArrayOffset(final Cigar cigar, final int offset, final boolean isInsertionAtBeginningOfRead, final boolean isDeletion, final int alignmentStart, final int refLocus) { + public static int calcAlignmentByteArrayOffset(final Cigar cigar, final int offset, final boolean isDeletion, final int alignmentStart, final int refLocus) { int pileupOffset = offset; - // Special case for reads starting with insertion - if (isInsertionAtBeginningOfRead) - return 0; - // Reassign the offset if we are in the middle of a deletion because of the modified representation of the read bases if (isDeletion) { pileupOffset = refLocus - alignmentStart; @@ -402,13 +339,13 @@ public class AlignmentUtils { switch (ce.getOperator()) { case I: if (alignPos > 0) { - if (alignment[alignPos - 1] == BaseUtils.A) { + if (alignment[alignPos - 1] == BaseUtils.Base.A.base) { alignment[alignPos - 1] = PileupElement.A_FOLLOWED_BY_INSERTION_BASE; - } else if (alignment[alignPos - 1] == BaseUtils.C) { + } else if (alignment[alignPos - 1] == BaseUtils.Base.C.base) { alignment[alignPos - 1] = PileupElement.C_FOLLOWED_BY_INSERTION_BASE; - } else if (alignment[alignPos - 1] == BaseUtils.T) { + } else if (alignment[alignPos - 1] == BaseUtils.Base.T.base) { alignment[alignPos - 1] = PileupElement.T_FOLLOWED_BY_INSERTION_BASE; - } else if (alignment[alignPos - 1] == BaseUtils.G) { + } else if (alignment[alignPos - 1] == BaseUtils.Base.G.base) { alignment[alignPos - 1] = PileupElement.G_FOLLOWED_BY_INSERTION_BASE; } } @@ -459,18 +396,21 @@ public class AlignmentUtils { * specification, one may need this convenience shortcut. Checks both 'read unmapped' flag and * alignment reference index/start. * - * @param r record + * Our life would be so much easier if all sam files followed the specs. In reality, + * sam files (including those generated by maq or bwa) miss headers altogether. When + * reading such a SAM file, reference name is set, but since there is no sequence dictionary, + * null is always returned for referenceIndex. Let's be paranoid here, and make sure that + * we do not call the read "unmapped" when it has only reference name set with ref. index missing + * or vice versa. + * + * @param r a non-null record * @return true if read is unmapped */ public static boolean isReadUnmapped(final SAMRecord r) { + if ( r == null ) throw new IllegalArgumentException("Read cannot be null"); + if (r.getReadUnmappedFlag()) return true; - // our life would be so much easier if all sam files followed the specs. In reality, - // sam files (including those generated by maq or bwa) miss headers altogether. When - // reading such a SAM file, reference name is set, but since there is no sequence dictionary, - // null is always returned for referenceIndex. Let's be paranoid here, and make sure that - // we do not call the read "unmapped" when it has only reference name set with ref. index missing - // or vice versa. if ((r.getReferenceIndex() != null && r.getReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX || r.getReferenceName() != null && !r.getReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) && r.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START) return false; @@ -478,26 +418,27 @@ public class AlignmentUtils { } /** - * Due to (unfortunate) multiple ways to indicate that read/mate is unmapped allowed by SAM format - * specification, one may need this convenience shortcut. Checks both 'mate unmapped' flag and - * alignment reference index/start of the mate. - * - * @param r sam record for the read - * @return true if read's mate is unmapped + * Need a well-formed, consolidated Cigar string so that the left aligning code works properly. + * For example, 1M1M1M1D2M1M --> 3M1D3M + * If the given cigar is empty then the returned cigar will also be empty + * @param c the cigar to consolidate + * @return a non-null cigar with consecutive matching operators merged into single operators. */ - public static boolean isMateUnmapped(final SAMRecord r) { - if (r.getMateUnmappedFlag()) return true; + @Ensures({"result != null"}) + public static Cigar consolidateCigar( final Cigar c ) { + if( c == null ) { throw new IllegalArgumentException("Cigar cannot be null"); } + if( c.isEmpty() ) { return c; } - // our life would be so much easier if all sam files followed the specs. In reality, - // sam files (including those generated by maq or bwa) miss headers altogether. When - // reading such a SAM file, reference name is set, but since there is no sequence dictionary, - // null is always returned for referenceIndex. Let's be paranoid here, and make sure that - // we do not call the read "unmapped" when it has only reference name set with ref. index missing - // or vice versa. - if ((r.getMateReferenceIndex() != null && r.getMateReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX - || r.getMateReferenceName() != null && !r.getMateReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) - && r.getMateAlignmentStart() != SAMRecord.NO_ALIGNMENT_START) return false; - return true; + final Cigar returnCigar = new Cigar(); + int sumLength = 0; + for( int iii = 0; iii < c.numCigarElements(); iii++ ) { + sumLength += c.getCigarElement(iii).getLength(); + if( iii == c.numCigarElements() - 1 || !c.getCigarElement(iii).getOperator().equals(c.getCigarElement(iii+1).getOperator())) { // at the end so finish the current element + returnCigar.add(new CigarElement(sumLength, c.getCigarElement(iii).getOperator())); + sumLength = 0; + } + } + return returnCigar; } /** @@ -566,22 +507,41 @@ public class AlignmentUtils { return cigar; } - private static boolean cigarHasZeroSizeElement(Cigar c) { - for (CigarElement ce : c.getCigarElements()) { + /** + * Does one of the elements in cigar have a 0 length? + * + * @param c a non-null cigar + * @return true if any element has 0 size + */ + @Requires("c != null") + protected static boolean cigarHasZeroSizeElement(final Cigar c) { + for (final CigarElement ce : c.getCigarElements()) { if (ce.getLength() == 0) return true; } return false; } - private static Cigar cleanUpCigar(Cigar c) { - ArrayList elements = new ArrayList(c.numCigarElements() - 1); - for (CigarElement ce : c.getCigarElements()) { - if (ce.getLength() != 0 && - (elements.size() != 0 || ce.getOperator() != CigarOperator.D)) { + /** + * Clean up the incoming cigar + * + * Removes elements with zero size + * Clips away beginning deletion operators + * + * @param c the cigar string we want to clean up + * @return a newly allocated, cleaned up Cigar + */ + @Requires("c != null") + @Ensures("result != null") + private static Cigar cleanUpCigar(final Cigar c) { + final List elements = new ArrayList(c.numCigarElements() - 1); + + for (final CigarElement ce : c.getCigarElements()) { + if (ce.getLength() != 0 && (! elements.isEmpty() || ce.getOperator() != CigarOperator.D)) { elements.add(ce); } } + return new Cigar(elements); } diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java new file mode 100644 index 000000000..bf3045c71 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java @@ -0,0 +1,237 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.sam; + +import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.samtools.*; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.NGSPlatform; + +import java.io.File; +import java.io.IOException; +import java.util.*; + +/** + * Easy to use creator of artificial BAM files for testing + * + * Allows us to make a stream of reads or an index BAM file with read having the following properties + * + * - coming from n samples + * - of fixed read length and aligned to the genome with M operator + * - having N reads per alignment start + * - skipping N bases between each alignment start + * - starting at a given alignment start + * + * User: depristo + * Date: 1/15/13 + * Time: 9:22 AM + */ +public class ArtificialBAMBuilder { + public final static int BAM_SHARD_SIZE = 16384; + + private final IndexedFastaSequenceFile reference; + private final GenomeLocParser parser; + + final int nReadsPerLocus; + final int nLoci; + + int skipNLoci = 0; + int alignmentStart = 1; + int readLength = 10; + private final ArrayList samples = new ArrayList(); + private List createdReads = null; + + private LinkedList additionalReads = new LinkedList(); + + final SAMFileWriterFactory factory = new SAMFileWriterFactory(); + { + factory.setCreateIndex(true); + } + + SAMFileHeader header; + + public ArtificialBAMBuilder(final IndexedFastaSequenceFile reference, int nReadsPerLocus, int nLoci) { + this.nReadsPerLocus = nReadsPerLocus; + this.nLoci = nLoci; + + this.reference = reference; + this.parser = new GenomeLocParser(reference); + createAndSetHeader(1); + } + + public ArtificialBAMBuilder(int nReadsPerLocus, int nLoci) { + this(ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000).getSequenceDictionary(), nReadsPerLocus, nLoci); + } + + public ArtificialBAMBuilder(final SAMSequenceDictionary dict, int nReadsPerLocus, int nLoci) { + this.nReadsPerLocus = nReadsPerLocus; + this.nLoci = nLoci; + this.reference = null; + this.parser = new GenomeLocParser(dict); + createAndSetHeader(1); + } + + public IndexedFastaSequenceFile getReference() { + return reference; + } + + public GenomeLocParser getGenomeLocParser() { + return parser; + } + + public ArtificialBAMBuilder createAndSetHeader(final int nSamples) { + createdReads = null; + this.header = new SAMFileHeader(); + header.setSortOrder(SAMFileHeader.SortOrder.coordinate); + header.setSequenceDictionary(parser.getContigs()); + samples.clear(); + + for ( int i = 0; i < nSamples; i++ ) { + final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("rg" + i); + final String sample = "sample" + i; + samples.add(sample); + rg.setSample(sample); + rg.setPlatform(NGSPlatform.ILLUMINA.getDefaultPlatform()); + header.addReadGroup(rg); + } + + return this; + } + + public void addReads(final GATKSAMRecord readToAdd) { + createdReads = null; + additionalReads.add(readToAdd); + } + + public void addReads(final Collection readsToAdd) { + createdReads = null; + additionalReads.addAll(readsToAdd); + } + + public List getSamples() { + return samples; + } + + /** + * Create a read stream based on the parameters. The cigar string for each + * read will be *M, where * is the length of the read. + * + * Useful for testing things like LocusIteratorBystate + * + * @return a ordered list of reads + */ + public List makeReads() { + if ( createdReads == null ) { + final String baseName = "read"; + final LinkedList readGroups = new LinkedList(); + for ( final SAMReadGroupRecord rg : header.getReadGroups()) + readGroups.add(new GATKSAMReadGroupRecord(rg)); + + List reads = new ArrayList(nReadsPerLocus*nLoci); + for ( int locusI = 0; locusI < nLoci; locusI++) { + final int locus = locusI * (skipNLoci + 1); + for ( int readI = 0; readI < nReadsPerLocus; readI++ ) { + for ( final GATKSAMReadGroupRecord rg : readGroups ) { + final String readName = String.format("%s.%d.%d.%s", baseName, locus, readI, rg.getId()); + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, readName, 0, alignmentStart + locus, readLength); + read.setReadGroup(rg); + reads.add(read); + } + } + } + + if ( ! additionalReads.isEmpty() ) { + reads.addAll(additionalReads); + Collections.sort(reads, new SAMRecordCoordinateComparator()); + } + + createdReads = new ArrayList(reads); + } + + return createdReads; + } + + /** + * Make an indexed BAM file contains the reads in the builder, marking it for deleteOnExit() + * @return the BAM file + */ + public File makeTemporarilyBAMFile() { + try { + final File file = File.createTempFile("tempBAM", ".bam"); + file.deleteOnExit(); + return makeBAMFile(file); + } catch ( IOException e ) { + throw new RuntimeException(e); + } + } + + /** + * Write the reads from this builder to output, creating an index as well + * @param output the output BAM file we want to use + * @return + */ + public File makeBAMFile(final File output) { + final SAMFileWriter writer = factory.makeBAMWriter(header, true, output, 0); + for ( final GATKSAMRecord read : makeReads() ) + writer.addAlignment(read); + writer.close(); + return output; + } + + public int getnReadsPerLocus() { return nReadsPerLocus; } + public int getnLoci() { return nLoci; } + public int getSkipNLoci() { return skipNLoci; } + public ArtificialBAMBuilder setSkipNLoci(int skipNLoci) { this.skipNLoci = skipNLoci; createdReads = null; return this; } + public int getAlignmentStart() { return alignmentStart; } + public ArtificialBAMBuilder setAlignmentStart(int alignmentStart) { this.alignmentStart = alignmentStart; createdReads = null; return this; } + public int getReadLength() { return readLength; } + public ArtificialBAMBuilder setReadLength(int readLength) { this.readLength = readLength; createdReads = null; return this; } + public SAMFileHeader getHeader() { return header; } + public ArtificialBAMBuilder setHeader(SAMFileHeader header) { this.header = header; createdReads = null; return this; } + + public int getAlignmentEnd() { + return alignmentStart + nLoci * (skipNLoci + 1) + readLength; + } + + + public int getNSamples() { return samples.size(); } + + public int expectedNumberOfReads() { + return nLoci * nReadsPerLocus * header.getReadGroups().size(); + } + + @Override + public String toString() { + return "ArtificialBAMBuilder{" + + "samples=" + samples + + ", readLength=" + readLength + + ", alignmentStart=" + alignmentStart + + ", skipNLoci=" + skipNLoci + + ", nLoci=" + nLoci + + ", nReadsPerLocus=" + nReadsPerLocus + + '}'; + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java index 4af6555d9..1bf24814b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java @@ -115,6 +115,19 @@ public class ArtificialSAMUtils { return header; } + /** + * Creates an artificial sam header based on the sequence dictionary dict + * + * @return + */ + public static SAMFileHeader createArtificialSamHeader(final SAMSequenceDictionary dict) { + SAMFileHeader header = new SAMFileHeader(); + header.setSortOrder(net.sf.samtools.SAMFileHeader.SortOrder.coordinate); + header.setSequenceDictionary(dict); + return header; + } + + /** * setup a default read group for a SAMFileHeader * @@ -327,35 +340,6 @@ public class ArtificialSAMUtils { return stack; } - /** - * Create a read stream based on the parameters. The cigar string for each - * read will be *M, where * is the length of the read. - * - * Useful for testing things like LocusIteratorBystate - * - * @return a collection of stackSize reads all sharing the above properties - */ - public static List createReadStream( final int nReadsPerLocus, - final int nLoci, - final SAMFileHeader header, - final int alignmentStart, - final int length ) { - final String baseName = "read"; - List reads = new ArrayList(nReadsPerLocus*nLoci); - for ( int locus = 0; locus < nLoci; locus++ ) { - for ( int readI = 0; readI < nReadsPerLocus; readI++ ) { - for ( final SAMReadGroupRecord rg : header.getReadGroups() ) { - final String readName = String.format("%s.%d.%d.%s", baseName, locus, readI, rg.getId()); - final GATKSAMRecord read = createArtificialRead(header, readName, 0, alignmentStart + locus, length); - read.setReadGroup(new GATKSAMReadGroupRecord(rg)); - reads.add(read); - } - } - } - - return reads; - } - /** * create an iterator containing the specified read piles * diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java index 9cd584d1b..01a8c1996 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -25,15 +25,13 @@ package org.broadinstitute.sting.utils.sam; +import com.google.java.contract.Ensures; import net.sf.samtools.*; import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.recalibration.EventType; -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; +import java.util.*; /** * @author ebanks, depristo @@ -46,6 +44,10 @@ import java.util.Map; * if they are ever modified externally then one must also invoke the * setReadGroup() method here to ensure that the cache is kept up-to-date. * + * WARNING -- GATKSAMRecords cache several values (that are expensive to compute) + * that depending on the inferred insert size and alignment starts and stops of this read and its mate. + * Changing these values in any way will invalidate the cached value. However, we do not monitor those setter + * functions, so modifying a GATKSAMRecord in any way may result in stale cached values. */ public class GATKSAMRecord extends BAMRecord { // ReduceReads specific attribute tags @@ -70,6 +72,7 @@ public class GATKSAMRecord extends BAMRecord { private final static int UNINITIALIZED = -1; private int softStart = UNINITIALIZED; private int softEnd = UNINITIALIZED; + private Integer adapterBoundary = null; // because some values can be null, we don't want to duplicate effort private boolean retrievedReadGroup = false; @@ -131,6 +134,13 @@ public class GATKSAMRecord extends BAMRecord { flags, readLen, mateReferenceSequenceIndex, mateAlignmentStart, insertSize, variableLengthBlock); } + public static GATKSAMRecord createRandomRead(int length) { + List cigarElements = new LinkedList(); + cigarElements.add(new CigarElement(length, CigarOperator.M)); + Cigar cigar = new Cigar(cigarElements); + return ArtificialSAMUtils.createArtificialRead(cigar); + } + /////////////////////////////////////////////////////////////////////////////// // *** The following methods are overloaded to cache the appropriate data ***// /////////////////////////////////////////////////////////////////////////////// @@ -561,4 +571,23 @@ public class GATKSAMRecord extends BAMRecord { } return clone; } + + /** + * A caching version of ReadUtils.getAdaptorBoundary() + * + * @see ReadUtils.getAdaptorBoundary(SAMRecord) for more information about the meaning of this function + * + * WARNING -- this function caches a value depending on the inferred insert size and alignment starts + * and stops of this read and its mate. Changing these values in any way will invalidate the cached value. + * However, we do not monitor those setter functions, so modifying a GATKSAMRecord in any way may + * result in stale cached values. + * + * @return the result of calling ReadUtils.getAdaptorBoundary on this read + */ + @Ensures("result == ReadUtils.getAdaptorBoundary(this)") + public int getAdaptorBoundary() { + if ( adapterBoundary == null ) + adapterBoundary = ReadUtils.getAdaptorBoundary(this); + return adapterBoundary; + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index b61628d4d..39d058aea 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -34,6 +34,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.BaseUtils; import java.io.File; import java.util.*; @@ -169,8 +170,8 @@ public class ReadUtils { * @return whether or not the base is in the adaptor */ public static boolean isBaseInsideAdaptor(final GATKSAMRecord read, long basePos) { - Integer adaptorBoundary = getAdaptorBoundary(read); - if (adaptorBoundary == null || read.getInferredInsertSize() > DEFAULT_ADAPTOR_SIZE) + final int adaptorBoundary = read.getAdaptorBoundary(); + if (adaptorBoundary == CANNOT_COMPUTE_ADAPTOR_BOUNDARY || read.getInferredInsertSize() > DEFAULT_ADAPTOR_SIZE) return false; return read.getReadNegativeStrandFlag() ? basePos <= adaptorBoundary : basePos >= adaptorBoundary; @@ -199,26 +200,28 @@ public class ReadUtils { * in these cases the adaptor boundary is at the start of the read plus the inferred insert size (plus one) * * @param read the read being tested for the adaptor boundary - * @return the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read. NULL if the read is unmapped or the mate is mapped to another contig. + * @return the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read. + * CANNOT_COMPUTE_ADAPTOR_BOUNDARY if the read is unmapped or the mate is mapped to another contig. */ - public static Integer getAdaptorBoundary(final SAMRecord read) { + public static int getAdaptorBoundary(final SAMRecord read) { final int MAXIMUM_ADAPTOR_LENGTH = 8; final int insertSize = Math.abs(read.getInferredInsertSize()); // the inferred insert size can be negative if the mate is mapped before the read (so we take the absolute value) if (insertSize == 0 || read.getReadUnmappedFlag()) // no adaptors in reads with mates in another chromosome or unmapped pairs - return null; + return CANNOT_COMPUTE_ADAPTOR_BOUNDARY; - Integer adaptorBoundary; // the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read) + int adaptorBoundary; // the reference coordinate for the adaptor boundary (effectively the first base IN the adaptor, closest to the read) if (read.getReadNegativeStrandFlag()) adaptorBoundary = read.getMateAlignmentStart() - 1; // case 1 (see header) else adaptorBoundary = read.getAlignmentStart() + insertSize + 1; // case 2 (see header) if ( (adaptorBoundary < read.getAlignmentStart() - MAXIMUM_ADAPTOR_LENGTH) || (adaptorBoundary > read.getAlignmentEnd() + MAXIMUM_ADAPTOR_LENGTH) ) - adaptorBoundary = null; // we are being conservative by not allowing the adaptor boundary to go beyond what we belive is the maximum size of an adaptor + adaptorBoundary = CANNOT_COMPUTE_ADAPTOR_BOUNDARY; // we are being conservative by not allowing the adaptor boundary to go beyond what we belive is the maximum size of an adaptor return adaptorBoundary; } + public static int CANNOT_COMPUTE_ADAPTOR_BOUNDARY = Integer.MIN_VALUE; /** * is the read a 454 read? @@ -392,6 +395,11 @@ public class ReadUtils { return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refCoord, tail, false); } + public static int getReadCoordinateForReferenceCoordinateUpToEndOfRead(GATKSAMRecord read, int refCoord, ClippingTail tail) { + final int leftmostSafeVariantPosition = Math.max(read.getSoftStart(), refCoord); + return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), leftmostSafeVariantPosition, tail, false); + } + public static int getReadCoordinateForReferenceCoordinate(final int alignmentStart, final Cigar cigar, final int refCoord, final ClippingTail tail, final boolean allowGoalNotReached) { Pair result = getReadCoordinateForReferenceCoordinate(alignmentStart, cigar, refCoord, allowGoalNotReached); int readCoord = result.getFirst(); @@ -843,4 +851,66 @@ public class ReadUtils { return events; } + /** + * Given a read, outputs the read bases in a string format + * + * @param read the read + * @return a string representation of the read bases + */ + public static String convertReadBasesToString(GATKSAMRecord read) { + String bases = ""; + for (byte b : read.getReadBases()) { + bases += (char) b; + } + return bases.toUpperCase(); + } + + /** + * Given a read, outputs the base qualities in a string format + * + * @param quals the read qualities + * @return a string representation of the base qualities + */ + public static String convertReadQualToString(byte[] quals) { + String result = ""; + for (byte b : quals) { + result += (char) (33 + b); + } + return result; + } + + /** + * Given a read, outputs the base qualities in a string format + * + * @param read the read + * @return a string representation of the base qualities + */ + public static String convertReadQualToString(GATKSAMRecord read) { + return convertReadQualToString(read.getBaseQualities()); + } + + /** + * Returns the reverse complement of the read bases + * + * @param bases the read bases + * @return the reverse complement of the read bases + */ + public static String getBasesReverseComplement(byte[] bases) { + String reverse = ""; + for (int i = bases.length-1; i >=0; i--) { + reverse += (char) BaseUtils.getComplement(bases[i]); + } + return reverse; + } + + /** + * Returns the reverse complement of the read bases + * + * @param read the read + * @return the reverse complement of the read bases + */ + public static String getBasesReverseComplement(GATKSAMRecord read) { + return getBasesReverseComplement(read.getReadBases()); + } + } diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java index 8602a2bd3..cbc7c01ed 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java @@ -147,9 +147,26 @@ public class GATKVCFUtils { return VCFUtils.withUpdatedContigs(header, engine.getArguments().referenceFile, engine.getMasterSequenceDictionary()); } + public static String rsIDOfFirstRealVariant(List VCs, VariantContext.Type type) { + if ( VCs == null ) + return null; + + String rsID = null; + for ( VariantContext vc : VCs ) { + if ( vc.getType() == type ) { + rsID = vc.getID(); + break; + } + } + + return rsID; + } + /** * Read all of the VCF records from source into memory, returning the header and the VariantContexts * + * SHOULD ONLY BE USED FOR UNIT/INTEGRATION TESTING PURPOSES! + * * @param source the file to read, must be in VCF4 format * @return * @throws java.io.IOException diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java index 8accb1643..b0f3cc5fe 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java @@ -27,19 +27,74 @@ package org.broadinstitute.sting.utils.variant; import com.google.java.contract.Requires; import org.apache.commons.lang.ArrayUtils; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.MathUtils; +import org.apache.log4j.Logger; +import org.broad.tribble.TribbleException; +import org.broad.tribble.util.popgen.HardyWeinbergCalculation; +import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.vcf.VCFConstants; +import java.io.Serializable; import java.util.*; public class GATKVariantContextUtils { + private static Logger logger = Logger.getLogger(GATKVariantContextUtils.class); + public static final int DEFAULT_PLOIDY = 2; public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call. private static final List NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL); + public final static String MERGE_FILTER_PREFIX = "filterIn"; + public final static String MERGE_REF_IN_ALL = "ReferenceInAll"; + public final static String MERGE_FILTER_IN_ALL = "FilteredInAll"; + public final static String MERGE_INTERSECTION = "Intersection"; + + + public enum GenotypeMergeType { + /** + * Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD. + */ + UNIQUIFY, + /** + * Take genotypes in priority order (see the priority argument). + */ + PRIORITIZE, + /** + * Take the genotypes in any order. + */ + UNSORTED, + /** + * Require that all samples/genotypes be unique between all inputs. + */ + REQUIRE_UNIQUE + } + + public enum FilteredRecordMergeType { + /** + * Union - leaves the record if any record is unfiltered. + */ + KEEP_IF_ANY_UNFILTERED, + /** + * Requires all records present at site to be unfiltered. VCF files that don't contain the record don't influence this. + */ + KEEP_IF_ALL_UNFILTERED, + /** + * If any record is present at this site (regardless of possibly being filtered), then all such records are kept and the filters are reset. + */ + KEEP_UNCONDITIONAL + } + + public enum MultipleAllelesMergeType { + /** + * Combine only alleles of the same type (SNP, indel, etc.) into a single VCF record. + */ + BY_TYPE, + /** + * Merge all allele types at the same start position into the same VCF record. + */ + MIX_TYPES + } /** * create a genome location, given a variant context @@ -51,6 +106,68 @@ public class GATKVariantContextUtils { return genomeLocParser.createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd(), true); } + public static BaseUtils.BaseSubstitutionType getSNPSubstitutionType(VariantContext context) { + if (!context.isSNP() || !context.isBiallelic()) + throw new IllegalStateException("Requested SNP substitution type for bialleic non-SNP " + context); + return BaseUtils.SNPSubstitutionType(context.getReference().getBases()[0], context.getAlternateAllele(0).getBases()[0]); + } + + /** + * If this is a BiAlleic SNP, is it a transition? + */ + public static boolean isTransition(VariantContext context) { + return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSITION; + } + + /** + * If this is a BiAlleic SNP, is it a transversion? + */ + public static boolean isTransversion(VariantContext context) { + return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSVERSION; + } + + public static boolean isTransition(Allele ref, Allele alt) { + return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSITION; + } + + public static boolean isTransversion(Allele ref, Allele alt) { + return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSVERSION; + } + + /** + * Returns a context identical to this with the REF and ALT alleles reverse complemented. + * + * @param vc variant context + * @return new vc + */ + public static VariantContext reverseComplement(VariantContext vc) { + // create a mapping from original allele to reverse complemented allele + HashMap alleleMap = new HashMap(vc.getAlleles().size()); + for ( Allele originalAllele : vc.getAlleles() ) { + Allele newAllele; + if ( originalAllele.isNoCall() ) + newAllele = originalAllele; + else + newAllele = Allele.create(BaseUtils.simpleReverseComplement(originalAllele.getBases()), originalAllele.isReference()); + alleleMap.put(originalAllele, newAllele); + } + + // create new Genotype objects + GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples()); + for ( final Genotype genotype : vc.getGenotypes() ) { + List newAlleles = new ArrayList(); + for ( Allele allele : genotype.getAlleles() ) { + Allele newAllele = alleleMap.get(allele); + if ( newAllele == null ) + newAllele = Allele.NO_CALL; + newAlleles.add(newAllele); + } + newGenotypes.add(new GenotypeBuilder(genotype).alleles(newAlleles).make()); + } + + return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).make(); + } + /** * Returns true iff VC is an non-complex indel where every allele represents an expansion or * contraction of a series of identical bases in the reference. @@ -137,9 +254,9 @@ public class GATKVariantContextUtils { return new Pair, byte[]>(lengths,repeatUnit); } - protected static Pair getNumTandemRepeatUnits(final byte[] refBases, final byte[] altBases, final byte[] remainingRefContext) { + public static Pair getNumTandemRepeatUnits(final byte[] refBases, final byte[] altBases, final byte[] remainingRefContext) { /* we can't exactly apply same logic as in basesAreRepeated() to compute tandem unit and number of repeated units. - Consider case where ref =ATATAT and we have an insertion of ATAT. Natural description is (AT)3 -> (AT)5. + Consider case where ref =ATATAT and we have an insertion of ATAT. Natural description is (AT)3 -> (AT)2. */ byte[] longB; @@ -155,11 +272,10 @@ public class GATKVariantContextUtils { final byte[] repeatUnit = Arrays.copyOf(longB, repeatUnitLength); final int[] repetitionCount = new int[2]; -// repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext)); -// repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext)); - int repetitionsInRef = findNumberofRepetitions(repeatUnit,refBases); - repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext))-repetitionsInRef; - repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext))-repetitionsInRef; + // look for repetitions forward on the ref bases (i.e. starting at beginning of ref bases) + int repetitionsInRef = findNumberofRepetitions(repeatUnit,refBases, true); + repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext), true)-repetitionsInRef; + repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext), true)-repetitionsInRef; return new Pair(repetitionCount, repeatUnit); @@ -200,17 +316,33 @@ public class GATKVariantContextUtils { * For example, for string ATAT and repeat unit AT, number of repetitions = 2 * @param repeatUnit Substring * @param testString String to test + * @oaram lookForward Look for repetitions forward (at beginning of string) or backward (at end of string) * @return Number of repetitions (0 if testString is not a concatenation of n repeatUnit's */ - public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) { + public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString, boolean lookForward) { int numRepeats = 0; - for (int start = 0; start < testString.length; start += repeatUnit.length) { + if (lookForward) { + // look forward on the test string + for (int start = 0; start < testString.length; start += repeatUnit.length) { + int end = start + repeatUnit.length; + byte[] unit = Arrays.copyOfRange(testString,start, end); + if(Arrays.equals(unit,repeatUnit)) + numRepeats++; + else + break; + } + return numRepeats; + } + + // look backward. For example, if repeatUnit = AT and testString = GATAT, number of repeat units is still 2 + // look forward on the test string + for (int start = testString.length - repeatUnit.length; start >= 0; start -= repeatUnit.length) { int end = start + repeatUnit.length; byte[] unit = Arrays.copyOfRange(testString,start, end); if(Arrays.equals(unit,repeatUnit)) numRepeats++; else - return numRepeats; + break; } return numRepeats; } @@ -240,7 +372,7 @@ public class GATKVariantContextUtils { final int start = i * potentialRepeat.length(); final int end = (i+1) * potentialRepeat.length(); if ( ref.length() < end ) - return false; // we ran out of bases to test + return false; // we ran out of bases to test final String refSub = ref.substring(start, end); if ( ! refSub.equals(potentialRepeat) ) return false; // repeat didn't match, fail @@ -249,50 +381,6 @@ public class GATKVariantContextUtils { return true; // we passed all tests, we matched } - /** - * Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs - * - * @param vc variant context with genotype likelihoods - * @return genotypes context - */ - public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) { - return subsetDiploidAlleles(vc, vc.getAlleles(), true); - } - - /** - * 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 - * - * Chromosome counts are updated (but they are by definition 0) - * - * @param vc a potentially multi-allelic variant context - * @return a list of bi-allelic (or monomorphic) variant context - */ - public static List splitVariantContextToBiallelics(final VariantContext vc) { - if ( ! vc.isVariant() || vc.isBiallelic() ) - // non variant or biallelics already satisfy the contract - return Collections.singletonList(vc); - else { - final List biallelics = new LinkedList(); - - for ( final Allele alt : vc.getAlternateAlleles() ) { - VariantContextBuilder builder = new VariantContextBuilder(vc); - final List alleles = Arrays.asList(vc.getReference(), alt); - builder.alleles(alleles); - builder.genotypes(subsetDiploidAlleles(vc, alleles, false)); - VariantContextUtils.calculateChromosomeCounts(builder, true); - biallelics.add(reverseTrimAlleles(builder.make())); - } - - return biallelics; - } - } - /** * subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately) * @@ -396,6 +484,424 @@ public class GATKVariantContextUtils { return newGTs; } + /** + * Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs + * + * @param vc variant context with genotype likelihoods + * @return genotypes context + */ + public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) { + return subsetDiploidAlleles(vc, vc.getAlleles(), true); + } + + /** + * 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 + * + * Chromosome counts are updated (but they are by definition 0) + * + * @param vc a potentially multi-allelic variant context + * @return a list of bi-allelic (or monomorphic) variant context + */ + public static List splitVariantContextToBiallelics(final VariantContext vc) { + if ( ! vc.isVariant() || vc.isBiallelic() ) + // non variant or biallelics already satisfy the contract + return Collections.singletonList(vc); + else { + final List biallelics = new LinkedList(); + + for ( final Allele alt : vc.getAlternateAlleles() ) { + VariantContextBuilder builder = new VariantContextBuilder(vc); + final List alleles = Arrays.asList(vc.getReference(), alt); + builder.alleles(alleles); + builder.genotypes(subsetDiploidAlleles(vc, alleles, false)); + VariantContextUtils.calculateChromosomeCounts(builder, true); + biallelics.add(reverseTrimAlleles(builder.make())); + } + + return biallelics; + } + } + + public static Genotype removePLsAndAD(final Genotype g) { + return ( g.hasLikelihoods() || g.hasAD() ) ? new GenotypeBuilder(g).noPL().noAD().make() : g; + } + + /** + * Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority order, if provided. + * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with + * the sample name + * + * @param unsortedVCs collection of unsorted VCs + * @param priorityListOfVCs priority list detailing the order in which we should grab the VCs + * @param filteredRecordMergeType merge type for filtered records + * @param genotypeMergeOptions merge option for genotypes + * @param annotateOrigin should we annotate the set it came from? + * @param printMessages should we print messages? + * @param setKey the key name of the set + * @param filteredAreUncalled are filtered records uncalled? + * @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count? + * @return new VariantContext representing the merge of unsortedVCs + */ + public static VariantContext simpleMerge(final Collection unsortedVCs, + final List priorityListOfVCs, + final FilteredRecordMergeType filteredRecordMergeType, + final GenotypeMergeType genotypeMergeOptions, + final boolean annotateOrigin, + final boolean printMessages, + final String setKey, + final boolean filteredAreUncalled, + final boolean mergeInfoWithMaxAC ) { + int originalNumOfVCs = priorityListOfVCs == null ? 0 : priorityListOfVCs.size(); + return simpleMerge(unsortedVCs,priorityListOfVCs,originalNumOfVCs,filteredRecordMergeType,genotypeMergeOptions,annotateOrigin,printMessages,setKey,filteredAreUncalled,mergeInfoWithMaxAC); + } + + /** + * Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority order, if provided. + * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with + * the sample name. + * simpleMerge does not verify any more unique sample names EVEN if genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE. One should use + * SampleUtils.verifyUniqueSamplesNames to check that before using sempleMerge. + * + * @param unsortedVCs collection of unsorted VCs + * @param priorityListOfVCs priority list detailing the order in which we should grab the VCs + * @param filteredRecordMergeType merge type for filtered records + * @param genotypeMergeOptions merge option for genotypes + * @param annotateOrigin should we annotate the set it came from? + * @param printMessages should we print messages? + * @param setKey the key name of the set + * @param filteredAreUncalled are filtered records uncalled? + * @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count? + * @return new VariantContext representing the merge of unsortedVCs + */ + public static VariantContext simpleMerge(final Collection unsortedVCs, + final List priorityListOfVCs, + final int originalNumOfVCs, + final FilteredRecordMergeType filteredRecordMergeType, + final GenotypeMergeType genotypeMergeOptions, + final boolean annotateOrigin, + final boolean printMessages, + final String setKey, + final boolean filteredAreUncalled, + final boolean mergeInfoWithMaxAC ) { + + if ( unsortedVCs == null || unsortedVCs.size() == 0 ) + return null; + + if (priorityListOfVCs != null && originalNumOfVCs != priorityListOfVCs.size()) + throw new IllegalArgumentException("the number of the original VariantContexts must be the same as the number of VariantContexts in the priority list"); + + if ( annotateOrigin && priorityListOfVCs == null && originalNumOfVCs == 0) + throw new IllegalArgumentException("Cannot merge calls and annotate their origins without a complete priority list of VariantContexts or the number of original VariantContexts"); + + final List preFilteredVCs = sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions); + // Make sure all variant contexts are padded with reference base in case of indels if necessary + final List VCs = new ArrayList(); + + for (final VariantContext vc : preFilteredVCs) { + if ( ! filteredAreUncalled || vc.isNotFiltered() ) + VCs.add(vc); + } + if ( VCs.size() == 0 ) // everything is filtered out and we're filteredAreUncalled + return null; + + // establish the baseline info from the first VC + final VariantContext first = VCs.get(0); + final String name = first.getSource(); + final Allele refAllele = determineReferenceAllele(VCs); + + final Set alleles = new LinkedHashSet(); + final Set filters = new HashSet(); + final Map attributes = new LinkedHashMap(); + final Set inconsistentAttributes = new HashSet(); + final Set variantSources = new HashSet(); // contains the set of sources we found in our set of VCs that are variant + final Set rsIDs = new LinkedHashSet(1); // most of the time there's one id + + VariantContext longestVC = first; + int depth = 0; + int maxAC = -1; + final Map attributesWithMaxAC = new LinkedHashMap(); + double log10PError = CommonInfo.NO_LOG10_PERROR; + VariantContext vcWithMaxAC = null; + GenotypesContext genotypes = GenotypesContext.create(); + + // counting the number of filtered and variant VCs + int nFiltered = 0; + + boolean remapped = false; + + // cycle through and add info from the other VCs, making sure the loc/reference matches + + for ( final VariantContext vc : VCs ) { + if ( longestVC.getStart() != vc.getStart() ) + throw new IllegalStateException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString()); + + if ( VariantContextUtils.getSize(vc) > VariantContextUtils.getSize(longestVC) ) + longestVC = vc; // get the longest location + + nFiltered += vc.isFiltered() ? 1 : 0; + if ( vc.isVariant() ) variantSources.add(vc.getSource()); + + AlleleMapper alleleMapping = resolveIncompatibleAlleles(refAllele, vc, alleles); + remapped = remapped || alleleMapping.needsRemapping(); + + alleles.addAll(alleleMapping.values()); + + mergeGenotypes(genotypes, vc, alleleMapping, genotypeMergeOptions == GenotypeMergeType.UNIQUIFY); + + // We always take the QUAL of the first VC with a non-MISSING qual for the combined value + if ( log10PError == CommonInfo.NO_LOG10_PERROR ) + log10PError = vc.getLog10PError(); + + filters.addAll(vc.getFilters()); + + // + // add attributes + // + // special case DP (add it up) and ID (just preserve it) + // + if (vc.hasAttribute(VCFConstants.DEPTH_KEY)) + depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0); + if ( vc.hasID() ) rsIDs.add(vc.getID()); + if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) { + String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null); + // lets see if the string contains a , separator + if (rawAlleleCounts.contains(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)) { + List alleleCountArray = Arrays.asList(rawAlleleCounts.substring(1, rawAlleleCounts.length() - 1).split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)); + for (String alleleCount : alleleCountArray) { + final int ac = Integer.valueOf(alleleCount.trim()); + if (ac > maxAC) { + maxAC = ac; + vcWithMaxAC = vc; + } + } + } else { + final int ac = Integer.valueOf(rawAlleleCounts); + if (ac > maxAC) { + maxAC = ac; + vcWithMaxAC = vc; + } + } + } + + for (final Map.Entry p : vc.getAttributes().entrySet()) { + String key = p.getKey(); + // if we don't like the key already, don't go anywhere + if ( ! inconsistentAttributes.contains(key) ) { + final boolean alreadyFound = attributes.containsKey(key); + final Object boundValue = attributes.get(key); + final boolean boundIsMissingValue = alreadyFound && boundValue.equals(VCFConstants.MISSING_VALUE_v4); + + if ( alreadyFound && ! boundValue.equals(p.getValue()) && ! boundIsMissingValue ) { + // we found the value but we're inconsistent, put it in the exclude list + //System.out.printf("Inconsistent INFO values: %s => %s and %s%n", key, boundValue, p.getValue()); + inconsistentAttributes.add(key); + attributes.remove(key); + } else if ( ! alreadyFound || boundIsMissingValue ) { // no value + //if ( vc != first ) System.out.printf("Adding key %s => %s%n", p.getKey(), p.getValue()); + attributes.put(key, p.getValue()); + } + } + } + } + + // if we have more alternate alleles in the merged VC than in one or more of the + // original VCs, we need to strip out the GL/PLs (because they are no longer accurate), as well as allele-dependent attributes like AC,AF, and AD + for ( final VariantContext vc : VCs ) { + if (vc.getAlleles().size() == 1) + continue; + if ( hasPLIncompatibleAlleles(alleles, vc.getAlleles())) { + if ( ! genotypes.isEmpty() ) { + logger.debug(String.format("Stripping PLs at %s:%d-%d due to incompatible alleles merged=%s vs. single=%s", + vc.getChr(), vc.getStart(), vc.getEnd(), alleles, vc.getAlleles())); + } + genotypes = stripPLsAndAD(genotypes); + // this will remove stale AC,AF attributed from vc + VariantContextUtils.calculateChromosomeCounts(vc, attributes, true); + break; + } + } + + // take the VC with the maxAC and pull the attributes into a modifiable map + if ( mergeInfoWithMaxAC && vcWithMaxAC != null ) { + attributesWithMaxAC.putAll(vcWithMaxAC.getAttributes()); + } + + // if at least one record was unfiltered and we want a union, clear all of the filters + if ( (filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size()) || filteredRecordMergeType == FilteredRecordMergeType.KEEP_UNCONDITIONAL ) + filters.clear(); + + + if ( annotateOrigin ) { // we care about where the call came from + String setValue; + if ( nFiltered == 0 && variantSources.size() == originalNumOfVCs ) // nothing was unfiltered + setValue = MERGE_INTERSECTION; + else if ( nFiltered == VCs.size() ) // everything was filtered out + setValue = MERGE_FILTER_IN_ALL; + else if ( variantSources.isEmpty() ) // everyone was reference + setValue = MERGE_REF_IN_ALL; + else { + final LinkedHashSet s = new LinkedHashSet(); + for ( final VariantContext vc : VCs ) + if ( vc.isVariant() ) + s.add( vc.isFiltered() ? MERGE_FILTER_PREFIX + vc.getSource() : vc.getSource() ); + setValue = Utils.join("-", s); + } + + if ( setKey != null ) { + attributes.put(setKey, setValue); + if( mergeInfoWithMaxAC && vcWithMaxAC != null ) { + attributesWithMaxAC.put(setKey, setValue); + } + } + } + + if ( depth > 0 ) + attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth)); + + final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs); + + final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID); + builder.loc(longestVC.getChr(), longestVC.getStart(), longestVC.getEnd()); + builder.alleles(alleles); + builder.genotypes(genotypes); + builder.log10PError(log10PError); + builder.filters(filters.isEmpty() ? filters : new TreeSet(filters)); + builder.attributes(new TreeMap(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes)); + + // Trim the padded bases of all alleles if necessary + final VariantContext merged = builder.make(); + if ( printMessages && remapped ) System.out.printf("Remapped => %s%n", merged); + return merged; + } + + private static final boolean hasPLIncompatibleAlleles(final Collection alleleSet1, final Collection alleleSet2) { + final Iterator it1 = alleleSet1.iterator(); + final Iterator it2 = alleleSet2.iterator(); + + while ( it1.hasNext() && it2.hasNext() ) { + final Allele a1 = it1.next(); + final Allele a2 = it2.next(); + if ( ! a1.equals(a2) ) + return true; + } + + // by this point, at least one of the iterators is empty. All of the elements + // we've compared are equal up until this point. But it's possible that the + // sets aren't the same size, which is indicated by the test below. If they + // are of the same size, though, the sets are compatible + return it1.hasNext() || it2.hasNext(); + } + + public static GenotypesContext stripPLsAndAD(GenotypesContext genotypes) { + GenotypesContext newGs = GenotypesContext.create(genotypes.size()); + + for ( final Genotype g : genotypes ) { + newGs.add(removePLsAndAD(g)); + } + + return newGs; + } + + static private Allele determineReferenceAllele(List VCs) { + Allele ref = null; + + for ( VariantContext vc : VCs ) { + Allele myRef = vc.getReference(); + if ( ref == null || ref.length() < myRef.length() ) + ref = myRef; + else if ( ref.length() == myRef.length() && ! ref.equals(myRef) ) + throw new TribbleException(String.format("The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s", vc.getChr(), vc.getStart(), ref, myRef)); + } + + return ref; + } + + static private AlleleMapper resolveIncompatibleAlleles(Allele refAllele, VariantContext vc, Set allAlleles) { + if ( refAllele.equals(vc.getReference()) ) + return new AlleleMapper(vc); + else { + // we really need to do some work. The refAllele is the longest reference allele seen at this + // start site. So imagine it is: + // + // refAllele: ACGTGA + // myRef: ACGT + // myAlt: A + // + // We need to remap all of the alleles in vc to include the extra GA so that + // myRef => refAllele and myAlt => AGA + // + + Allele myRef = vc.getReference(); + if ( refAllele.length() <= myRef.length() ) throw new IllegalStateException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele); + byte[] extraBases = Arrays.copyOfRange(refAllele.getBases(), myRef.length(), refAllele.length()); + +// System.out.printf("Remapping allele at %s%n", vc); +// System.out.printf("ref %s%n", refAllele); +// System.out.printf("myref %s%n", myRef ); +// System.out.printf("extrabases %s%n", new String(extraBases)); + + Map map = new HashMap(); + for ( Allele a : vc.getAlleles() ) { + if ( a.isReference() ) + map.put(a, refAllele); + else { + Allele extended = Allele.extend(a, extraBases); + for ( Allele b : allAlleles ) + if ( extended.equals(b) ) + extended = b; +// System.out.printf(" Extending %s => %s%n", a, extended); + map.put(a, extended); + } + } + + // debugging +// System.out.printf("mapping %s%n", map); + + return new AlleleMapper(map); + } + } + + public static List sortVariantContextsByPriority(Collection unsortedVCs, List priorityListOfVCs, GenotypeMergeType mergeOption ) { + if ( mergeOption == GenotypeMergeType.PRIORITIZE && priorityListOfVCs == null ) + throw new IllegalArgumentException("Cannot merge calls by priority with a null priority list"); + + if ( priorityListOfVCs == null || mergeOption == GenotypeMergeType.UNSORTED ) + return new ArrayList(unsortedVCs); + else { + ArrayList sorted = new ArrayList(unsortedVCs); + Collections.sort(sorted, new CompareByPriority(priorityListOfVCs)); + return sorted; + } + } + + private static void mergeGenotypes(GenotypesContext mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) { + //TODO: should we add a check for cases when the genotypeMergeOption is REQUIRE_UNIQUE + for ( Genotype g : oneVC.getGenotypes() ) { + String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples); + if ( ! mergedGenotypes.containsSample(name) ) { + // only add if the name is new + Genotype newG = g; + + if ( uniqifySamples || alleleMapping.needsRemapping() ) { + final List alleles = alleleMapping.needsRemapping() ? alleleMapping.remap(g.getAlleles()) : g.getAlleles(); + newG = new GenotypeBuilder(g).name(name).alleles(alleles).make(); + } + + mergedGenotypes.add(newG); + } + } + } + + public static String mergedSampleName(String trackName, String sampleName, boolean uniqify ) { + return uniqify ? sampleName + "." + trackName : sampleName; + } + public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) { // see whether we need to trim common reference base from all alleles @@ -472,4 +978,193 @@ public class GATKVariantContextUtils { return clipping; } + + public static double computeHardyWeinbergPvalue(VariantContext vc) { + if ( vc.getCalledChrCount() == 0 ) + return 0.0; + return HardyWeinbergCalculation.hwCalculate(vc.getHomRefCount(), vc.getHetCount(), vc.getHomVarCount()); + } + + public static boolean requiresPaddingBase(final List alleles) { + + // see whether one of the alleles would be null if trimmed through + + for ( final String allele : alleles ) { + if ( allele.isEmpty() ) + return true; + } + + int clipping = 0; + Character currentBase = null; + + while ( true ) { + for ( final String allele : alleles ) { + if ( allele.length() - clipping == 0 ) + return true; + + char myBase = allele.charAt(clipping); + if ( currentBase == null ) + currentBase = myBase; + else if ( currentBase != myBase ) + return false; + } + + clipping++; + currentBase = null; + } + } + + private final static Map subsetAttributes(final CommonInfo igc, final Collection keysToPreserve) { + Map attributes = new HashMap(keysToPreserve.size()); + for ( final String key : keysToPreserve ) { + if ( igc.hasAttribute(key) ) + attributes.put(key, igc.getAttribute(key)); + } + return attributes; + } + + /** + * @deprecated use variant context builder version instead + * @param vc the variant context + * @param keysToPreserve the keys to preserve + * @return a pruned version of the original variant context + */ + @Deprecated + public static VariantContext pruneVariantContext(final VariantContext vc, Collection keysToPreserve ) { + return pruneVariantContext(new VariantContextBuilder(vc), keysToPreserve).make(); + } + + public static VariantContextBuilder pruneVariantContext(final VariantContextBuilder builder, Collection keysToPreserve ) { + final VariantContext vc = builder.make(); + if ( keysToPreserve == null ) keysToPreserve = Collections.emptyList(); + + // VC info + final Map attributes = subsetAttributes(vc.getCommonInfo(), keysToPreserve); + + // Genotypes + final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples()); + for ( final Genotype g : vc.getGenotypes() ) { + final GenotypeBuilder gb = new GenotypeBuilder(g); + // remove AD, DP, PL, and all extended attributes, keeping just GT and GQ + gb.noAD().noDP().noPL().noAttributes(); + genotypes.add(gb.make()); + } + + return builder.genotypes(genotypes).attributes(attributes); + } + + public static boolean allelesAreSubset(VariantContext vc1, VariantContext vc2) { + // if all alleles of vc1 are a contained in alleles of vc2, return true + if (!vc1.getReference().equals(vc2.getReference())) + return false; + + for (Allele a :vc1.getAlternateAlleles()) { + if (!vc2.getAlternateAlleles().contains(a)) + return false; + } + + return true; + } + + public static Map> separateVariantContextsByType(Collection VCs) { + HashMap> mappedVCs = new HashMap>(); + for ( VariantContext vc : VCs ) { + + // look at previous variant contexts of different type. If: + // a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list + // b) vc has alleles which are subset of otherVC. Then, add vc to otherVC's type list (rather, do nothing since vc will be added automatically to its list) + // c) neither: do nothing, just add vc to its own list + boolean addtoOwnList = true; + for (VariantContext.Type type : VariantContext.Type.values()) { + if (type.equals(vc.getType())) + continue; + + if (!mappedVCs.containsKey(type)) + continue; + + List vcList = mappedVCs.get(type); + for (int k=0; k < vcList.size(); k++) { + VariantContext otherVC = vcList.get(k); + if (allelesAreSubset(otherVC,vc)) { + // otherVC has a type different than vc and its alleles are a subset of vc: remove otherVC from its list and add it to vc's type list + vcList.remove(k); + // avoid having empty lists + if (vcList.size() == 0) + mappedVCs.remove(type); + if ( !mappedVCs.containsKey(vc.getType()) ) + mappedVCs.put(vc.getType(), new ArrayList()); + mappedVCs.get(vc.getType()).add(otherVC); + break; + } + else if (allelesAreSubset(vc,otherVC)) { + // vc has a type different than otherVC and its alleles are a subset of VC: add vc to otherVC's type list and don't add to its own + mappedVCs.get(type).add(vc); + addtoOwnList = false; + break; + } + } + } + if (addtoOwnList) { + if ( !mappedVCs.containsKey(vc.getType()) ) + mappedVCs.put(vc.getType(), new ArrayList()); + mappedVCs.get(vc.getType()).add(vc); + } + } + + return mappedVCs; + } + + public static VariantContext purgeUnallowedGenotypeAttributes(VariantContext vc, Set allowedAttributes) { + if ( allowedAttributes == null ) + return vc; + + GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples()); + for ( final Genotype genotype : vc.getGenotypes() ) { + Map attrs = new HashMap(); + for ( Map.Entry attr : genotype.getExtendedAttributes().entrySet() ) { + if ( allowedAttributes.contains(attr.getKey()) ) + attrs.put(attr.getKey(), attr.getValue()); + } + newGenotypes.add(new GenotypeBuilder(genotype).attributes(attrs).make()); + } + + return new VariantContextBuilder(vc).genotypes(newGenotypes).make(); + } + + + private static class AlleleMapper { + private VariantContext vc = null; + private Map map = null; + public AlleleMapper(VariantContext vc) { this.vc = vc; } + public AlleleMapper(Map map) { this.map = map; } + public boolean needsRemapping() { return this.map != null; } + public Collection values() { return map != null ? map.values() : vc.getAlleles(); } + public Allele remap(Allele a) { return map != null && map.containsKey(a) ? map.get(a) : a; } + + public List remap(List as) { + List newAs = new ArrayList(); + for ( Allele a : as ) { + //System.out.printf(" Remapping %s => %s%n", a, remap(a)); + newAs.add(remap(a)); + } + return newAs; + } + } + + private static class CompareByPriority implements Comparator, Serializable { + List priorityListOfVCs; + public CompareByPriority(List priorityListOfVCs) { + this.priorityListOfVCs = priorityListOfVCs; + } + + private int getIndex(VariantContext vc) { + int i = priorityListOfVCs.indexOf(vc.getSource()); + if ( i == -1 ) throw new IllegalArgumentException("Priority list " + priorityListOfVCs + " doesn't contain variant context " + vc.getSource()); + return i; + } + + public int compare(VariantContext vc1, VariantContext vc2) { + return Integer.valueOf(getIndex(vc1)).compareTo(getIndex(vc2)); + } + } } diff --git a/public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java index 2dcd775c0..098b2a5b0 100644 --- a/public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java @@ -27,13 +27,13 @@ package org.broadinstitute.variant.bcf2; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodecHeader; import org.broad.tribble.TribbleException; import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.PositionalBufferedStream; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.vcf.*; import org.broadinstitute.variant.variantcontext.*; @@ -50,8 +50,6 @@ import java.util.Map; * Decode BCF2 files */ public final class BCF2Codec implements FeatureCodec { - final protected static Logger logger = Logger.getLogger(BCF2Codec.class); - private final static int ALLOWED_MAJOR_VERSION = 2; private final static int MIN_MINOR_VERSION = 1; @@ -149,7 +147,9 @@ public final class BCF2Codec implements FeatureCodec { if ( bcfVersion.getMinorVersion() < MIN_MINOR_VERSION ) error("BCF2Codec can only process BCF2 files with minor version >= " + MIN_MINOR_VERSION + " but this file has minor version " + bcfVersion.getMinorVersion()); - logger.debug("Parsing data stream with BCF version " + bcfVersion); + if ( GeneralUtils.DEBUG_MODE_ENABLED ) { + System.err.println("Parsing data stream with BCF version " + bcfVersion); + } final int headerSizeInBytes = BCF2Type.INT32.read(inputStream); diff --git a/public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java index c3a1b5f15..b9970706b 100644 --- a/public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java @@ -27,9 +27,8 @@ package org.broadinstitute.variant.bcf2; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.apache.log4j.Logger; -import org.broad.tribble.FeatureCodec; import org.broad.tribble.TribbleException; +import org.broadinstitute.variant.utils.GeneralUtils; import java.io.ByteArrayInputStream; import java.io.IOException; @@ -38,8 +37,6 @@ import java.util.ArrayList; import java.util.Arrays; public final class BCF2Decoder { - final protected static Logger logger = Logger.getLogger(FeatureCodec.class); - byte[] recordBytes = null; ByteArrayInputStream recordStream = null; @@ -343,8 +340,9 @@ public final class BCF2Decoder { bytesRead += read1; } - if ( nReadAttempts > 1 ) // TODO -- remove me - logger.warn("Required multiple read attempts to actually get the entire BCF2 block, unexpected behavior"); + if ( GeneralUtils.DEBUG_MODE_ENABLED && nReadAttempts > 1 ) { // TODO -- remove me + System.err.println("Required multiple read attempts to actually get the entire BCF2 block, unexpected behavior"); + } validateReadBytes(bytesRead, nReadAttempts, blockSizeInBytes); } catch ( IOException e ) { diff --git a/public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java index 1b624a1b8..87d676526 100644 --- a/public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java @@ -27,7 +27,6 @@ package org.broadinstitute.variant.bcf2; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.apache.log4j.Logger; import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.variant.variantcontext.Allele; @@ -46,7 +45,6 @@ import java.util.*; * @since 6/12 */ public class BCF2GenotypeFieldDecoders { - final protected static Logger logger = Logger.getLogger(BCF2GenotypeFieldDecoders.class); private final static boolean ENABLE_FASTPATH_GT = true; private final static int MIN_SAMPLES_FOR_FASTPATH_GENOTYPES = 0; // TODO -- update to reasonable number diff --git a/public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java index bcd8e41d8..ffbfe81e6 100644 --- a/public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java @@ -26,7 +26,6 @@ package org.broadinstitute.variant.bcf2; import com.google.java.contract.Requires; -import org.apache.log4j.Logger; import org.broad.tribble.TribbleException; import org.broadinstitute.variant.variantcontext.*; @@ -40,8 +39,6 @@ import java.util.*; * @since 5/12 */ public class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser { - final protected static Logger logger = Logger.getLogger(BCF2LazyGenotypesDecoder.class); - // the essential information for us to use to decode the genotypes data // initialized when this lazy decoder is created, as we know all of this from the BCF2Codec // and its stored here again for code cleanliness @@ -63,8 +60,6 @@ public class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser @Override public LazyGenotypesContext.LazyData parse(final Object data) { -// if ( logger.isDebugEnabled() ) -// logger.debug("Decoding BCF genotypes for " + nSamples + " samples with " + nFields + " fields each"); try { // load our byte[] data into the decoder diff --git a/public/java/src/org/broadinstitute/variant/utils/Utils.java b/public/java/src/org/broadinstitute/variant/utils/GeneralUtils.java similarity index 65% rename from public/java/src/org/broadinstitute/variant/utils/Utils.java rename to public/java/src/org/broadinstitute/variant/utils/GeneralUtils.java index e61ce2ef3..2dbc865b5 100644 --- a/public/java/src/org/broadinstitute/variant/utils/Utils.java +++ b/public/java/src/org/broadinstitute/variant/utils/GeneralUtils.java @@ -25,10 +25,18 @@ package org.broadinstitute.variant.utils; -import java.util.Collection; -import java.util.Iterator; +import java.util.*; -public class Utils { +/** + * Constants and utility methods used throughout the VCF/BCF/VariantContext classes + */ +public class GeneralUtils { + + /** + * Setting this to true causes the VCF/BCF/VariantContext classes to emit debugging information + * to standard error + */ + public static final boolean DEBUG_MODE_ENABLED = false; /** * The smallest log10 value we'll emit from normalizeFromLog10 and other functions @@ -66,7 +74,6 @@ public class Utils { } } - /** * normalizes the log10-based array. ASSUMES THAT ALL ARRAY ENTRIES ARE <= 0 (<= 1 IN REAL-SPACE). * @@ -138,6 +145,10 @@ public class Utils { return array[maxElementIndex(array, array.length)]; } + public static int maxElementIndex(final double[] array) { + return maxElementIndex(array, array.length); + } + public static int maxElementIndex(final double[] array, final int endIndex) { if (array == null || array.length == 0) throw new IllegalArgumentException("Array cannot be null!"); @@ -150,6 +161,82 @@ public class Utils { return maxI; } + + public static List cons(final T elt, final List l) { + List l2 = new ArrayList(); + l2.add(elt); + if (l != null) l2.addAll(l); + return l2; + } + + /** + * Make all combinations of N size of objects + * + * if objects = [A, B, C] + * if N = 1 => [[A], [B], [C]] + * if N = 2 => [[A, A], [B, A], [C, A], [A, B], [B, B], [C, B], [A, C], [B, C], [C, C]] + * + * @param objects + * @param n + * @param + * @param withReplacement if false, the resulting permutations will only contain unique objects from objects + * @return + */ + public static List> makePermutations(final List objects, final int n, final boolean withReplacement) { + final List> combinations = new ArrayList>(); + + if ( n <= 0 ) + ; + else if ( n == 1 ) { + for ( final T o : objects ) + combinations.add(Collections.singletonList(o)); + } else { + final List> sub = makePermutations(objects, n - 1, withReplacement); + for ( List subI : sub ) { + for ( final T a : objects ) { + if ( withReplacement || ! subI.contains(a) ) + combinations.add(cons(a, subI)); + } + } + } + + return combinations; + } + + /** + * Compares double values for equality (within 1e-6), or inequality. + * + * @param a the first double value + * @param b the second double value + * @return -1 if a is greater than b, 0 if a is equal to be within 1e-6, 1 if b is greater than a. + */ + public static byte compareDoubles(double a, double b) { + return compareDoubles(a, b, 1e-6); + } + + /** + * Compares double values for equality (within epsilon), or inequality. + * + * @param a the first double value + * @param b the second double value + * @param epsilon the precision within which two double values will be considered equal + * @return -1 if a is greater than b, 0 if a is equal to be within epsilon, 1 if b is greater than a. + */ + public static byte compareDoubles(double a, double b, double epsilon) { + if (Math.abs(a - b) < epsilon) { + return 0; + } + if (a > b) { + return -1; + } + return 1; + } + + static public final List reverse(final List l) { + final List newL = new ArrayList(l); + Collections.reverse(newL); + return newL; + } } diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/Allele.java b/public/java/src/org/broadinstitute/variant/variantcontext/Allele.java index 33bca1a8a..e0a6495a5 100644 --- a/public/java/src/org/broadinstitute/variant/variantcontext/Allele.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/Allele.java @@ -25,7 +25,7 @@ package org.broadinstitute.variant.variantcontext; -import org.broadinstitute.variant.utils.BaseUtils; +import net.sf.samtools.util.StringUtil; import java.util.Arrays; import java.util.Collection; @@ -111,7 +111,7 @@ public class Allele implements Comparable { /** A generic static NO_CALL allele for use */ // no public way to create an allele - private Allele(byte[] bases, boolean isRef) { + protected Allele(byte[] bases, boolean isRef) { // null alleles are no longer allowed if ( wouldBeNullAllele(bases) ) { throw new IllegalArgumentException("Null alleles are not supported"); @@ -130,7 +130,7 @@ public class Allele implements Comparable { if ( isRef ) throw new IllegalArgumentException("Cannot tag a symbolic allele as the reference allele"); } else { - BaseUtils.convertToUpperCase(bases); + StringUtil.toUpperCase(bases); } this.isRef = isRef; @@ -140,7 +140,7 @@ public class Allele implements Comparable { throw new IllegalArgumentException("Unexpected base in allele bases \'" + new String(bases)+"\'"); } - private Allele(String bases, boolean isRef) { + protected Allele(String bases, boolean isRef) { this(bases.getBytes(), isRef); } diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java b/public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java index fd3227dbf..16fa52ee0 100644 --- a/public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java @@ -36,7 +36,7 @@ import java.util.*; * * @author depristo */ -final class CommonInfo { +public final class CommonInfo { public static final double NO_LOG10_PERROR = 1.0; private static Set NO_FILTERS = Collections.emptySet(); diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java index 7d804fd1b..1f6da6ecc 100644 --- a/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java @@ -28,7 +28,7 @@ package org.broadinstitute.variant.variantcontext; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.broad.tribble.TribbleException; -import org.broadinstitute.variant.utils.Utils; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.vcf.VCFConstants; import java.util.Arrays; @@ -155,7 +155,7 @@ public class GenotypeLikelihoods { //Returns null in case of missing likelihoods public EnumMap getAsMap(boolean normalizeFromLog10){ //Make sure that the log10likelihoods are set - double[] likelihoods = normalizeFromLog10 ? Utils.normalizeFromLog10(getAsVector()) : getAsVector(); + double[] likelihoods = normalizeFromLog10 ? GeneralUtils.normalizeFromLog10(getAsVector()) : getAsVector(); if(likelihoods == null) return null; EnumMap likelihoodsMap = new EnumMap(GenotypeType.class); @@ -215,7 +215,7 @@ public class GenotypeLikelihoods { if (qual < 0) { // QUAL can be negative if the chosen genotype is not the most likely one individually. // In this case, we compute the actual genotype probability and QUAL is the likelihood of it not being the chosen one - double[] normalized = Utils.normalizeFromLog10(likelihoods); + double[] normalized = GeneralUtils.normalizeFromLog10(likelihoods); double chosenGenotype = normalized[iOfChoosenGenotype]; return Math.log10(1.0 - chosenGenotype); } else { diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java index 003877088..1fce89431 100644 --- a/public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java @@ -25,10 +25,10 @@ package org.broadinstitute.variant.variantcontext; -import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broad.tribble.TribbleException; import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.vcf.*; import java.util.*; @@ -202,7 +202,6 @@ import java.util.*; public class VariantContext implements Feature { // to enable tribble integration private final static boolean WARN_ABOUT_BAD_END = true; private final static int MAX_ALLELE_SIZE_FOR_NON_SV = 150; - final protected static Logger logger = Logger.getLogger(VariantContext.class); private boolean fullyDecoded = false; protected CommonInfo commonInfo = null; public final static double NO_LOG10_PERROR = CommonInfo.NO_LOG10_PERROR; @@ -626,6 +625,10 @@ public class VariantContext implements Feature { // to enable tribble integratio public double getAttributeAsDouble(String key, double defaultValue) { return commonInfo.getAttributeAsDouble(key, defaultValue); } public boolean getAttributeAsBoolean(String key, boolean defaultValue) { return commonInfo.getAttributeAsBoolean(key, defaultValue); } + public CommonInfo getCommonInfo() { + return commonInfo; + } + // --------------------------------------------------------------------------------------------------------- // // Working with alleles @@ -1176,10 +1179,12 @@ public class VariantContext implements Feature { // to enable tribble integratio final String message = "Badly formed variant context at location " + getChr() + ":" + getStart() + "; getEnd() was " + getEnd() + " but this VariantContext contains an END key with value " + end; - if ( WARN_ABOUT_BAD_END ) - logger.warn(message); - else + if ( GeneralUtils.DEBUG_MODE_ENABLED && WARN_ABOUT_BAD_END ) { + System.err.println(message); + } + else { throw new TribbleException(message); + } } } else { final long length = (stop - start) + 1; diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java index b07040748..a5b7b6c04 100644 --- a/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java @@ -29,22 +29,13 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.commons.jexl2.Expression; import org.apache.commons.jexl2.JexlEngine; -import org.apache.log4j.Logger; import org.broad.tribble.TribbleException; -import org.broad.tribble.util.popgen.HardyWeinbergCalculation; -import org.broadinstitute.variant.utils.BaseUtils; -import org.broadinstitute.variant.utils.Utils; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.vcf.*; -import java.io.Serializable; import java.util.*; public class VariantContextUtils { - private static Logger logger = Logger.getLogger(VariantContextUtils.class); - public final static String MERGE_INTERSECTION = "Intersection"; - public final static String MERGE_FILTER_IN_ALL = "FilteredInAll"; - public final static String MERGE_REF_IN_ALL = "ReferenceInAll"; - public final static String MERGE_FILTER_PREFIX = "filterIn"; private static Set MISSING_KEYS_WARNED_ABOUT = new HashSet(); @@ -155,10 +146,6 @@ public class VariantContextUtils { builder.attributes(calculateChromosomeCounts(vc, new HashMap(vc.getAttributes()), removeStaleValues, founderIds)); } - public static Genotype removePLsAndAD(final Genotype g) { - return ( g.hasLikelihoods() || g.hasAD() ) ? new GenotypeBuilder(g).noPL().noAD().make() : g; - } - public final static VCFCompoundHeaderLine getMetaDataForField(final VCFHeader header, final String field) { VCFCompoundHeaderLine metaData = header.getFormatHeaderLine(field); if ( metaData == null ) metaData = header.getInfoHeaderLine(field); @@ -166,7 +153,8 @@ public class VariantContextUtils { if ( ASSUME_MISSING_FIELDS_ARE_STRINGS ) { if ( ! MISSING_KEYS_WARNED_ABOUT.contains(field) ) { MISSING_KEYS_WARNED_ABOUT.add(field); - logger.warn("Field " + field + " missing from VCF header, assuming it is an unbounded string type"); + if ( GeneralUtils.DEBUG_MODE_ENABLED ) + System.err.println("Field " + field + " missing from VCF header, assuming it is an unbounded string type"); } return new VCFInfoHeaderLine(field, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Auto-generated string header for " + field); } @@ -303,12 +291,6 @@ public class VariantContextUtils { return new JEXLMap(exps,vc,g); } - public static double computeHardyWeinbergPvalue(VariantContext vc) { - if ( vc.getCalledChrCount() == 0 ) - return 0.0; - return HardyWeinbergCalculation.hwCalculate(vc.getHomRefCount(), vc.getHetCount(), vc.getHomVarCount()); - } - /** * Returns a newly allocated VC that is the same as VC, but without genotypes * @param vc variant context @@ -334,648 +316,20 @@ public class VariantContextUtils { return r; } - private final static Map subsetAttributes(final CommonInfo igc, final Collection keysToPreserve) { - Map attributes = new HashMap(keysToPreserve.size()); - for ( final String key : keysToPreserve ) { - if ( igc.hasAttribute(key) ) - attributes.put(key, igc.getAttribute(key)); - } - return attributes; - } + // TODO: remove that after testing +// static private void verifyUniqueSampleNames(Collection unsortedVCs) { +// Set names = new HashSet(); +// for ( VariantContext vc : unsortedVCs ) { +// for ( String name : vc.getSampleNames() ) { +// //System.out.printf("Checking %s %b%n", name, names.contains(name)); +// if ( names.contains(name) ) +// throw new IllegalStateException("REQUIRE_UNIQUE sample names is true but duplicate names were discovered " + name); +// } +// +// names.addAll(vc.getSampleNames()); +// } +// } - /** - * @deprecated use variant context builder version instead - * @param vc the variant context - * @param keysToPreserve the keys to preserve - * @return a pruned version of the original variant context - */ - @Deprecated - public static VariantContext pruneVariantContext(final VariantContext vc, Collection keysToPreserve ) { - return pruneVariantContext(new VariantContextBuilder(vc), keysToPreserve).make(); - } - - public static VariantContextBuilder pruneVariantContext(final VariantContextBuilder builder, Collection keysToPreserve ) { - final VariantContext vc = builder.make(); - if ( keysToPreserve == null ) keysToPreserve = Collections.emptyList(); - - // VC info - final Map attributes = subsetAttributes(vc.commonInfo, keysToPreserve); - - // Genotypes - final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples()); - for ( final Genotype g : vc.getGenotypes() ) { - final GenotypeBuilder gb = new GenotypeBuilder(g); - // remove AD, DP, PL, and all extended attributes, keeping just GT and GQ - gb.noAD().noDP().noPL().noAttributes(); - genotypes.add(gb.make()); - } - - return builder.genotypes(genotypes).attributes(attributes); - } - - public enum GenotypeMergeType { - /** - * Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD. - */ - UNIQUIFY, - /** - * Take genotypes in priority order (see the priority argument). - */ - PRIORITIZE, - /** - * Take the genotypes in any order. - */ - UNSORTED, - /** - * Require that all samples/genotypes be unique between all inputs. - */ - REQUIRE_UNIQUE - } - - public enum FilteredRecordMergeType { - /** - * Union - leaves the record if any record is unfiltered. - */ - KEEP_IF_ANY_UNFILTERED, - /** - * Requires all records present at site to be unfiltered. VCF files that don't contain the record don't influence this. - */ - KEEP_IF_ALL_UNFILTERED, - /** - * If any record is present at this site (regardless of possibly being filtered), then all such records are kept and the filters are reset. - */ - KEEP_UNCONDITIONAL - } - - public enum MultipleAllelesMergeType { - /** - * Combine only alleles of the same type (SNP, indel, etc.) into a single VCF record. - */ - BY_TYPE, - /** - * Merge all allele types at the same start position into the same VCF record. - */ - MIX_TYPES - } - - /** - * Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority order, if provided. - * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with - * the sample name - * - * @param unsortedVCs collection of unsorted VCs - * @param priorityListOfVCs priority list detailing the order in which we should grab the VCs - * @param filteredRecordMergeType merge type for filtered records - * @param genotypeMergeOptions merge option for genotypes - * @param annotateOrigin should we annotate the set it came from? - * @param printMessages should we print messages? - * @param setKey the key name of the set - * @param filteredAreUncalled are filtered records uncalled? - * @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count? - * @return new VariantContext representing the merge of unsortedVCs - */ - public static VariantContext simpleMerge(final Collection unsortedVCs, - final List priorityListOfVCs, - final FilteredRecordMergeType filteredRecordMergeType, - final GenotypeMergeType genotypeMergeOptions, - final boolean annotateOrigin, - final boolean printMessages, - final String setKey, - final boolean filteredAreUncalled, - final boolean mergeInfoWithMaxAC ) { - int originalNumOfVCs = priorityListOfVCs == null ? 0 : priorityListOfVCs.size(); - return simpleMerge(unsortedVCs,priorityListOfVCs,originalNumOfVCs,filteredRecordMergeType,genotypeMergeOptions,annotateOrigin,printMessages,setKey,filteredAreUncalled,mergeInfoWithMaxAC); - } - - /** - * Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority order, if provided. - * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with - * the sample name - * - * @param unsortedVCs collection of unsorted VCs - * @param priorityListOfVCs priority list detailing the order in which we should grab the VCs - * @param filteredRecordMergeType merge type for filtered records - * @param genotypeMergeOptions merge option for genotypes - * @param annotateOrigin should we annotate the set it came from? - * @param printMessages should we print messages? - * @param setKey the key name of the set - * @param filteredAreUncalled are filtered records uncalled? - * @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count? - * @return new VariantContext representing the merge of unsortedVCs - */ - public static VariantContext simpleMerge(final Collection unsortedVCs, - final List priorityListOfVCs, - final int originalNumOfVCs, - final FilteredRecordMergeType filteredRecordMergeType, - final GenotypeMergeType genotypeMergeOptions, - final boolean annotateOrigin, - final boolean printMessages, - final String setKey, - final boolean filteredAreUncalled, - final boolean mergeInfoWithMaxAC ) { - - if ( unsortedVCs == null || unsortedVCs.size() == 0 ) - return null; - - if (priorityListOfVCs != null && originalNumOfVCs != priorityListOfVCs.size()) - throw new IllegalArgumentException("the number of the original VariantContexts must be the same as the number of VariantContexts in the priority list"); - - if ( annotateOrigin && priorityListOfVCs == null && originalNumOfVCs == 0) - throw new IllegalArgumentException("Cannot merge calls and annotate their origins without a complete priority list of VariantContexts or the number of original VariantContexts"); - - if ( genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE ) - verifyUniqueSampleNames(unsortedVCs); - - final List preFilteredVCs = sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions); - // Make sure all variant contexts are padded with reference base in case of indels if necessary - final List VCs = new ArrayList(); - - for (final VariantContext vc : preFilteredVCs) { - if ( ! filteredAreUncalled || vc.isNotFiltered() ) - VCs.add(vc); - } - if ( VCs.size() == 0 ) // everything is filtered out and we're filteredAreUncalled - return null; - - // establish the baseline info from the first VC - final VariantContext first = VCs.get(0); - final String name = first.getSource(); - final Allele refAllele = determineReferenceAllele(VCs); - - final Set alleles = new LinkedHashSet(); - final Set filters = new HashSet(); - final Map attributes = new LinkedHashMap(); - final Set inconsistentAttributes = new HashSet(); - final Set variantSources = new HashSet(); // contains the set of sources we found in our set of VCs that are variant - final Set rsIDs = new LinkedHashSet(1); // most of the time there's one id - - VariantContext longestVC = first; - int depth = 0; - int maxAC = -1; - final Map attributesWithMaxAC = new LinkedHashMap(); - double log10PError = CommonInfo.NO_LOG10_PERROR; - VariantContext vcWithMaxAC = null; - GenotypesContext genotypes = GenotypesContext.create(); - - // counting the number of filtered and variant VCs - int nFiltered = 0; - - boolean remapped = false; - - // cycle through and add info from the other VCs, making sure the loc/reference matches - - for ( final VariantContext vc : VCs ) { - if ( longestVC.getStart() != vc.getStart() ) - throw new IllegalStateException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString()); - - if ( getSize(vc) > getSize(longestVC) ) - longestVC = vc; // get the longest location - - nFiltered += vc.isFiltered() ? 1 : 0; - if ( vc.isVariant() ) variantSources.add(vc.getSource()); - - AlleleMapper alleleMapping = resolveIncompatibleAlleles(refAllele, vc, alleles); - remapped = remapped || alleleMapping.needsRemapping(); - - alleles.addAll(alleleMapping.values()); - - mergeGenotypes(genotypes, vc, alleleMapping, genotypeMergeOptions == GenotypeMergeType.UNIQUIFY); - - // We always take the QUAL of the first VC with a non-MISSING qual for the combined value - if ( log10PError == CommonInfo.NO_LOG10_PERROR ) - log10PError = vc.getLog10PError(); - - filters.addAll(vc.getFilters()); - - // - // add attributes - // - // special case DP (add it up) and ID (just preserve it) - // - if (vc.hasAttribute(VCFConstants.DEPTH_KEY)) - depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0); - if ( vc.hasID() ) rsIDs.add(vc.getID()); - if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) { - String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null); - // lets see if the string contains a , separator - if (rawAlleleCounts.contains(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)) { - List alleleCountArray = Arrays.asList(rawAlleleCounts.substring(1, rawAlleleCounts.length() - 1).split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)); - for (String alleleCount : alleleCountArray) { - final int ac = Integer.valueOf(alleleCount.trim()); - if (ac > maxAC) { - maxAC = ac; - vcWithMaxAC = vc; - } - } - } else { - final int ac = Integer.valueOf(rawAlleleCounts); - if (ac > maxAC) { - maxAC = ac; - vcWithMaxAC = vc; - } - } - } - - for (final Map.Entry p : vc.getAttributes().entrySet()) { - String key = p.getKey(); - // if we don't like the key already, don't go anywhere - if ( ! inconsistentAttributes.contains(key) ) { - final boolean alreadyFound = attributes.containsKey(key); - final Object boundValue = attributes.get(key); - final boolean boundIsMissingValue = alreadyFound && boundValue.equals(VCFConstants.MISSING_VALUE_v4); - - if ( alreadyFound && ! boundValue.equals(p.getValue()) && ! boundIsMissingValue ) { - // we found the value but we're inconsistent, put it in the exclude list - //System.out.printf("Inconsistent INFO values: %s => %s and %s%n", key, boundValue, p.getValue()); - inconsistentAttributes.add(key); - attributes.remove(key); - } else if ( ! alreadyFound || boundIsMissingValue ) { // no value - //if ( vc != first ) System.out.printf("Adding key %s => %s%n", p.getKey(), p.getValue()); - attributes.put(key, p.getValue()); - } - } - } - } - - // if we have more alternate alleles in the merged VC than in one or more of the - // original VCs, we need to strip out the GL/PLs (because they are no longer accurate), as well as allele-dependent attributes like AC,AF, and AD - for ( final VariantContext vc : VCs ) { - if (vc.alleles.size() == 1) - continue; - if ( hasPLIncompatibleAlleles(alleles, vc.alleles)) { - if ( ! genotypes.isEmpty() ) - logger.debug(String.format("Stripping PLs at %s:%d-%d due to incompatible alleles merged=%s vs. single=%s", - vc.getChr(), vc.getStart(), vc.getEnd(), alleles, vc.alleles)); - genotypes = stripPLsAndAD(genotypes); - // this will remove stale AC,AF attributed from vc - calculateChromosomeCounts(vc, attributes, true); - break; - } - } - - // take the VC with the maxAC and pull the attributes into a modifiable map - if ( mergeInfoWithMaxAC && vcWithMaxAC != null ) { - attributesWithMaxAC.putAll(vcWithMaxAC.getAttributes()); - } - - // if at least one record was unfiltered and we want a union, clear all of the filters - if ( (filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size()) || filteredRecordMergeType == FilteredRecordMergeType.KEEP_UNCONDITIONAL ) - filters.clear(); - - - if ( annotateOrigin ) { // we care about where the call came from - String setValue; - if ( nFiltered == 0 && variantSources.size() == originalNumOfVCs ) // nothing was unfiltered - setValue = MERGE_INTERSECTION; - else if ( nFiltered == VCs.size() ) // everything was filtered out - setValue = MERGE_FILTER_IN_ALL; - else if ( variantSources.isEmpty() ) // everyone was reference - setValue = MERGE_REF_IN_ALL; - else { - final LinkedHashSet s = new LinkedHashSet(); - for ( final VariantContext vc : VCs ) - if ( vc.isVariant() ) - s.add( vc.isFiltered() ? MERGE_FILTER_PREFIX + vc.getSource() : vc.getSource() ); - setValue = Utils.join("-", s); - } - - if ( setKey != null ) { - attributes.put(setKey, setValue); - if( mergeInfoWithMaxAC && vcWithMaxAC != null ) { - attributesWithMaxAC.put(setKey, setValue); - } - } - } - - if ( depth > 0 ) - attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth)); - - final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs); - - final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID); - builder.loc(longestVC.getChr(), longestVC.getStart(), longestVC.getEnd()); - builder.alleles(alleles); - builder.genotypes(genotypes); - builder.log10PError(log10PError); - builder.filters(filters.isEmpty() ? filters : new TreeSet(filters)); - builder.attributes(new TreeMap(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes)); - - // Trim the padded bases of all alleles if necessary - final VariantContext merged = builder.make(); - if ( printMessages && remapped ) System.out.printf("Remapped => %s%n", merged); - return merged; - } - - private static final boolean hasPLIncompatibleAlleles(final Collection alleleSet1, final Collection alleleSet2) { - final Iterator it1 = alleleSet1.iterator(); - final Iterator it2 = alleleSet2.iterator(); - - while ( it1.hasNext() && it2.hasNext() ) { - final Allele a1 = it1.next(); - final Allele a2 = it2.next(); - if ( ! a1.equals(a2) ) - return true; - } - - // by this point, at least one of the iterators is empty. All of the elements - // we've compared are equal up until this point. But it's possible that the - // sets aren't the same size, which is indicated by the test below. If they - // are of the same size, though, the sets are compatible - return it1.hasNext() || it2.hasNext(); - } - - public static boolean allelesAreSubset(VariantContext vc1, VariantContext vc2) { - // if all alleles of vc1 are a contained in alleles of vc2, return true - if (!vc1.getReference().equals(vc2.getReference())) - return false; - - for (Allele a :vc1.getAlternateAlleles()) { - if (!vc2.getAlternateAlleles().contains(a)) - return false; - } - - return true; - } - - public static GenotypesContext stripPLsAndAD(GenotypesContext genotypes) { - GenotypesContext newGs = GenotypesContext.create(genotypes.size()); - - for ( final Genotype g : genotypes ) { - newGs.add(removePLsAndAD(g)); - } - - return newGs; - } - - public static Map> separateVariantContextsByType(Collection VCs) { - HashMap> mappedVCs = new HashMap>(); - for ( VariantContext vc : VCs ) { - - // look at previous variant contexts of different type. If: - // a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list - // b) vc has alleles which are subset of otherVC. Then, add vc to otherVC's type list (rather, do nothing since vc will be added automatically to its list) - // c) neither: do nothing, just add vc to its own list - boolean addtoOwnList = true; - for (VariantContext.Type type : VariantContext.Type.values()) { - if (type.equals(vc.getType())) - continue; - - if (!mappedVCs.containsKey(type)) - continue; - - List vcList = mappedVCs.get(type); - for (int k=0; k < vcList.size(); k++) { - VariantContext otherVC = vcList.get(k); - if (allelesAreSubset(otherVC,vc)) { - // otherVC has a type different than vc and its alleles are a subset of vc: remove otherVC from its list and add it to vc's type list - vcList.remove(k); - // avoid having empty lists - if (vcList.size() == 0) - mappedVCs.remove(type); - if ( !mappedVCs.containsKey(vc.getType()) ) - mappedVCs.put(vc.getType(), new ArrayList()); - mappedVCs.get(vc.getType()).add(otherVC); - break; - } - else if (allelesAreSubset(vc,otherVC)) { - // vc has a type different than otherVC and its alleles are a subset of VC: add vc to otherVC's type list and don't add to its own - mappedVCs.get(type).add(vc); - addtoOwnList = false; - break; - } - } - } - if (addtoOwnList) { - if ( !mappedVCs.containsKey(vc.getType()) ) - mappedVCs.put(vc.getType(), new ArrayList()); - mappedVCs.get(vc.getType()).add(vc); - } - } - - return mappedVCs; - } - - private static class AlleleMapper { - private VariantContext vc = null; - private Map map = null; - public AlleleMapper(VariantContext vc) { this.vc = vc; } - public AlleleMapper(Map map) { this.map = map; } - public boolean needsRemapping() { return this.map != null; } - public Collection values() { return map != null ? map.values() : vc.getAlleles(); } - public Allele remap(Allele a) { return map != null && map.containsKey(a) ? map.get(a) : a; } - - public List remap(List as) { - List newAs = new ArrayList(); - for ( Allele a : as ) { - //System.out.printf(" Remapping %s => %s%n", a, remap(a)); - newAs.add(remap(a)); - } - return newAs; - } - } - - static private void verifyUniqueSampleNames(Collection unsortedVCs) { - Set names = new HashSet(); - for ( VariantContext vc : unsortedVCs ) { - for ( String name : vc.getSampleNames() ) { - //System.out.printf("Checking %s %b%n", name, names.contains(name)); - if ( names.contains(name) ) - throw new IllegalStateException("REQUIRE_UNIQUE sample names is true but duplicate names were discovered " + name); - } - - names.addAll(vc.getSampleNames()); - } - } - - - static private Allele determineReferenceAllele(List VCs) { - Allele ref = null; - - for ( VariantContext vc : VCs ) { - Allele myRef = vc.getReference(); - if ( ref == null || ref.length() < myRef.length() ) - ref = myRef; - else if ( ref.length() == myRef.length() && ! ref.equals(myRef) ) - throw new TribbleException(String.format("The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s", vc.getChr(), vc.getStart(), ref, myRef)); - } - - return ref; - } - - static private AlleleMapper resolveIncompatibleAlleles(Allele refAllele, VariantContext vc, Set allAlleles) { - if ( refAllele.equals(vc.getReference()) ) - return new AlleleMapper(vc); - else { - // we really need to do some work. The refAllele is the longest reference allele seen at this - // start site. So imagine it is: - // - // refAllele: ACGTGA - // myRef: ACGT - // myAlt: A - // - // We need to remap all of the alleles in vc to include the extra GA so that - // myRef => refAllele and myAlt => AGA - // - - Allele myRef = vc.getReference(); - if ( refAllele.length() <= myRef.length() ) throw new IllegalStateException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele); - byte[] extraBases = Arrays.copyOfRange(refAllele.getBases(), myRef.length(), refAllele.length()); - -// System.out.printf("Remapping allele at %s%n", vc); -// System.out.printf("ref %s%n", refAllele); -// System.out.printf("myref %s%n", myRef ); -// System.out.printf("extrabases %s%n", new String(extraBases)); - - Map map = new HashMap(); - for ( Allele a : vc.getAlleles() ) { - if ( a.isReference() ) - map.put(a, refAllele); - else { - Allele extended = Allele.extend(a, extraBases); - for ( Allele b : allAlleles ) - if ( extended.equals(b) ) - extended = b; -// System.out.printf(" Extending %s => %s%n", a, extended); - map.put(a, extended); - } - } - - // debugging -// System.out.printf("mapping %s%n", map); - - return new AlleleMapper(map); - } - } - - static class CompareByPriority implements Comparator, Serializable { - List priorityListOfVCs; - public CompareByPriority(List priorityListOfVCs) { - this.priorityListOfVCs = priorityListOfVCs; - } - - private int getIndex(VariantContext vc) { - int i = priorityListOfVCs.indexOf(vc.getSource()); - if ( i == -1 ) throw new IllegalArgumentException("Priority list " + priorityListOfVCs + " doesn't contain variant context " + vc.getSource()); - return i; - } - - public int compare(VariantContext vc1, VariantContext vc2) { - return Integer.valueOf(getIndex(vc1)).compareTo(getIndex(vc2)); - } - } - - public static List sortVariantContextsByPriority(Collection unsortedVCs, List priorityListOfVCs, GenotypeMergeType mergeOption ) { - if ( mergeOption == GenotypeMergeType.PRIORITIZE && priorityListOfVCs == null ) - throw new IllegalArgumentException("Cannot merge calls by priority with a null priority list"); - - if ( priorityListOfVCs == null || mergeOption == GenotypeMergeType.UNSORTED ) - return new ArrayList(unsortedVCs); - else { - ArrayList sorted = new ArrayList(unsortedVCs); - Collections.sort(sorted, new CompareByPriority(priorityListOfVCs)); - return sorted; - } - } - - private static void mergeGenotypes(GenotypesContext mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) { - for ( Genotype g : oneVC.getGenotypes() ) { - String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples); - if ( ! mergedGenotypes.containsSample(name) ) { - // only add if the name is new - Genotype newG = g; - - if ( uniqifySamples || alleleMapping.needsRemapping() ) { - final List alleles = alleleMapping.needsRemapping() ? alleleMapping.remap(g.getAlleles()) : g.getAlleles(); - newG = new GenotypeBuilder(g).name(name).alleles(alleles).make(); - } - - mergedGenotypes.add(newG); - } - } - } - - public static String mergedSampleName(String trackName, String sampleName, boolean uniqify ) { - return uniqify ? sampleName + "." + trackName : sampleName; - } - - /** - * Returns a context identical to this with the REF and ALT alleles reverse complemented. - * - * @param vc variant context - * @return new vc - */ - public static VariantContext reverseComplement(VariantContext vc) { - // create a mapping from original allele to reverse complemented allele - HashMap alleleMap = new HashMap(vc.getAlleles().size()); - for ( Allele originalAllele : vc.getAlleles() ) { - Allele newAllele; - if ( originalAllele.isNoCall() ) - newAllele = originalAllele; - else - newAllele = Allele.create(BaseUtils.simpleReverseComplement(originalAllele.getBases()), originalAllele.isReference()); - alleleMap.put(originalAllele, newAllele); - } - - // create new Genotype objects - GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples()); - for ( final Genotype genotype : vc.getGenotypes() ) { - List newAlleles = new ArrayList(); - for ( Allele allele : genotype.getAlleles() ) { - Allele newAllele = alleleMap.get(allele); - if ( newAllele == null ) - newAllele = Allele.NO_CALL; - newAlleles.add(newAllele); - } - newGenotypes.add(new GenotypeBuilder(genotype).alleles(newAlleles).make()); - } - - return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).make(); - } - - public static VariantContext purgeUnallowedGenotypeAttributes(VariantContext vc, Set allowedAttributes) { - if ( allowedAttributes == null ) - return vc; - - GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples()); - for ( final Genotype genotype : vc.getGenotypes() ) { - Map attrs = new HashMap(); - for ( Map.Entry attr : genotype.getExtendedAttributes().entrySet() ) { - if ( allowedAttributes.contains(attr.getKey()) ) - attrs.put(attr.getKey(), attr.getValue()); - } - newGenotypes.add(new GenotypeBuilder(genotype).attributes(attrs).make()); - } - - return new VariantContextBuilder(vc).genotypes(newGenotypes).make(); - } - - public static BaseUtils.BaseSubstitutionType getSNPSubstitutionType(VariantContext context) { - if (!context.isSNP() || !context.isBiallelic()) - throw new IllegalStateException("Requested SNP substitution type for bialleic non-SNP " + context); - return BaseUtils.SNPSubstitutionType(context.getReference().getBases()[0], context.getAlternateAllele(0).getBases()[0]); - } - - /** - * If this is a BiAlleic SNP, is it a transition? - */ - public static boolean isTransition(VariantContext context) { - return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSITION; - } - - /** - * If this is a BiAlleic SNP, is it a transversion? - */ - public static boolean isTransversion(VariantContext context) { - return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSVERSION; - } - - public static boolean isTransition(Allele ref, Allele alt) { - return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSITION; - } - - public static boolean isTransversion(Allele ref, Allele alt) { - return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSVERSION; - } public static int getSize( VariantContext vc ) { return vc.getEnd() - vc.getStart() + 1; @@ -1017,33 +371,4 @@ public class VariantContextUtils { } } - public static boolean requiresPaddingBase(final List alleles) { - - // see whether one of the alleles would be null if trimmed through - - for ( final String allele : alleles ) { - if ( allele.isEmpty() ) - return true; - } - - int clipping = 0; - Character currentBase = null; - - while ( true ) { - for ( final String allele : alleles ) { - if ( allele.length() - clipping == 0 ) - return true; - - char myBase = allele.charAt(clipping); - if ( currentBase == null ) - currentBase = myBase; - else if ( currentBase != myBase ) - return false; - } - - clipping++; - currentBase = null; - } - } - } diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java index 2df3e3227..efdd54b57 100644 --- a/public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java @@ -27,7 +27,7 @@ package org.broadinstitute.variant.variantcontext; import org.apache.commons.jexl2.JexlContext; import org.apache.commons.jexl2.MapContext; -import org.broadinstitute.variant.utils.Utils; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.vcf.VCFConstants; import java.util.Collection; @@ -168,7 +168,7 @@ class JEXLMap implements Map { infoMap.put("QUAL", String.valueOf(vc.getPhredScaledQual())); // add alleles - infoMap.put("ALLELES", Utils.join(";", vc.getAlleles())); + infoMap.put("ALLELES", GeneralUtils.join(";", vc.getAlleles())); infoMap.put("N_ALLELES", String.valueOf(vc.getNAlleles())); // add attributes diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java index c80f83855..a3cbc5bf3 100644 --- a/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java @@ -27,7 +27,7 @@ package org.broadinstitute.variant.variantcontext.writer; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.apache.log4j.Logger; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.vcf.*; import java.util.HashMap; @@ -40,7 +40,6 @@ import java.util.Map; * @since 06/12 */ public class BCF2FieldWriterManager { - final protected static Logger logger = Logger.getLogger(BCF2FieldWriterManager.class); final Map siteWriters = new HashMap(); final Map genotypesWriters = new HashMap(); final IntGenotypeFieldAccessors intGenotypeFieldAccessors = new IntGenotypeFieldAccessors(); @@ -98,8 +97,8 @@ public class BCF2FieldWriterManager { final boolean createGenotypesEncoders ) { if ( createGenotypesEncoders && intGenotypeFieldAccessors.getAccessor(line.getID()) != null ) { - if ( line.getType() != VCFHeaderLineType.Integer ) - logger.warn("Warning: field " + line.getID() + " expected to encode an integer but saw " + line.getType() + " for record " + line); + if ( GeneralUtils.DEBUG_MODE_ENABLED && line.getType() != VCFHeaderLineType.Integer ) + System.err.println("Warning: field " + line.getID() + " expected to encode an integer but saw " + line.getType() + " for record " + line); return new BCF2FieldEncoder.IntArray(line, dict); } else if ( createGenotypesEncoders && line.getID().equals(VCFConstants.GENOTYPE_KEY) ) { return new BCF2FieldEncoder.GenericInts(line, dict); diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java index e01a39cfb..c24ffec48 100644 --- a/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java @@ -28,11 +28,11 @@ package org.broadinstitute.variant.variantcontext.writer; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.SAMSequenceDictionary; -import org.apache.log4j.Logger; import org.broadinstitute.variant.bcf2.BCF2Codec; import org.broadinstitute.variant.bcf2.BCF2Type; import org.broadinstitute.variant.bcf2.BCF2Utils; import org.broadinstitute.variant.bcf2.BCFVersion; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFContigHeaderLine; import org.broadinstitute.variant.vcf.VCFHeader; @@ -89,7 +89,6 @@ class BCF2Writer extends IndexingVariantContextWriter { public static final int MAJOR_VERSION = 2; public static final int MINOR_VERSION = 1; - final protected static Logger logger = Logger.getLogger(BCF2Writer.class); final private static boolean ALLOW_MISSING_CONTIG_LINES = false; private final OutputStream outputStream; // Note: do not flush until completely done writing, to avoid issues with eventual BGZF support @@ -129,7 +128,9 @@ class BCF2Writer extends IndexingVariantContextWriter { // create the config offsets map if ( header.getContigLines().isEmpty() ) { if ( ALLOW_MISSING_CONTIG_LINES ) { - logger.warn("No contig dictionary found in header, falling back to reference sequence dictionary"); + if ( GeneralUtils.DEBUG_MODE_ENABLED ) { + System.err.println("No contig dictionary found in header, falling back to reference sequence dictionary"); + } createContigDictionary(VCFUtils.makeContigHeaderLines(getRefDict(), null)); } else { throw new IllegalStateException("Cannot write BCF2 file with missing contig lines"); @@ -275,10 +276,8 @@ class BCF2Writer extends IndexingVariantContextWriter { if ( lgc.getUnparsedGenotypeData() instanceof BCF2Codec.LazyData && canSafelyWriteRawGenotypesBytes((BCF2Codec.LazyData) lgc.getUnparsedGenotypeData())) { - //logger.info("Passing on raw BCF2 genotypes data"); return (BCF2Codec.LazyData)lgc.getUnparsedGenotypeData(); } else { - //logger.info("Decoding raw BCF2 genotypes data"); lgc.decode(); // WARNING -- required to avoid keeping around bad lazy data for too long } } diff --git a/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java index 8ad79364b..a4ccd050a 100644 --- a/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java @@ -25,14 +25,14 @@ package org.broadinstitute.variant.vcf; -import org.apache.log4j.Logger; import org.broad.tribble.AsciiFeatureCodec; import org.broad.tribble.Feature; import org.broad.tribble.NameAwareCodec; import org.broad.tribble.TribbleException; import org.broad.tribble.readers.LineReader; -import org.broad.tribble.util.BlockCompressedInputStream; +import net.sf.samtools.util.BlockCompressedInputStream; import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.variantcontext.*; import java.io.FileInputStream; @@ -46,7 +46,6 @@ import java.util.zip.GZIPInputStream; public abstract class AbstractVCFCodec extends AsciiFeatureCodec implements NameAwareCodec { public final static int MAX_ALLELE_SIZE_BEFORE_WARNING = (int)Math.pow(2, 20); - protected final static Logger log = Logger.getLogger(AbstractVCFCodec.class); protected final static int NUM_STANDARD_FIELDS = 8; // INFO is the 8th column // we have to store the list of strings that make up the header until they're needed @@ -397,9 +396,9 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec key = infoFieldArray[i]; final VCFInfoHeaderLine headerLine = header.getInfoHeaderLine(key); if ( headerLine != null && headerLine.getType() != VCFHeaderLineType.Flag ) { - if ( ! warnedAboutNoEqualsForNonFlag ) { - log.warn("Found info key " + key + " without a = value, but the header says the field is of type " - + headerLine.getType() + " but this construct is only value for FLAG type fields"); + if ( GeneralUtils.DEBUG_MODE_ENABLED && ! warnedAboutNoEqualsForNonFlag ) { + System.err.println("Found info key " + key + " without a = value, but the header says the field is of type " + + headerLine.getType() + " but this construct is only value for FLAG type fields"); warnedAboutNoEqualsForNonFlag = true; } @@ -517,8 +516,9 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec if ( allele == null || allele.length() == 0 ) generateException("Empty alleles are not permitted in VCF records", lineNo); - if ( MAX_ALLELE_SIZE_BEFORE_WARNING != -1 && allele.length() > MAX_ALLELE_SIZE_BEFORE_WARNING ) - log.warn(String.format("Allele detected with length %d exceeding max size %d at approximately line %d, likely resulting in degraded VCF processing performance", allele.length(), MAX_ALLELE_SIZE_BEFORE_WARNING, lineNo)); + if ( GeneralUtils.DEBUG_MODE_ENABLED && MAX_ALLELE_SIZE_BEFORE_WARNING != -1 && allele.length() > MAX_ALLELE_SIZE_BEFORE_WARNING ) { + System.err.println(String.format("Allele detected with length %d exceeding max size %d at approximately line %d, likely resulting in degraded VCF processing performance", allele.length(), MAX_ALLELE_SIZE_BEFORE_WARNING, lineNo)); + } if ( isSymbolicAllele(allele) ) { if ( isRef ) { diff --git a/public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java index 7aa378642..3fc790f80 100644 --- a/public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java @@ -25,8 +25,8 @@ package org.broadinstitute.variant.vcf; -import org.apache.log4j.Logger; import org.broad.tribble.TribbleException; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; import org.broadinstitute.variant.variantcontext.VariantContext; @@ -38,7 +38,6 @@ import java.util.Map; * a base class for compound header lines, which include info lines and format lines (so far) */ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCFIDHeaderLine { - final protected static Logger logger = Logger.getLogger(VCFHeader.class); public enum SupportedHeaderLineType { INFO(true), FORMAT(false); @@ -197,7 +196,9 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF if ( type == VCFHeaderLineType.Flag && count != 0 ) { count = 0; - logger.warn("FLAG fields must have a count value of 0, but saw " + count + " for header line " + getID() + ". Changing it to 0 inside the code"); + if ( GeneralUtils.DEBUG_MODE_ENABLED ) { + System.err.println("FLAG fields must have a count value of 0, but saw " + count + " for header line " + getID() + ". Changing it to 0 inside the code"); + } } } diff --git a/public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java index 583a01417..9d4c4d576 100644 --- a/public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java @@ -25,9 +25,9 @@ package org.broadinstitute.variant.vcf; -import org.apache.log4j.Logger; import org.broad.tribble.TribbleException; import org.broad.tribble.util.ParsingUtils; +import org.broadinstitute.variant.utils.GeneralUtils; import java.util.*; @@ -45,7 +45,6 @@ import java.util.*; * A class representing the VCF header */ public class VCFHeader { - final protected static Logger logger = Logger.getLogger(VCFHeader.class); // the mandatory header fields public enum HEADER_FIELDS { @@ -73,6 +72,10 @@ public class VCFHeader { public static final String REFERENCE_KEY = "reference"; public static final String CONTIG_KEY = "contig"; public static final String INTERVALS_KEY = "intervals"; + public static final String EXCLUDE_INTERVALS_KEY = "excludeIntervals"; + public static final String INTERVAL_MERGING_KEY = "interval_merging"; + public static final String INTERVAL_SET_RULE_KEY = "interval_set_rule"; + public static final String INTERVAL_PADDING_KEY = "interval_padding"; // were the input samples sorted originally (or are we sorting them)? private boolean samplesWereAlreadySorted = true; @@ -234,9 +237,11 @@ public class VCFHeader { } if ( hasFormatLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && ! hasFormatLine(VCFConstants.GENOTYPE_PL_KEY) ) { - logger.warn("Found " + VCFConstants.GENOTYPE_LIKELIHOODS_KEY + " format, but no " - + VCFConstants.GENOTYPE_PL_KEY + " field. We now only manage PL fields internally" - + " automatically adding a corresponding PL field to your VCF header"); + if ( GeneralUtils.DEBUG_MODE_ENABLED ) { + System.err.println("Found " + VCFConstants.GENOTYPE_LIKELIHOODS_KEY + " format, but no " + + VCFConstants.GENOTYPE_PL_KEY + " field. We now only manage PL fields internally" + + " automatically adding a corresponding PL field to your VCF header"); + } addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification")); } } @@ -250,10 +255,14 @@ public class VCFHeader { */ private final void addMetaDataMapBinding(final Map map, T line) { final String key = line.getID(); - if ( map.containsKey(key) ) - logger.debug("Found duplicate VCF header lines for " + key + "; keeping the first only" ); - else + if ( map.containsKey(key) ) { + if ( GeneralUtils.DEBUG_MODE_ENABLED ) { + System.err.println("Found duplicate VCF header lines for " + key + "; keeping the first only" ); + } + } + else { map.put(key, line); + } } /** diff --git a/public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java b/public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java index b6f982193..d289c679e 100644 --- a/public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java @@ -27,8 +27,8 @@ package org.broadinstitute.variant.vcf; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.apache.log4j.Logger; import org.broad.tribble.TribbleException; +import org.broadinstitute.variant.utils.GeneralUtils; import java.util.*; @@ -46,7 +46,6 @@ public class VCFStandardHeaderLines { * Enabling this causes us to repair header lines even if only their descriptions differ */ private final static boolean REPAIR_BAD_DESCRIPTIONS = false; - protected final static Logger logger = Logger.getLogger(VCFStandardHeaderLines.class); private static Standards formatStandards = new Standards(); private static Standards infoStandards = new Standards(); @@ -216,11 +215,13 @@ public class VCFStandardHeaderLines { final boolean needsRepair = badCountType || badCount || badType || (REPAIR_BAD_DESCRIPTIONS && badDesc); if ( needsRepair ) { - logger.warn("Repairing standard header line for field " + line.getID() + " because" - + (badCountType ? " -- count types disagree; header has " + line.getCountType() + " but standard is " + standard.getCountType() : "") - + (badType ? " -- type disagree; header has " + line.getType() + " but standard is " + standard.getType() : "") - + (badCount ? " -- counts disagree; header has " + line.getCount() + " but standard is " + standard.getCount() : "") - + (badDesc ? " -- descriptions disagree; header has '" + line.getDescription() + "' but standard is '" + standard.getDescription() + "'": "")); + if ( GeneralUtils.DEBUG_MODE_ENABLED ) { + System.err.println("Repairing standard header line for field " + line.getID() + " because" + + (badCountType ? " -- count types disagree; header has " + line.getCountType() + " but standard is " + standard.getCountType() : "") + + (badType ? " -- type disagree; header has " + line.getType() + " but standard is " + standard.getType() : "") + + (badCount ? " -- counts disagree; header has " + line.getCount() + " but standard is " + standard.getCount() : "") + + (badDesc ? " -- descriptions disagree; header has '" + line.getDescription() + "' but standard is '" + standard.getDescription() + "'": "")); + } return standard; } else return line; diff --git a/public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java index f7d4c5b45..f61761652 100644 --- a/public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java @@ -28,17 +28,16 @@ package org.broadinstitute.variant.vcf; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; import org.apache.commons.io.FilenameUtils; -import org.apache.log4j.Logger; -import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.utils.GeneralUtils; import java.io.File; import java.util.*; public class VCFUtils { - public static Set smartMergeHeaders(Collection headers, Logger logger) throws IllegalStateException { + public static Set smartMergeHeaders(Collection headers, boolean emitWarnings) throws IllegalStateException { HashMap map = new HashMap(); // from KEY.NAME -> line - HeaderConflictWarner conflictWarner = new HeaderConflictWarner(logger); + HeaderConflictWarner conflictWarner = new HeaderConflictWarner(emitWarnings); // todo -- needs to remove all version headers from sources and add its own VCF version line for ( VCFHeader source : headers ) { @@ -101,21 +100,6 @@ public class VCFUtils { return new HashSet(map.values()); } - public static String rsIDOfFirstRealVariant(List VCs, VariantContext.Type type) { - if ( VCs == null ) - return null; - - String rsID = null; - for ( VariantContext vc : VCs ) { - if ( vc.getType() == type ) { - rsID = vc.getID(); - break; - } - } - - return rsID; - } - /** * Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary * @@ -193,19 +177,19 @@ public class VCFUtils { return assembly; } - /** Only displays a warning if a logger is provided and an identical warning hasn't been already issued */ + /** Only displays a warning if warnings are enabled and an identical warning hasn't been already issued */ private static final class HeaderConflictWarner { - Logger logger; + boolean emitWarnings; Set alreadyIssued = new HashSet(); - private HeaderConflictWarner(final Logger logger) { - this.logger = logger; + private HeaderConflictWarner( final boolean emitWarnings ) { + this.emitWarnings = emitWarnings; } public void warn(final VCFHeaderLine line, final String msg) { - if ( logger != null && ! alreadyIssued.contains(line.getKey()) ) { + if ( GeneralUtils.DEBUG_MODE_ENABLED && emitWarnings && ! alreadyIssued.contains(line.getKey()) ) { alreadyIssued.add(line.getKey()); - logger.warn(msg); + System.err.println(msg); } } } diff --git a/public/java/test/org/broadinstitute/sting/ExampleToCopyUnitTest.java b/public/java/test/org/broadinstitute/sting/ExampleToCopyUnitTest.java new file mode 100644 index 000000000..765511ae6 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/ExampleToCopyUnitTest.java @@ -0,0 +1,212 @@ +/* + * Copyright (c) 2012 The Broad Institute + * + * 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.sting; + + +// the imports for unit testing. + + +import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMFileReader; +import net.sf.samtools.SAMRecord; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.sting.utils.activeregion.ActiveRegion; +import org.broadinstitute.sting.utils.activeregion.ActivityProfileState; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; +import org.broadinstitute.sting.utils.sam.ArtificialBAMBuilder; +import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.VariantContextTestProvider; +import org.broadinstitute.variant.vcf.VCFCodec; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.*; + +public class ExampleToCopyUnitTest extends BaseTest { + // example genome loc parser for this test, can be deleted if you don't use the reference + private GenomeLocParser genomeLocParser; + + // example fasta index file, can be deleted if you don't use the reference + private IndexedFastaSequenceFile seq; + + @BeforeClass + public void setup() throws FileNotFoundException { + // sequence + seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + genomeLocParser = new GenomeLocParser(seq); + } + + /** + * Combinatorial unit test data provider example. + * + * Creates data for testMyData test function, containing two arguments, start and size at each value + * + * @return Object[][] for testng DataProvider + */ + @DataProvider(name = "MyDataProvider") + public Object[][] makeMyDataProvider() { + List tests = new ArrayList(); + + // this functionality can be adapted to provide input data for whatever you might want in your data + for ( final int start : Arrays.asList(1, 10, 100) ) { + for ( final int size : Arrays.asList(1, 10, 100, 1000) ) { + tests.add(new Object[]{start, size}); + } + } + + return tests.toArray(new Object[][]{}); + } + + /** + * Example testng test using MyDataProvider + */ + @Test(dataProvider = "MyDataProvider") + public void testMyData(final int start, final int size) { + // adaptor this code to do whatever testing you want given the arguments start and size + Assert.assertTrue(start >= 0); + Assert.assertTrue(size >= 0); + } + + /** + * A unit test that creates an artificial read for testing some code that uses reads + */ + @Test() + public void testWithARead() { + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10); + Assert.assertEquals(read.getReadLength(), 10); + // TODO -- add some tests here using read + } + + /** + * A unit test that creates a GenomeLoc for testing + */ + @Test() + public void testWithAGenomeLoc() { + final GenomeLoc loc = genomeLocParser.createGenomeLoc("1", 1, 10); + Assert.assertEquals(loc.size(), 10); + // TODO -- add some tests here using the loc + } + + /** + * A unit test that creates an artificial read for testing some code that uses reads + * + * Note that effective creation of RBPs isn't so good. If you need pileups of specific properties, you shoud + * look into building them yourself as in the example below + */ + @Test() + public void testWithAPileup() { + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); + final GenomeLoc myLocation = genomeLocParser.createGenomeLoc("1", 10); + final ReadBackedPileup pileup = ArtificialSAMUtils.createReadBackedPileup(header, myLocation, 10, 400, 10); + Assert.assertFalse(pileup.isEmpty()); + // TODO -- add some tests here using pileup + } + + /** + * A unit test that creates an artificial read for testing some code that uses reads + * + * Builds the pileup from scratch to have specific properties + */ + @Test() + public void testBuildingAPileupWithSpecificProperties() { + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); + final GenomeLoc myLocation = genomeLocParser.createGenomeLoc("1", 10); + + final int pileupSize = 100; + final int readLength = 10; + final List reads = new LinkedList(); + for ( int i = 0; i < pileupSize; i++ ) { + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead" + i, 0, 1, readLength); + final byte[] bases = Utils.dupBytes((byte)'A', readLength); + bases[0] = (byte)(i % 2 == 0 ? 'A' : 'C'); // every other base is a C + + // set the read's bases and quals + read.setReadBases(bases); + read.setBaseQualities(Utils.dupBytes((byte)30, readLength)); + reads.add(read); + } + + // create a pileup with all reads having offset 0 + final ReadBackedPileup pileup = new ReadBackedPileupImpl(myLocation, reads, 0); + // TODO -- add some tests here using pileup + + // this code ensures that the pileup example is correct. Can be deleted + Assert.assertEquals(pileup.getNumberOfElements(), pileupSize); + int nA = 0, nC = 0; + for ( final PileupElement p : pileup ) { + if ( p.getBase() == 'A' ) nA++; + if ( p.getBase() == 'C' ) nC++; + } + Assert.assertEquals(nA, pileupSize / 2); + Assert.assertEquals(nC, pileupSize / 2); + + } + + /** + * A unit test that creates an artificial read for testing some code that uses reads + */ + @Test() + public void testWithBAMFile() { + // create a fake BAM file, and iterate through it + final ArtificialBAMBuilder bamBuilder = new ArtificialBAMBuilder(seq, 20, 10); + final File bam = bamBuilder.makeTemporarilyBAMFile(); + final SAMFileReader reader = new SAMFileReader(bam); + reader.setSAMRecordFactory(new GATKSamRecordFactory()); + + final Iterator bamIt = reader.iterator(); + while ( bamIt.hasNext() ) { + final GATKSAMRecord read = (GATKSAMRecord)bamIt.next(); // all reads are actually GATKSAMRecords + // TODO -- add some tests that use reads from a BAM + } + } + + /** + * Test code that creates VariantContexts + */ + @Test() + public void testWithVariantContext() throws Exception { + final List alleles = Arrays.asList(Allele.create("A", true), Allele.create("C")); + final VariantContext vc = new VariantContextBuilder("test", "1", 10, 10, alleles).make(); + Assert.assertTrue(vc.getAlleles().size() >= 0); + // TODO -- add some tests that use VariantContext + } +} \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/MD5DB.java b/public/java/test/org/broadinstitute/sting/MD5DB.java index aed98b78a..2b0d52a11 100644 --- a/public/java/test/org/broadinstitute/sting/MD5DB.java +++ b/public/java/test/org/broadinstitute/sting/MD5DB.java @@ -28,11 +28,10 @@ package org.broadinstitute.sting; import org.apache.commons.io.FileUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine; +import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.*; -import java.math.BigInteger; -import java.security.MessageDigest; import java.util.Arrays; /** @@ -252,11 +251,7 @@ public class MD5DB { */ public String testFileMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) { try { - byte[] bytesOfMessage = getBytesFromFile(resultsFile); - byte[] thedigest = MessageDigest.getInstance("MD5").digest(bytesOfMessage); - BigInteger bigInt = new BigInteger(1, thedigest); - String filemd5sum = bigInt.toString(16); - while (filemd5sum.length() < 32) filemd5sum = "0" + filemd5sum; // pad to length 32 + final String filemd5sum = Utils.calcMD5(getBytesFromFile(resultsFile)); // // copy md5 to integrationtests diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java index 9e4612de5..eec0f653a 100644 --- a/public/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java @@ -35,8 +35,8 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.variant.bcf2.BCF2Utils; -import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.variant.variantcontext.VariantContextTestProvider; diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java index d960177d9..00389be97 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java +++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java @@ -86,7 +86,7 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark { }, PER_SAMPLE { @Override - DownsamplingMethod create() { return DownsamplingMethod.getDefaultDownsamplingMethod(new CountLoci(), false); } + DownsamplingMethod create() { return DownsamplingMethod.getDefaultDownsamplingMethod(new CountLoci()); } }; abstract DownsamplingMethod create(); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java index 049e8d6bb..40ec42ef1 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java @@ -52,7 +52,7 @@ public class ReadShardBalancerUnitTest extends BaseTest { * Tests to ensure that ReadShardBalancer works as expected and does not place shard boundaries * at inappropriate places, such as within an alignment start position */ - private static class ExperimentalReadShardBalancerTest extends TestDataProvider { + private static class ReadShardBalancerTest extends TestDataProvider { private int numContigs; private int numStacksPerContig; private int stackSize; @@ -63,19 +63,19 @@ public class ReadShardBalancerUnitTest extends BaseTest { private SAMFileHeader header; private SAMReaderID testBAM; - public ExperimentalReadShardBalancerTest( int numContigs, - int numStacksPerContig, - int stackSize, - int numUnmappedReads, - int downsamplingTargetCoverage ) { - super(ExperimentalReadShardBalancerTest.class); + public ReadShardBalancerTest( int numContigs, + int numStacksPerContig, + int stackSize, + int numUnmappedReads, + int downsamplingTargetCoverage ) { + super(ReadShardBalancerTest.class); this.numContigs = numContigs; this.numStacksPerContig = numStacksPerContig; this.stackSize = stackSize; this.numUnmappedReads = numUnmappedReads; - this.downsamplingMethod = new DownsamplingMethod(DownsampleType.BY_SAMPLE, downsamplingTargetCoverage, null, false); + this.downsamplingMethod = new DownsamplingMethod(DownsampleType.BY_SAMPLE, downsamplingTargetCoverage, null); this.expectedReadCount = Math.min(stackSize, downsamplingTargetCoverage) * numStacksPerContig * numContigs + numUnmappedReads; setName(String.format("%s: numContigs=%d numStacksPerContig=%d stackSize=%d numUnmappedReads=%d downsamplingTargetCoverage=%d", @@ -176,8 +176,8 @@ public class ReadShardBalancerUnitTest extends BaseTest { } } - @DataProvider(name = "ExperimentalReadShardBalancerTestDataProvider") - public Object[][] createExperimentalReadShardBalancerTests() { + @DataProvider(name = "ReadShardBalancerTestDataProvider") + public Object[][] createReadShardBalancerTests() { for ( int numContigs = 1; numContigs <= 3; numContigs++ ) { for ( int numStacksPerContig : Arrays.asList(1, 2, 4) ) { // Use crucial read shard boundary values as the stack sizes @@ -185,18 +185,18 @@ public class ReadShardBalancerUnitTest extends BaseTest { for ( int numUnmappedReads : Arrays.asList(0, ReadShard.DEFAULT_MAX_READS / 2, ReadShard.DEFAULT_MAX_READS * 2) ) { // The first value will result in no downsampling at all, the others in some downsampling for ( int downsamplingTargetCoverage : Arrays.asList(ReadShard.DEFAULT_MAX_READS * 10, ReadShard.DEFAULT_MAX_READS, ReadShard.DEFAULT_MAX_READS / 2) ) { - new ExperimentalReadShardBalancerTest(numContigs, numStacksPerContig, stackSize, numUnmappedReads, downsamplingTargetCoverage); + new ReadShardBalancerTest(numContigs, numStacksPerContig, stackSize, numUnmappedReads, downsamplingTargetCoverage); } } } } } - return ExperimentalReadShardBalancerTest.getTests(ExperimentalReadShardBalancerTest.class); + return ReadShardBalancerTest.getTests(ReadShardBalancerTest.class); } - @Test(dataProvider = "ExperimentalReadShardBalancerTestDataProvider") - public void runExperimentalReadShardBalancerTest( ExperimentalReadShardBalancerTest test ) { + @Test(dataProvider = "ReadShardBalancerTestDataProvider") + public void runReadShardBalancerTest( ReadShardBalancerTest test ) { logger.warn("Running test: " + test); test.run(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/DummyActiveRegionWalker.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/DummyActiveRegionWalker.java new file mode 100644 index 000000000..e2cad88a1 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/DummyActiveRegionWalker.java @@ -0,0 +1,116 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.traversals; + +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocSortedSet; +import org.broadinstitute.sting.utils.activeregion.ActiveRegion; +import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; +import org.broadinstitute.sting.utils.activeregion.ActivityProfileState; + +import java.util.*; + +/** + * ActiveRegionWalker for unit testing + * + * User: depristo + * Date: 1/15/13 + * Time: 1:28 PM + */ +class DummyActiveRegionWalker extends ActiveRegionWalker { + private final double prob; + private EnumSet states = super.desiredReadStates(); + private GenomeLocSortedSet activeRegions = null; + + protected List isActiveCalls = new ArrayList(); + protected Map mappedActiveRegions = new LinkedHashMap(); + private boolean declareHavingPresetRegions = false; + + public DummyActiveRegionWalker() { + this(1.0); + } + + public DummyActiveRegionWalker(double constProb) { + this.prob = constProb; + } + + public DummyActiveRegionWalker(GenomeLocSortedSet activeRegions, EnumSet wantStates, final boolean declareHavingPresetRegions) { + this(activeRegions, declareHavingPresetRegions); + this.states = wantStates; + } + + public DummyActiveRegionWalker(GenomeLocSortedSet activeRegions, final boolean declareHavingPresetRegions) { + this(1.0); + this.activeRegions = activeRegions; + this.declareHavingPresetRegions = declareHavingPresetRegions; + } + + public void setStates(EnumSet states) { + this.states = states; + } + + @Override + public boolean hasPresetActiveRegions() { + return declareHavingPresetRegions; + } + + @Override + public GenomeLocSortedSet getPresetActiveRegions() { + return declareHavingPresetRegions ? activeRegions : null; + } + + @Override + public EnumSet desiredReadStates() { + return states; + } + + @Override + public ActivityProfileState isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + isActiveCalls.add(ref.getLocus()); + final double p = activeRegions == null || activeRegions.overlaps(ref.getLocus()) ? prob : 0.0; + return new ActivityProfileState(ref.getLocus(), p); + } + + @Override + public Integer map(ActiveRegion activeRegion, RefMetaDataTracker metaDataTracker) { + mappedActiveRegions.put(activeRegion.getLocation(), activeRegion); + return 0; + } + + @Override + public Integer reduceInit() { + return 0; + } + + @Override + public Integer reduce(Integer value, Integer sum) { + return 0; + } +} diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOriginalUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOriginalUnitTest.java deleted file mode 100644 index 35a0931df..000000000 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOriginalUnitTest.java +++ /dev/null @@ -1,523 +0,0 @@ -/* - * Copyright (c) 2012 The Broad Institute - * - * 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.sting.gatk.traversals; - -import com.google.java.contract.PreconditionError; -import net.sf.samtools.*; -import org.broadinstitute.sting.commandline.Tags; -import org.broadinstitute.sting.gatk.datasources.reads.*; -import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; -import org.broadinstitute.sting.utils.interval.IntervalMergingRule; -import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.gatk.executive.WindowMaker; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.testng.Assert; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - - -import java.io.File; -import java.io.FileNotFoundException; -import java.util.*; - - -/** - * Created with IntelliJ IDEA. - * User: depristo - * Date: 1/10/13 - * Time: 8:03 PM - * To change this template use File | Settings | File Templates. - */ -public class TraverseActiveRegionsOriginalUnitTest extends BaseTest { - - private class DummyActiveRegionWalker extends ActiveRegionWalker { - private final double prob; - private EnumSet states = super.desiredReadStates(); - - protected List isActiveCalls = new ArrayList(); - protected Map mappedActiveRegions = new HashMap(); - - public DummyActiveRegionWalker() { - this.prob = 1.0; - } - - public DummyActiveRegionWalker(double constProb) { - this.prob = constProb; - } - - public DummyActiveRegionWalker(EnumSet wantStates) { - this.prob = 1.0; - this.states = wantStates; - } - - @Override - public EnumSet desiredReadStates() { - return states; - } - - @Override - public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - isActiveCalls.add(ref.getLocus()); - return new ActivityProfileResult(ref.getLocus(), prob); - } - - @Override - public Integer map(ActiveRegion activeRegion, RefMetaDataTracker metaDataTracker) { - mappedActiveRegions.put(activeRegion.getLocation(), activeRegion); - return 0; - } - - @Override - public Integer reduceInit() { - return 0; - } - - @Override - public Integer reduce(Integer value, Integer sum) { - return 0; - } - } - - private final TraverseActiveRegions t = new TraverseActiveRegionsOriginal(); - - private IndexedFastaSequenceFile reference; - private SAMSequenceDictionary dictionary; - private GenomeLocParser genomeLocParser; - - private List intervals; - - private static final String testBAM = "TraverseActiveRegionsUnitTest.bam"; - private static final String testBAI = "TraverseActiveRegionsUnitTest.bai"; - - @BeforeClass - private void init() throws FileNotFoundException { - reference = new CachingIndexedFastaSequenceFile(new File(hg19Reference)); - dictionary = reference.getSequenceDictionary(); - genomeLocParser = new GenomeLocParser(dictionary); - - // TODO: reads with indels - // TODO: reads which span many regions - // TODO: reads which are partially between intervals (in/outside extension) - // TODO: duplicate reads - // TODO: read at the end of a contig - // TODO: reads which are completely outside intervals but within extension - // TODO: test the extension itself - // TODO: unmapped reads - - intervals = new ArrayList(); - intervals.add(genomeLocParser.createGenomeLoc("1", 10, 20)); - intervals.add(genomeLocParser.createGenomeLoc("1", 1, 999)); - intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999)); - intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999)); - intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000)); - intervals.add(genomeLocParser.createGenomeLoc("2", 1, 100)); - intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100)); - intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList(); - - List reads = new ArrayList(); - reads.add(buildSAMRecord("simple", "1", 100, 200)); - reads.add(buildSAMRecord("overlap_equal", "1", 10, 20)); - reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21)); - reads.add(buildSAMRecord("boundary_equal", "1", 1990, 2009)); - reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008)); - reads.add(buildSAMRecord("boundary_1_pre", "1", 1950, 2000)); - reads.add(buildSAMRecord("boundary_1_post", "1", 1999, 2050)); - reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990)); - reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000)); - reads.add(buildSAMRecord("shard_boundary_1_pre", "1", 16300, 16385)); - reads.add(buildSAMRecord("shard_boundary_1_post", "1", 16384, 16400)); - reads.add(buildSAMRecord("shard_boundary_equal", "1", 16355, 16414)); - reads.add(buildSAMRecord("simple20", "20", 10025, 10075)); - - createBAM(reads); - } - - private void createBAM(List reads) { - File outFile = new File(testBAM); - outFile.deleteOnExit(); - File indexFile = new File(testBAI); - indexFile.deleteOnExit(); - - SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, outFile); - for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) { - out.addAlignment(read); - } - out.close(); - } - - @Test - public void testAllBasesSeen() { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker(); - - List activeIntervals = getIsActiveIntervals(walker, intervals); - // Contract: Every genome position in the analysis interval(s) is processed by the walker's isActive() call - verifyEqualIntervals(intervals, activeIntervals); - } - - private List getIsActiveIntervals(DummyActiveRegionWalker walker, List intervals) { - List activeIntervals = new ArrayList(); - for (LocusShardDataProvider dataProvider : createDataProviders(walker, intervals, testBAM)) { - t.traverse(walker, dataProvider, 0); - activeIntervals.addAll(walker.isActiveCalls); - } - - return activeIntervals; - } - - @Test (expectedExceptions = PreconditionError.class) - public void testIsActiveRangeLow () { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker(-0.1); - getActiveRegions(walker, intervals).values(); - } - - @Test (expectedExceptions = PreconditionError.class) - public void testIsActiveRangeHigh () { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker(1.1); - getActiveRegions(walker, intervals).values(); - } - - @Test - public void testActiveRegionCoverage() { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker(); - - Collection activeRegions = getActiveRegions(walker, intervals).values(); - verifyActiveRegionCoverage(intervals, activeRegions); - } - - private void verifyActiveRegionCoverage(List intervals, Collection activeRegions) { - List intervalStarts = new ArrayList(); - List intervalStops = new ArrayList(); - - for (GenomeLoc interval : intervals) { - intervalStarts.add(interval.getStartLocation()); - intervalStops.add(interval.getStopLocation()); - } - - Map baseRegionMap = new HashMap(); - - for (ActiveRegion activeRegion : activeRegions) { - for (GenomeLoc activeLoc : toSingleBaseLocs(activeRegion.getLocation())) { - // Contract: Regions do not overlap - Assert.assertFalse(baseRegionMap.containsKey(activeLoc), "Genome location " + activeLoc + " is assigned to more than one region"); - baseRegionMap.put(activeLoc, activeRegion); - } - - GenomeLoc start = activeRegion.getLocation().getStartLocation(); - if (intervalStarts.contains(start)) - intervalStarts.remove(start); - - GenomeLoc stop = activeRegion.getLocation().getStopLocation(); - if (intervalStops.contains(stop)) - intervalStops.remove(stop); - } - - for (GenomeLoc baseLoc : toSingleBaseLocs(intervals)) { - // Contract: Each location in the interval(s) is in exactly one region - // Contract: The total set of regions exactly matches the analysis interval(s) - Assert.assertTrue(baseRegionMap.containsKey(baseLoc), "Genome location " + baseLoc + " is not assigned to any region"); - baseRegionMap.remove(baseLoc); - } - - // Contract: The total set of regions exactly matches the analysis interval(s) - Assert.assertEquals(baseRegionMap.size(), 0, "Active regions contain base(s) outside of the given intervals"); - - // Contract: All explicit interval boundaries must also be region boundaries - Assert.assertEquals(intervalStarts.size(), 0, "Interval start location does not match an active region start location"); - Assert.assertEquals(intervalStops.size(), 0, "Interval stop location does not match an active region stop location"); - } - - @Test - public void testActiveRegionExtensionOnContig() { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker(); - - Collection activeRegions = getActiveRegions(walker, intervals).values(); - for (ActiveRegion activeRegion : activeRegions) { - GenomeLoc loc = activeRegion.getExtendedLoc(); - - // Contract: active region extensions must stay on the contig - Assert.assertTrue(loc.getStart() > 0, "Active region extension begins at location " + loc.getStart() + ", past the left end of the contig"); - int refLen = dictionary.getSequence(loc.getContigIndex()).getSequenceLength(); - Assert.assertTrue(loc.getStop() <= refLen, "Active region extension ends at location " + loc.getStop() + ", past the right end of the contig"); - } - } - - @Test - public void testPrimaryReadMapping() { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker(); - - // Contract: Each read has the Primary state in a single region (or none) - // This is the region of maximum overlap for the read (earlier if tied) - - // simple: Primary in 1:1-999 - // overlap_equal: Primary in 1:1-999 - // overlap_unequal: Primary in 1:1-999 - // boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 - // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 - // boundary_1_pre: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 - // boundary_1_post: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 - // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999 - // outside_intervals: none - // shard_boundary_1_pre: Primary in 1:14908-16384, Non-Primary in 1:16385-16927 - // shard_boundary_1_post: Non-Primary in 1:14908-16384, Primary in 1:16385-16927 - // shard_boundary_equal: Non-Primary in 1:14908-16384, Primary in 1:16385-16927 - // simple20: Primary in 20:10000-10100 - - Map activeRegions = getActiveRegions(walker, intervals); - ActiveRegion region; - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999)); - verifyReadMapping(region, "simple", "overlap_equal", "overlap_unequal"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999)); - verifyReadMapping(region, "boundary_unequal", "extended_and_np", "boundary_1_pre"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); - verifyReadMapping(region, "boundary_equal", "boundary_1_post"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 14908, 16384)); - verifyReadMapping(region, "shard_boundary_1_pre"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 16385, 16927)); - verifyReadMapping(region, "shard_boundary_1_post", "shard_boundary_equal"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); - verifyReadMapping(region, "simple20"); - } - - @Test - public void testNonPrimaryReadMapping() { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker( - EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY)); - - // Contract: Each read has the Primary state in a single region (or none) - // This is the region of maximum overlap for the read (earlier if tied) - - // Contract: Each read has the Non-Primary state in all other regions it overlaps - - // simple: Primary in 1:1-999 - // overlap_equal: Primary in 1:1-999 - // overlap_unequal: Primary in 1:1-999 - // boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 - // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 - // boundary_1_pre: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 - // boundary_1_post: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 - // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999 - // outside_intervals: none - // shard_boundary_1_pre: Primary in 1:14908-16384, Non-Primary in 1:16385-16927 - // shard_boundary_1_post: Non-Primary in 1:14908-16384, Primary in 1:16385-16927 - // shard_boundary_equal: Non-Primary in 1:14908-16384, Primary in 1:16385-16927 - // simple20: Primary in 20:10000-10100 - - Map activeRegions = getActiveRegions(walker, intervals); - ActiveRegion region; - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999)); - verifyReadMapping(region, "simple", "overlap_equal", "overlap_unequal", "extended_and_np"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999)); - verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np", "boundary_1_pre", "boundary_1_post"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); - verifyReadMapping(region, "boundary_equal", "boundary_unequal", "boundary_1_pre", "boundary_1_post"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 14908, 16384)); - verifyReadMapping(region, "shard_boundary_1_pre", "shard_boundary_1_post", "shard_boundary_equal"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 16385, 16927)); - verifyReadMapping(region, "shard_boundary_1_pre", "shard_boundary_1_post", "shard_boundary_equal"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); - verifyReadMapping(region, "simple20"); - } - - @Test - public void testExtendedReadMapping() { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker( - EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY, ActiveRegionReadState.EXTENDED)); - - // Contract: Each read has the Primary state in a single region (or none) - // This is the region of maximum overlap for the read (earlier if tied) - - // Contract: Each read has the Non-Primary state in all other regions it overlaps - // Contract: Each read has the Extended state in regions where it only overlaps if the region is extended - - // simple: Primary in 1:1-999 - // overlap_equal: Primary in 1:1-999 - // overlap_unequal: Primary in 1:1-999 - // boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 - // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 - // boundary_1_pre: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 - // boundary_1_post: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 - // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999 - // outside_intervals: none - // shard_boundary_1_pre: Primary in 1:14908-16384, Non-Primary in 1:16385-16927 - // shard_boundary_1_post: Non-Primary in 1:14908-16384, Primary in 1:16385-16927 - // shard_boundary_equal: Non-Primary in 1:14908-16384, Primary in 1:16385-16927 - // simple20: Primary in 20:10000-10100 - - Map activeRegions = getActiveRegions(walker, intervals); - ActiveRegion region; - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1, 999)); - verifyReadMapping(region, "simple", "overlap_equal", "overlap_unequal", "extended_and_np"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999)); - verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np", "boundary_1_pre", "boundary_1_post"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); - verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np", "boundary_1_pre", "boundary_1_post"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 14908, 16384)); - verifyReadMapping(region, "shard_boundary_1_pre", "shard_boundary_1_post", "shard_boundary_equal"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 16385, 16927)); - verifyReadMapping(region, "shard_boundary_1_pre", "shard_boundary_1_post", "shard_boundary_equal"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); - verifyReadMapping(region, "simple20"); - } - - @Test - public void testUnmappedReads() { - // TODO - } - - private void verifyReadMapping(ActiveRegion region, String... reads) { - Collection wantReads = new ArrayList(Arrays.asList(reads)); - for (SAMRecord read : region.getReads()) { - String regionReadName = read.getReadName(); - Assert.assertTrue(wantReads.contains(regionReadName), "Read " + regionReadName + " assigned to active region " + region); - wantReads.remove(regionReadName); - } - - Assert.assertTrue(wantReads.isEmpty(), "Reads missing in active region " + region); - } - - private Map getActiveRegions(DummyActiveRegionWalker walker, List intervals) { - for (LocusShardDataProvider dataProvider : createDataProviders(walker, intervals, testBAM)) - t.traverse(walker, dataProvider, 0); - - t.endTraversal(walker, 0); - - return walker.mappedActiveRegions; - } - - private Collection toSingleBaseLocs(GenomeLoc interval) { - List bases = new ArrayList(); - if (interval.size() == 1) - bases.add(interval); - else { - for (int location = interval.getStart(); location <= interval.getStop(); location++) - bases.add(genomeLocParser.createGenomeLoc(interval.getContig(), location, location)); - } - - return bases; - } - - private Collection toSingleBaseLocs(List intervals) { - Set bases = new TreeSet(); // for sorting and uniqueness - for (GenomeLoc interval : intervals) - bases.addAll(toSingleBaseLocs(interval)); - - return bases; - } - - private void verifyEqualIntervals(List aIntervals, List bIntervals) { - Collection aBases = toSingleBaseLocs(aIntervals); - Collection bBases = toSingleBaseLocs(bIntervals); - - Assert.assertTrue(aBases.size() == bBases.size(), "Interval lists have a differing number of bases: " + aBases.size() + " vs. " + bBases.size()); - - Iterator aIter = aBases.iterator(); - Iterator bIter = bBases.iterator(); - while (aIter.hasNext() && bIter.hasNext()) { - GenomeLoc aLoc = aIter.next(); - GenomeLoc bLoc = bIter.next(); - Assert.assertTrue(aLoc.equals(bLoc), "Interval locations do not match: " + aLoc + " vs. " + bLoc); - } - } - - // copied from LocusViewTemplate - protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) { - SAMFileHeader header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test"); - header.setSequenceDictionary(dictionary); - header.setSortOrder(SAMFileHeader.SortOrder.coordinate); - GATKSAMRecord record = new GATKSAMRecord(header); - - record.setReadName(readName); - record.setReferenceIndex(dictionary.getSequenceIndex(contig)); - record.setAlignmentStart(alignmentStart); - - Cigar cigar = new Cigar(); - int len = alignmentEnd - alignmentStart + 1; - cigar.add(new CigarElement(len, CigarOperator.M)); - record.setCigar(cigar); - record.setReadString(new String(new char[len]).replace("\0", "A")); - record.setBaseQualities(new byte[len]); - - return record; - } - - private List createDataProviders(final Walker walker, List intervals, String bamFile) { - GenomeAnalysisEngine engine = new GenomeAnalysisEngine(); - engine.setGenomeLocParser(genomeLocParser); - t.initialize(engine, walker); - - Collection samFiles = new ArrayList(); - SAMReaderID readerID = new SAMReaderID(new File(bamFile), new Tags()); - samFiles.add(readerID); - - SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser); - - List providers = new ArrayList(); - for (Shard shard : dataSource.createShardIteratorOverIntervals(new GenomeLocSortedSet(genomeLocParser, intervals), new LocusShardBalancer())) { - for (WindowMaker.WindowMakerIterator window : new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs())) { - providers.add(new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList())); - } - } - - return providers; - } -} diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOptimizedUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java similarity index 65% rename from public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOptimizedUnitTest.java rename to public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java index 038cd2853..a574932a7 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOptimizedUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.gatk.traversals; @@ -30,33 +30,26 @@ import net.sf.samtools.*; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.datasources.reads.*; -import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod; import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.iterators.ReadTransformer; import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.GenomeLocSortedSet; +import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.sting.utils.sam.*; import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.executive.WindowMaker; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.ReadUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; @@ -76,62 +69,14 @@ import java.util.*; * Test the Active Region Traversal Contract * http://iwww.broadinstitute.org/gsa/wiki/index.php/Active_Region_Traversal_Contract */ -public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { +public class TraverseActiveRegionsUnitTest extends BaseTest { private final static boolean ENFORCE_CONTRACTS = false; private final static boolean DEBUG = false; - private class DummyActiveRegionWalker extends ActiveRegionWalker { - private final double prob; - private EnumSet states = super.desiredReadStates(); - - protected List isActiveCalls = new ArrayList(); - protected Map mappedActiveRegions = new HashMap(); - - public DummyActiveRegionWalker() { - this.prob = 1.0; - } - - public DummyActiveRegionWalker(double constProb) { - this.prob = constProb; - } - - public DummyActiveRegionWalker(EnumSet wantStates) { - this.prob = 1.0; - this.states = wantStates; - } - - @Override - public EnumSet desiredReadStates() { - return states; - } - - @Override - public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - isActiveCalls.add(ref.getLocus()); - return new ActivityProfileResult(ref.getLocus(), prob); - } - - @Override - public Integer map(ActiveRegion activeRegion, RefMetaDataTracker metaDataTracker) { - mappedActiveRegions.put(activeRegion.getLocation(), activeRegion); - return 0; - } - - @Override - public Integer reduceInit() { - return 0; - } - - @Override - public Integer reduce(Integer value, Integer sum) { - return 0; - } - } - @DataProvider(name = "TraversalEngineProvider") public Object[][] makeTraversals() { final List traversals = new LinkedList(); - traversals.add(new Object[]{new TraverseActiveRegionsOptimized()}); + traversals.add(new Object[]{new TraverseActiveRegions()}); return traversals.toArray(new Object[][]{}); } @@ -234,7 +179,7 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { @Test(enabled = true && ! DEBUG, dataProvider = "TraversalEngineProvider") public void testActiveRegionCoverage(TraverseActiveRegions t) { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker(); + DummyActiveRegionWalker walker = new DummyActiveRegionWalker(new GenomeLocSortedSet(genomeLocParser, intervals), true); Collection activeRegions = getActiveRegions(t, walker, intervals).values(); verifyActiveRegionCoverage(intervals, activeRegions); @@ -297,9 +242,11 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { } } - @Test(enabled = true && ! DEBUG, dataProvider = "TraversalEngineProvider") + @Test(enabled = true && !DEBUG, dataProvider = "TraversalEngineProvider") public void testPrimaryReadMapping(TraverseActiveRegions t) { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker(); + DummyActiveRegionWalker walker = new DummyActiveRegionWalker(new GenomeLocSortedSet(genomeLocParser, intervals), + EnumSet.of(ActiveRegionReadState.PRIMARY), + true); // Contract: Each read has the Primary state in a single region (or none) // This is the region of maximum overlap for the read (earlier if tied) @@ -330,20 +277,18 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); verifyReadMapping(region); - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 14908, 16384)); + region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 10000, 20000)); verifyReadMapping(region, "shard_boundary_1_pre", "shard_boundary_1_post", "shard_boundary_equal"); - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 16385, 16927)); - verifyReadMapping(region); - region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); verifyReadMapping(region, "simple20"); } - @Test(enabled = true, dataProvider = "TraversalEngineProvider") + @Test(enabled = true && ! DEBUG, dataProvider = "TraversalEngineProvider") public void testNonPrimaryReadMapping(TraverseActiveRegions t) { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker( - EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY)); + DummyActiveRegionWalker walker = new DummyActiveRegionWalker(new GenomeLocSortedSet(genomeLocParser, intervals), + EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY), + true); // Contract: Each read has the Primary state in a single region (or none) // This is the region of maximum overlap for the read (earlier if tied) @@ -376,10 +321,7 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); verifyReadMapping(region, "boundary_equal", "boundary_unequal", "boundary_1_pre", "boundary_1_post"); - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 14908, 16384)); - verifyReadMapping(region, "shard_boundary_1_pre", "shard_boundary_1_post", "shard_boundary_equal"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 16385, 16927)); + region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 10000, 20000)); verifyReadMapping(region, "shard_boundary_1_pre", "shard_boundary_1_post", "shard_boundary_equal"); region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); @@ -388,8 +330,9 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { @Test(enabled = true && ! DEBUG, dataProvider = "TraversalEngineProvider") public void testExtendedReadMapping(TraverseActiveRegions t) { - DummyActiveRegionWalker walker = new DummyActiveRegionWalker( - EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY, ActiveRegionReadState.EXTENDED)); + DummyActiveRegionWalker walker = new DummyActiveRegionWalker(new GenomeLocSortedSet(genomeLocParser, intervals), + EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY, ActiveRegionReadState.EXTENDED), + true); // Contract: Each read has the Primary state in a single region (or none) // This is the region of maximum overlap for the read (earlier if tied) @@ -423,10 +366,7 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); verifyReadMapping(region, "boundary_equal", "boundary_unequal", "extended_and_np", "boundary_1_pre", "boundary_1_post"); - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 14908, 16384)); - verifyReadMapping(region, "shard_boundary_1_pre", "shard_boundary_1_post", "shard_boundary_equal"); - - region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 16385, 16927)); + region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 10000, 20000)); verifyReadMapping(region, "shard_boundary_1_pre", "shard_boundary_1_post", "shard_boundary_equal"); region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); @@ -439,6 +379,7 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { } private void verifyReadMapping(ActiveRegion region, String... reads) { + Assert.assertNotNull(region, "Region was unexpectedly null"); final Set regionReads = new HashSet(); for (SAMRecord read : region.getReads()) { Assert.assertFalse(regionReads.contains(read.getReadName()), "Duplicate reads detected in region " + region + " read " + read.getReadName()); @@ -456,7 +397,11 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { } private Map getActiveRegions(TraverseActiveRegions t, DummyActiveRegionWalker walker, List intervals) { - for (LocusShardDataProvider dataProvider : createDataProviders(t, walker, intervals, testBAM)) + return getActiveRegions(t, walker, intervals, testBAM); + } + + private Map getActiveRegions(TraverseActiveRegions t, DummyActiveRegionWalker walker, List intervals, final String bam) { + for (LocusShardDataProvider dataProvider : createDataProviders(t, walker, intervals, bam)) t.traverse(walker, dataProvider, 0); t.endTraversal(walker, 0); @@ -516,14 +461,15 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { record.setCigar(cigar); record.setReadString(new String(new char[len]).replace("\0", "A")); record.setBaseQualities(new byte[len]); + record.setReadGroup(new GATKSAMReadGroupRecord(header.getReadGroup("test"))); return record; } - private List createDataProviders(TraverseActiveRegions t, final Walker walker, List intervals, String bamFile) { + private List createDataProviders(TraverseActiveRegions traverseActiveRegions, final Walker walker, List intervals, String bamFile) { GenomeAnalysisEngine engine = new GenomeAnalysisEngine(); engine.setGenomeLocParser(genomeLocParser); - t.initialize(engine, walker); + traverseActiveRegions.initialize(engine, walker); Collection samFiles = new ArrayList(); SAMReaderID readerID = new SAMReaderID(new File(bamFile), new Tags()); @@ -537,15 +483,201 @@ public class TraverseActiveRegionsOptimizedUnitTest extends BaseTest { new ValidationExclusion(), new ArrayList(), new ArrayList(), - false, (byte)30, false, t instanceof TraverseActiveRegionsOptimized); + false, (byte)30, false, true); + + final Set samples = SampleUtils.getSAMFileSamples(dataSource.getHeader()); List providers = new ArrayList(); for (Shard shard : dataSource.createShardIteratorOverIntervals(new GenomeLocSortedSet(genomeLocParser, intervals), new LocusShardBalancer())) { - for (WindowMaker.WindowMakerIterator window : new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs())) { + for (WindowMaker.WindowMakerIterator window : new WindowMaker(shard, genomeLocParser, dataSource.seek(shard), shard.getGenomeLocs(), samples)) { providers.add(new LocusShardDataProvider(shard, shard.getReadProperties(), genomeLocParser, window.getLocus(), window, reference, new ArrayList())); } } return providers; } + + // --------------------------------------------------------------------------------------------------------- + // + // Combinatorial tests to ensure reads are going into the right regions + // + // --------------------------------------------------------------------------------------------------------- + + @DataProvider(name = "CombinatorialARTTilingProvider") + public Object[][] makeCombinatorialARTTilingProvider() { + final List tests = new LinkedList(); + + final List starts = Arrays.asList( + 1, // very start of the chromosome + ArtificialBAMBuilder.BAM_SHARD_SIZE - 100, // right before the shard boundary + ArtificialBAMBuilder.BAM_SHARD_SIZE + 100 // right after the shard boundary + ); + + final List> allReadStates = Arrays.asList( + EnumSet.of(ActiveRegionReadState.PRIMARY), + EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY), + EnumSet.of(ActiveRegionReadState.PRIMARY, ActiveRegionReadState.NONPRIMARY, ActiveRegionReadState.EXTENDED) + ); + + final int maxTests = Integer.MAX_VALUE; + int nTests = 0; + for ( final int readLength : Arrays.asList(10, 100) ) { + for ( final int skips : Arrays.asList(0, 1, 10) ) { + for ( final int start : starts ) { + for ( final int nReadsPerLocus : Arrays.asList(1, 2) ) { + for ( final int nLoci : Arrays.asList(1, 1000) ) { + final ArtificialBAMBuilder bamBuilder = new ArtificialBAMBuilder(reference, nReadsPerLocus, nLoci); + bamBuilder.setReadLength(readLength); + bamBuilder.setSkipNLoci(skips); + bamBuilder.setAlignmentStart(start); + for ( EnumSet readStates : allReadStates ) { + for ( final GenomeLocSortedSet activeRegions : enumerateActiveRegions(bamBuilder.getAlignmentStart(), bamBuilder.getAlignmentEnd())) { + nTests++; + if ( nTests < maxTests ) // && nTests == 1238 ) + tests.add(new Object[]{nTests, activeRegions, readStates, bamBuilder}); + } + } + } + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + private Collection enumerateActiveRegions(final int start, final int stop) { + // should basically cut up entire region into equal sized chunks, of + // size 10, 20, 50, 100, etc, alternating skipping pieces so they are inactive + // Need to make sure we include some edge cases: + final List activeRegions = new LinkedList(); + + for ( final int stepSize : Arrays.asList(11, 29, 53, 97) ) { + for ( final boolean startWithActive : Arrays.asList(true, false) ) { + activeRegions.add(makeActiveRegionMask(start, stop, stepSize, startWithActive)); + } + } + + // active region is the whole interval + activeRegions.add(new GenomeLocSortedSet(genomeLocParser, genomeLocParser.createGenomeLoc("1", start, stop))); + + // active region extends up to the end of the data, but doesn't include start + activeRegions.add(new GenomeLocSortedSet(genomeLocParser, genomeLocParser.createGenomeLoc("1", start+10, stop))); + + return activeRegions; + } + + private GenomeLocSortedSet makeActiveRegionMask(final int start, final int stop, final int stepSize, final boolean startWithActive) { + final GenomeLocSortedSet active = new GenomeLocSortedSet(genomeLocParser); + + boolean includeRegion = startWithActive; + for ( int left = start; left < stop; left += stepSize) { + final int right = left + stepSize; + final GenomeLoc region = genomeLocParser.createGenomeLoc("1", left, right); + if ( includeRegion ) + active.add(region); + includeRegion = ! includeRegion; + } + + return active; + } + + + @Test(enabled = true && ! DEBUG, dataProvider = "CombinatorialARTTilingProvider") + public void testARTReadsInActiveRegions(final int id, final GenomeLocSortedSet activeRegions, final EnumSet readStates, final ArtificialBAMBuilder bamBuilder) { + logger.warn("Running testARTReadsInActiveRegions id=" + id + " locs " + activeRegions + " against bam " + bamBuilder); + final List intervals = Arrays.asList( + genomeLocParser.createGenomeLoc("1", bamBuilder.getAlignmentStart(), bamBuilder.getAlignmentEnd()) + ); + + final DummyActiveRegionWalker walker = new DummyActiveRegionWalker(activeRegions, false); + walker.setStates(readStates); + + final TraverseActiveRegions traversal = new TraverseActiveRegions(); + final Map activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile().toString()); + + final Set alreadySeenReads = new HashSet(); // for use with the primary / non-primary + for ( final ActiveRegion region : activeRegionsMap.values() ) { + final Set readNamesInRegion = readNamesInRegion(region); + int nReadsExpectedInRegion = 0; + for ( final GATKSAMRecord read : bamBuilder.makeReads() ) { + final GenomeLoc readLoc = genomeLocParser.createGenomeLoc(read); + + boolean shouldBeInRegion = readStates.contains(ActiveRegionReadState.EXTENDED) + ? region.getExtendedLoc().overlapsP(readLoc) + : region.getLocation().overlapsP(readLoc); + + if ( ! readStates.contains(ActiveRegionReadState.NONPRIMARY) ) { + if ( alreadySeenReads.contains(read.getReadName()) ) + shouldBeInRegion = false; + else if ( shouldBeInRegion ) + alreadySeenReads.add(read.getReadName()); + } + + String msg = readNamesInRegion.contains(read.getReadName()) == shouldBeInRegion ? "" : "Region " + region + + " failed contains read check: read " + read + " with span " + readLoc + " should be in region is " + shouldBeInRegion + " but I got the opposite"; + Assert.assertEquals(readNamesInRegion.contains(read.getReadName()), shouldBeInRegion, msg); + + nReadsExpectedInRegion += shouldBeInRegion ? 1 : 0; + } + + Assert.assertEquals(region.size(), nReadsExpectedInRegion, "There are more reads in active region " + region + "than expected"); + } + } + + private Set readNamesInRegion(final ActiveRegion region) { + final Set readNames = new LinkedHashSet(region.getReads().size()); + for ( final SAMRecord read : region.getReads() ) + readNames.add(read.getReadName()); + return readNames; + } + + // --------------------------------------------------------------------------------------------------------- + // + // Make sure all insertion reads are properly included in the active regions + // + // --------------------------------------------------------------------------------------------------------- + + @Test(enabled = true && ! DEBUG) + public void ensureAllInsertionReadsAreInActiveRegions() { + + final int readLength = 10; + final int start = 20; + final int nReadsPerLocus = 10; + final int nLoci = 3; + + final ArtificialBAMBuilder bamBuilder = new ArtificialBAMBuilder(reference, nReadsPerLocus, nLoci); + bamBuilder.setReadLength(readLength); + bamBuilder.setAlignmentStart(start); + + // note that the position must be +1 as the read's all I cigar puts the end 1 bp before start, leaving it out of the region + GATKSAMRecord allI = ArtificialSAMUtils.createArtificialRead(bamBuilder.getHeader(),"allI",0,start+1,readLength); + allI.setCigarString(readLength + "I"); + allI.setReadGroup(new GATKSAMReadGroupRecord(bamBuilder.getHeader().getReadGroups().get(0))); + + bamBuilder.addReads(allI); + + final GenomeLocSortedSet activeRegions = new GenomeLocSortedSet(bamBuilder.getGenomeLocParser()); + activeRegions.add(bamBuilder.getGenomeLocParser().createGenomeLoc("1", 10, 30)); + final List intervals = Arrays.asList( + genomeLocParser.createGenomeLoc("1", bamBuilder.getAlignmentStart(), bamBuilder.getAlignmentEnd()) + ); + + final DummyActiveRegionWalker walker = new DummyActiveRegionWalker(activeRegions, false); + + final TraverseActiveRegions traversal = new TraverseActiveRegions(); + final Map activeRegionsMap = getActiveRegions(traversal, walker, intervals, bamBuilder.makeTemporarilyBAMFile().toString()); + + final ActiveRegion region = activeRegionsMap.values().iterator().next(); + int nReadsExpectedInRegion = 0; + + final Set readNamesInRegion = readNamesInRegion(region); + for ( final GATKSAMRecord read : bamBuilder.makeReads() ) { + Assert.assertTrue(readNamesInRegion.contains(read.getReadName()), + "Region " + region + " should contain read " + read + " with cigar " + read.getCigarString() + " but it wasn't"); + nReadsExpectedInRegion++; + } + + Assert.assertEquals(region.size(), nReadsExpectedInRegion, "There are more reads in active region " + region + "than expected"); + } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java index 4328e3047..8bc373fe8 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java @@ -31,10 +31,7 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; -import org.broadinstitute.sting.gatk.datasources.reads.LegacyReadShardBalancer; -import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; +import org.broadinstitute.sting.gatk.datasources.reads.*; import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.qc.CountReads; @@ -139,7 +136,7 @@ public class TraverseReadsUnitTest extends BaseTest { @Test public void testUnmappedReadCount() { SAMDataSource dataSource = new SAMDataSource(bamList,new ThreadAllocation(),null,genomeLocParser); - Iterable shardStrategy = dataSource.createShardIteratorOverAllReads(new LegacyReadShardBalancer()); + Iterable shardStrategy = dataSource.createShardIteratorOverAllReads(new ReadShardBalancer()); countReadWalker.initialize(); Object accumulator = countReadWalker.reduceInit(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java index 13cd2be73..6b0422c6a 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java @@ -43,13 +43,13 @@ public class BAQIntegrationTest extends WalkerTest { // -------------------------------------------------------------------------------------------------------------- @Test public void testPrintReadsNoBAQ() { - WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("d97340a2bba2c6320d1ebeb86024a27c")); + WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("11af64ba020262d06b490bae2c5e08f8")); executeTest(String.format("testPrintReadsNoBAQ"), spec); } @Test public void testPrintReadsRecalBAQ() { - WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("4ac691bde1ba1301a59857694fda6ae2")); + WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("96ec97cf92f1f660bd5244c6b44539b3")); executeTest(String.format("testPrintReadsRecalBAQ"), spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java index 76654fb74..a6191802b 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java @@ -31,9 +31,6 @@ import org.testng.annotations.Test; import java.util.Arrays; public class PileupWalkerIntegrationTest extends WalkerTest { - String gatkSpeedupArgs="-T Pileup -I " + validationDataLocation + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam " - + "-R " + hg19Reference + " -o %s "; - @Test public void testGnarleyFHSPileup() { String gatk_args = "-T Pileup -I " + validationDataLocation + "FHS_Pileup_Test.bam " @@ -67,31 +64,4 @@ public class PileupWalkerIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(SingleReadAligningOffChromosome1MD5)); executeTest("Testing single read spanning off chromosome 1 unindexed", spec); } - - /************************/ - - //testing speedup to GATKBAMIndex - - - @Test - public void testPileupOnLargeBamChr20(){ - WalkerTestSpec spec = new WalkerTestSpec(gatkSpeedupArgs + "-L 20:1-76,050", 1, Arrays.asList("8702701350de11a6d28204acefdc4775")); - executeTest("Testing single on big BAM at start of chromosome 20", spec); - } - @Test - public void testPileupOnLargeBamMid20(){ - WalkerTestSpec spec = new WalkerTestSpec(gatkSpeedupArgs + "-L 20:10,000,000-10,001,100", 1, Arrays.asList("818cf5a8229efe6f89fc1cd8145ccbe3")); - executeTest("Testing single on big BAM somewhere in chromosome 20", spec); - } - @Test - public void testPileupOnLargeBamEnd20(){ - WalkerTestSpec spec = new WalkerTestSpec(gatkSpeedupArgs + "-L 20:62,954,114-63,025,520", 1, Arrays.asList("22471ea4a12e5139aef62bf8ff2a5b63")); - executeTest("Testing single at end of chromosome 20", spec); - } - @Test - public void testPileupOnLargeBam20Many(){ - WalkerTestSpec spec = new WalkerTestSpec(gatkSpeedupArgs + "-L 20:1-76,050 -L 20:20,000,000-20,000,100 -L 20:40,000,000-40,000,100 -L 20:30,000,000-30,000,100 -L 20:50,000,000-50,000,100 -L 20:62,954,114-63,025,520 ", - 1, Arrays.asList("08d899ed7c5a76ef3947bf67338acda1")); - executeTest("Testing single on big BAM many places", spec); - } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java index ae4bce81b..b3d583ef1 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java @@ -47,22 +47,22 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { } final static String Q10ClipOutput = "b29c5bc1cb9006ed9306d826a11d444f"; - @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "33e781084379aae538954e30919e8fd3"); } - @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "57c05b6241db7110148a91fde2d431d0"); } - @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "57c05b6241db7110148a91fde2d431d0"); } - @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "67263a39d5127f2660a5b638ff32056a"); } + @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "12be03c817d94bab88457e5afe74256a"); } + @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); } + @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1cfc9da4867765c1e5b5bd6326984634"); } + @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "0bcfd177fe4be422898eda8e161ebd6c"); } - @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "764846d0592f346a33525af674fd7a10"); } - @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "3061cf742f9e5526a61130128ae761a3"); } + @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "aed836c97c6383dd80e39a093cc25e08"); } + @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "5f6e08bd44d6faf5b85cde5d4ec1a36f"); } - @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "b89459f373e40f0b835c1faff2208839"); } - @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "24e19116ef16a37a6d095ed5c22c2466"); } + @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "f3cb42759428df80d06e9789f9f9f762"); } + @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "44658c018378467f809b443d047d5778"); } - @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "ad8d30300cb43d5e300fcc4d2450da8e"); } + @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "bae38f83eb9b63857f5e6e3c6e62f80c"); } - @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "57c05b6241db7110148a91fde2d431d0"); } - @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "2a1a3153e0942ab355fd8a6e082b30e0"); } - @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "50d43d63d8e39f67a87a6359963c6f52"); } + @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); } + @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "3b32da2eaab7a2d4729fdb486cedbb2f"); } + @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "9d355b0f6d2076178e92bd7fcd8f5adb"); } @Test public void testUseOriginalQuals() { @@ -74,7 +74,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { " -OQ -QT 4 -CR WRITE_Q0S" + " -o %s -os %s", 2, - Arrays.asList("22db22749f811d30216215e047461621", "55c01ccc2e84481b22d3632cdb06c8ba")); + Arrays.asList("c83b4e2ade8654a2818fe9d405f07662", "55c01ccc2e84481b22d3632cdb06c8ba")); executeTest("clipOriginalQuals", spec); } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java index 83f801a98..b509fc1df 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java @@ -54,17 +54,17 @@ public class PrintReadsIntegrationTest extends WalkerTest { @DataProvider(name = "PRTest") public Object[][] createPrintReadsTestData() { return new Object[][]{ - {new PRTest(hg18Reference, "HiSeq.1mb.bam", "", "dc8e5451dd29757c336013146010f73a")}, - {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -compress 0", "fde82269c78c9e91e57286433531b4af")}, - {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -simplifyBAM", "0531717b32a7e21c0de70b1526b0751f")}, - {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -n 10", "cdc4ddf9ee1d2ecf37168da8ef23c270")}, + {new PRTest(hg18Reference, "HiSeq.1mb.bam", "", "fa9c66f66299fe5405512ac36ec9d0f2")}, + {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -compress 0", "488eb22abc31c6af7cbb1a3d41da1507")}, + {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -simplifyBAM", "1510dc4429f3ed49caf96da41e8ed396")}, + {new PRTest(hg18Reference, "HiSeq.1mb.bam", " -n 10", "0e3d1748ad1cb523e3295cab9d09d8fc")}, // See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance() - {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", "", "0a9ce949d07a84cb33a1a8e3358bf679")}, - {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1", "6e920b8505e7e95d67634b0905237dbc")}, - {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L unmapped", "13bb9a91b1d4dd2425f73302b8a1ac1c")}, - {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1 -L unmapped", "6e920b8505e7e95d67634b0905237dbc")}, - {new PRTest(b37KGReference, "oneReadAllInsertion.bam", "", "6caec4f8a25befb6aba562955401af93")}, - {new PRTest(b37KGReference, "NA12878.1_10mb_2_10mb.bam", "", "c43380ac39b98853af457b90e52f8427")} + {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", "", "e1cac555f3d720f611c47eec93e84bd9")}, + {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1", "6e2558317d409195eab3006dc9e5524c")}, + {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L unmapped", "2d32440e47e8d9d329902fe573ad94ce")}, + {new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1 -L unmapped", "6e2558317d409195eab3006dc9e5524c")}, + {new PRTest(b37KGReference, "oneReadAllInsertion.bam", "", "349650b6aa9e574b48a2a62627f37c7d")}, + {new PRTest(b37KGReference, "NA12878.1_10mb_2_10mb.bam", "", "0c1cbe67296637a85e80e7a182f828ab")} }; } diff --git a/public/java/test/org/broadinstitute/sting/AutoFormattingTimeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/AutoFormattingTimeUnitTest.java similarity index 98% rename from public/java/test/org/broadinstitute/sting/AutoFormattingTimeUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/AutoFormattingTimeUnitTest.java index b1aacd8b9..8bedfb547 100644 --- a/public/java/test/org/broadinstitute/sting/AutoFormattingTimeUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/AutoFormattingTimeUnitTest.java @@ -23,8 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting; +package org.broadinstitute.sting.utils; +import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.AutoFormattingTime; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java similarity index 67% rename from public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java index 372d13a7a..6f645b34d 100644 --- a/public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java @@ -1,33 +1,32 @@ /* -* Copyright (c) 2012 The Broad Institute -* -* 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. -*/ + * Copyright (c) 2012 The Broad Institute + * + * 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.variant.utils; +package org.broadinstitute.sting.utils; -import org.broadinstitute.sting.utils.MathUtils; -import org.testng.Assert; import org.broadinstitute.sting.BaseTest; +import org.testng.Assert; import org.testng.annotations.Test; import org.testng.annotations.BeforeClass; @@ -39,7 +38,7 @@ public class BaseUtilsUnitTest extends BaseTest { @Test public void testMostFrequentBaseFraction() { logger.warn("Executing testMostFrequentBaseFraction"); - + compareFrequentBaseFractionToExpected("AAAAA", 1.0); compareFrequentBaseFractionToExpected("ACCG", 0.5); compareFrequentBaseFractionToExpected("ACCCCTTTTG", 4.0/10.0); @@ -50,6 +49,21 @@ public class BaseUtilsUnitTest extends BaseTest { Assert.assertTrue(MathUtils.compareDoubles(fraction, expected) == 0); } + @Test + public void testConvertIUPACtoN() { + + checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'A', 'A', 'A'}, false, false), new byte[]{'A', 'A', 'A'}); + checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'W', 'A', 'A'}, false, false), new byte[]{'N', 'A', 'A'}); + checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'A', 'M', 'A'}, false, false), new byte[]{'A', 'N', 'A'}); + checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'A', 'A', 'K'}, false, false), new byte[]{'A', 'A', 'N'}); + checkBytesAreEqual(BaseUtils.convertIUPACtoN(new byte[]{'M', 'M', 'M'}, false, false), new byte[]{'N', 'N', 'N'}); + } + + private void checkBytesAreEqual(final byte[] b1, final byte[] b2) { + for ( int i = 0; i < b1.length; i++ ) + Assert.assertEquals(b1[i], b2[i]); + } + @Test public void testTransitionTransversion() { logger.warn("Executing testTransitionTransversion"); diff --git a/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserBenchmark.java b/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserBenchmark.java new file mode 100644 index 000000000..478f02530 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserBenchmark.java @@ -0,0 +1,81 @@ +/* + * Copyright (c) 2012 The Broad Institute + * + * 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.sting.utils; + +import com.google.caliper.Param; +import com.google.caliper.SimpleBenchmark; +import net.sf.picard.reference.IndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; + +import java.io.File; + +/** + * Caliper microbenchmark of genome loc parser + */ +public class GenomeLocParserBenchmark extends SimpleBenchmark { + private IndexedFastaSequenceFile seq; + private final int ITERATIONS = 1000000; + + @Param({"NEW", "NONE"}) + GenomeLocParser.ValidationLevel validationLevel; // set automatically by framework + + @Param({"true", "false"}) + boolean useContigIndex; // set automatically by framework + + @Override protected void setUp() throws Exception { + seq = new CachingIndexedFastaSequenceFile(new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta")); + } +// +// public void timeSequentialCreationFromGenomeLoc(int rep) { +// final GenomeLocParser genomeLocParser = new GenomeLocParser(seq.getSequenceDictionary(), validationLevel); +// GenomeLoc last = genomeLocParser.createGenomeLoc("1", 1, 1); +// for ( int i = 0; i < rep; i++ ) { +// for ( int j = 1; j < ITERATIONS; j++ ) { +// if ( useContigIndex ) +// last = genomeLocParser.createGenomeLoc(last.getContig(), last.getContigIndex(), last.getStart() + 1); +// else +// last = genomeLocParser.createGenomeLoc(last.getContig(), last.getStart() + 1); +// } +// } +// } +// +// public void timeSequentialCreationFromGenomeLocOriginal(int rep) { +// final GenomeLocParserOriginal genomeLocParser = new GenomeLocParserOriginal(seq.getSequenceDictionary()); +// GenomeLoc last = genomeLocParser.createGenomeLoc("1", 1, 1); +// for ( int i = 0; i < rep; i++ ) { +// for ( int j = 1; j < ITERATIONS; j++ ) { +// if ( useContigIndex ) +// last = genomeLocParser.createGenomeLoc(last.getContig(), last.getContigIndex(), last.getStart() + 1); +// else +// last = genomeLocParser.createGenomeLoc(last.getContig(), last.getStart() + 1); +// } +// } +// } + + public static void main(String[] args) { + com.google.caliper.Runner.main(GenomeLocParserBenchmark.class, args); + } +} diff --git a/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java index 4a989b984..9621aecda 100644 --- a/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java @@ -29,17 +29,31 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; +import org.broad.tribble.BasicFeature; +import org.broad.tribble.Feature; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; - -import static org.testng.Assert.assertEquals; -import static org.testng.Assert.assertTrue; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; 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 static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; + /** * @author aaron *

@@ -49,10 +63,11 @@ import org.testng.annotations.Test; */ public class GenomeLocParserUnitTest extends BaseTest { private GenomeLocParser genomeLocParser; + private SAMFileHeader header; @BeforeClass public void init() { - SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10); + header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10); genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); } @@ -231,7 +246,16 @@ public class GenomeLocParserUnitTest extends BaseTest { assertTrue(!genomeLocParser.isValidGenomeLoc("chr1",1,11)); // past the end of the contig assertTrue(!genomeLocParser.isValidGenomeLoc("chr1",-1,10)); // bad start assertTrue(!genomeLocParser.isValidGenomeLoc("chr1",1,-2)); // bad stop + assertTrue( genomeLocParser.isValidGenomeLoc("chr1",-1,2, false)); // bad stop assertTrue(!genomeLocParser.isValidGenomeLoc("chr1",10,11)); // bad start, past end + assertTrue( genomeLocParser.isValidGenomeLoc("chr1",10,11, false)); // bad start, past end + assertTrue(!genomeLocParser.isValidGenomeLoc("chr1",2,1)); // stop < start + } + + @Test(expectedExceptions = ReviewedStingException.class) + public void testValidateGenomeLoc() { + // bad contig index + genomeLocParser.validateGenomeLoc("chr1", 1, 1, 2, false); } private static class FlankingGenomeLocTestData extends TestDataProvider { @@ -333,4 +357,153 @@ public class GenomeLocParserUnitTest extends BaseTest { data.toString(), data.original, actual, data.flankStop); assertEquals(actual, data.flankStop, description); } + + @DataProvider(name = "parseGenomeLoc") + public Object[][] makeParsingTest() { + final List tests = new LinkedList(); + + tests.add(new Object[]{ "chr1:10", "chr1", 10 }); + tests.add(new Object[]{ "chr1:100", "chr1", 100 }); + tests.add(new Object[]{ "chr1:1000", "chr1", 1000 }); + tests.add(new Object[]{ "chr1:1,000", "chr1", 1000 }); + tests.add(new Object[]{ "chr1:10000", "chr1", 10000 }); + tests.add(new Object[]{ "chr1:10,000", "chr1", 10000 }); + tests.add(new Object[]{ "chr1:100000", "chr1", 100000 }); + tests.add(new Object[]{ "chr1:100,000", "chr1", 100000 }); + tests.add(new Object[]{ "chr1:1000000", "chr1", 1000000 }); + tests.add(new Object[]{ "chr1:1,000,000", "chr1", 1000000 }); + tests.add(new Object[]{ "chr1:1000,000", "chr1", 1000000 }); + tests.add(new Object[]{ "chr1:1,000000", "chr1", 1000000 }); + + return tests.toArray(new Object[][]{}); + } + + @Test( dataProvider = "parseGenomeLoc") + public void testParsingPositions(final String string, final String contig, final int start) { + SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10000000); + GenomeLocParser genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); + final GenomeLoc loc = genomeLocParser.parseGenomeLoc(string); + Assert.assertEquals(loc.getContig(), contig); + Assert.assertEquals(loc.getStart(), start); + Assert.assertEquals(loc.getStop(), start); + } + + @Test( ) + public void testCreationFromSAMRecord() { + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5); + final GenomeLoc loc = genomeLocParser.createGenomeLoc(read); + Assert.assertEquals(loc.getContig(), read.getReferenceName()); + Assert.assertEquals(loc.getContigIndex(), (int)read.getReferenceIndex()); + Assert.assertEquals(loc.getStart(), read.getAlignmentStart()); + Assert.assertEquals(loc.getStop(), read.getAlignmentEnd()); + } + + @Test( ) + public void testCreationFromSAMRecordUnmapped() { + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5); + read.setReadUnmappedFlag(true); + read.setReferenceIndex(-1); + final GenomeLoc loc = genomeLocParser.createGenomeLoc(read); + Assert.assertTrue(loc.isUnmapped()); + } + + @Test( ) + public void testCreationFromSAMRecordUnmappedButOnGenome() { + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5); + read.setReadUnmappedFlag(true); + read.setCigarString("*"); + final GenomeLoc loc = genomeLocParser.createGenomeLoc(read); + Assert.assertEquals(loc.getContig(), read.getReferenceName()); + Assert.assertEquals(loc.getContigIndex(), (int)read.getReferenceIndex()); + Assert.assertEquals(loc.getStart(), read.getAlignmentStart()); + Assert.assertEquals(loc.getStop(), read.getAlignmentStart()); + } + + @Test + public void testCreationFromFeature() { + final Feature feature = new BasicFeature("chr1", 1, 5); + final GenomeLoc loc = genomeLocParser.createGenomeLoc(feature); + Assert.assertEquals(loc.getContig(), feature.getChr()); + Assert.assertEquals(loc.getStart(), feature.getStart()); + Assert.assertEquals(loc.getStop(), feature.getEnd()); + } + + @Test + public void testCreationFromVariantContext() { + final VariantContext feature = new VariantContextBuilder("x", "chr1", 1, 5, Arrays.asList(Allele.create("AAAAA", true))).make(); + final GenomeLoc loc = genomeLocParser.createGenomeLoc(feature); + Assert.assertEquals(loc.getContig(), feature.getChr()); + Assert.assertEquals(loc.getStart(), feature.getStart()); + Assert.assertEquals(loc.getStop(), feature.getEnd()); + } + + @Test + public void testcreateGenomeLocOnContig() throws FileNotFoundException { + final CachingIndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + final SAMSequenceDictionary dict = seq.getSequenceDictionary(); + final GenomeLocParser genomeLocParser = new GenomeLocParser(dict); + + for ( final SAMSequenceRecord rec : dict.getSequences() ) { + final GenomeLoc loc = genomeLocParser.createOverEntireContig(rec.getSequenceName()); + Assert.assertEquals(loc.getContig(), rec.getSequenceName()); + Assert.assertEquals(loc.getStart(), 1); + Assert.assertEquals(loc.getStop(), rec.getSequenceLength()); + } + } + + @DataProvider(name = "GenomeLocOnContig") + public Object[][] makeGenomeLocOnContig() { + final List tests = new LinkedList(); + + final int contigLength = header.getSequence(0).getSequenceLength(); + for ( int start = -10; start < contigLength + 10; start++ ) { + for ( final int len : Arrays.asList(1, 10, 20) ) { + tests.add(new Object[]{ "chr1", start, start + len }); + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test( dataProvider = "GenomeLocOnContig") + public void testGenomeLocOnContig(final String contig, final int start, final int stop) { + final int contigLength = header.getSequence(0).getSequenceLength(); + final GenomeLoc loc = genomeLocParser.createGenomeLocOnContig(contig, start, stop); + + if ( stop < 1 || start > contigLength ) + Assert.assertNull(loc, "GenomeLoc should be null if the start/stops are not meaningful"); + else { + Assert.assertNotNull(loc); + Assert.assertEquals(loc.getContig(), contig); + Assert.assertEquals(loc.getStart(), Math.max(start, 1)); + Assert.assertEquals(loc.getStop(), Math.min(stop, contigLength)); + } + } + + @DataProvider(name = "GenomeLocPadding") + public Object[][] makeGenomeLocPadding() { + final List tests = new LinkedList(); + + final int contigLength = header.getSequence(0).getSequenceLength(); + for ( int pad = 0; pad < contigLength + 1; pad++) { + for ( int start = 1; start < contigLength; start++ ) { + for ( int stop = start; stop < contigLength; stop++ ) { + tests.add(new Object[]{ genomeLocParser.createGenomeLoc("chr1", start, stop), pad}); + } + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test( dataProvider = "GenomeLocPadding") + public void testGenomeLocPadding(final GenomeLoc input, final int pad) { + final int contigLength = header.getSequence(0).getSequenceLength(); + final GenomeLoc padded = genomeLocParser.createPaddedGenomeLoc(input, pad); + + Assert.assertNotNull(padded); + Assert.assertEquals(padded.getContig(), input.getContig()); + Assert.assertEquals(padded.getStart(), Math.max(input.getStart() - pad, 1)); + Assert.assertEquals(padded.getStop(), Math.min(input.getStop() + pad, contigLength)); + } } diff --git a/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java index b5d495ddc..ed91114a4 100644 --- a/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java @@ -29,6 +29,7 @@ package org.broadinstitute.sting.utils; // the imports for unit testing. +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.testng.Assert; @@ -40,10 +41,7 @@ import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import java.io.File; import java.io.FileNotFoundException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; +import java.util.*; import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile; @@ -291,4 +289,58 @@ public class GenomeLocUnitTest extends BaseTest { if ( expected == ComparisonResult.EQUALS ) Assert.assertEquals(g1.hashCode(), g2.hashCode(), "Equal genome locs don't have the same hash code"); } + + // ------------------------------------------------------------------------------------- + // + // testing merging functionality + // + // ------------------------------------------------------------------------------------- + + private static final GenomeLoc loc1 = new GenomeLoc("1", 0, 10, 20); + private static final GenomeLoc loc2 = new GenomeLoc("1", 0, 21, 30); + private static final GenomeLoc loc3 = new GenomeLoc("1", 0, 31, 40); + + private class MergeTest { + public List locs; + + private MergeTest(final List locs) { + this.locs = locs; + } + } + + @DataProvider(name = "SGLtest") + public Object[][] createFindVariantRegionsData() { + List tests = new ArrayList(); + + tests.add(new Object[]{new MergeTest(Arrays.asList(loc1))}); + tests.add(new Object[]{new MergeTest(Arrays.asList(loc1, loc2))}); + tests.add(new Object[]{new MergeTest(Arrays.asList(loc1, loc2, loc3))}); + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "SGLtest", enabled = true) + public void testSimpleGenomeLoc(MergeTest test) { + testMerge(test.locs); + } + + @Test(expectedExceptions = ReviewedStingException.class) + public void testNotContiguousLocs() { + final List locs = new ArrayList(1); + locs.add(loc1); + locs.add(loc3); + testMerge(locs); + } + + private void testMerge(final List locs) { + GenomeLoc result1 = locs.get(0); + for ( int i = 1; i < locs.size(); i++ ) + result1 = GenomeLoc.merge(result1, locs.get(i)); + + GenomeLoc result2 = GenomeLoc.merge(new TreeSet(locs)); + Assert.assertEquals(result1, result2); + Assert.assertEquals(result1.getStart(), locs.get(0).getStart()); + Assert.assertEquals(result1.getStop(), locs.get(locs.size() - 1).getStop()); + } + } diff --git a/public/java/test/org/broadinstitute/sting/utils/LegacyReservoirDownsamplerUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/LegacyReservoirDownsamplerUnitTest.java deleted file mode 100644 index bdcd4f600..000000000 --- a/public/java/test/org/broadinstitute/sting/utils/LegacyReservoirDownsamplerUnitTest.java +++ /dev/null @@ -1,191 +0,0 @@ -/* -* Copyright (c) 2012 The Broad Institute -* -* 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.sting.utils; - -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.testng.Assert; -import org.testng.annotations.Test; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMFileHeader; - -import java.util.*; - -/** - * Basic tests to prove the integrity of the reservoir downsampler. - * At the moment, always run tests on SAM records as that's the task - * for which the downsampler was conceived. - * - * @author mhanna - * @version 0.1 - */ -public class LegacyReservoirDownsamplerUnitTest { - private static final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,200); - - - @Test - public void testEmptyIterator() { - LegacyReservoirDownsampler downsampler = new LegacyReservoirDownsampler(1); - Assert.assertTrue(downsampler.isEmpty(),"Downsampler is not empty but should be."); - } - - @Test - public void testOneElementWithPoolSizeOne() { - List reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76)); - LegacyReservoirDownsampler downsampler = new LegacyReservoirDownsampler(1); - downsampler.addAll(reads); - - Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be"); - Collection batchedReads = downsampler.getDownsampledContents(); - Assert.assertEquals(batchedReads.size(), 1, "Downsampler is returning the wrong number of reads"); - Assert.assertSame(batchedReads.iterator().next(), reads.get(0), "Downsampler is returning an incorrect read"); - } - - @Test - public void testOneElementWithPoolSizeGreaterThanOne() { - List reads = Collections.singletonList(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76)); - LegacyReservoirDownsampler downsampler = new LegacyReservoirDownsampler(5); - downsampler.addAll(reads); - - Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be"); - Collection batchedReads = downsampler.getDownsampledContents(); - Assert.assertEquals(batchedReads.size(), 1, "Downsampler is returning the wrong number of reads"); - Assert.assertSame(batchedReads.iterator().next(), reads.get(0), "Downsampler is returning an incorrect read"); - - } - - @Test - public void testPoolFilledPartially() { - List reads = new ArrayList(); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,76)); - LegacyReservoirDownsampler downsampler = new LegacyReservoirDownsampler(5); - downsampler.addAll(reads); - - Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be"); - List batchedReads = new ArrayList(downsampler.getDownsampledContents()); - Assert.assertEquals(batchedReads.size(), 3, "Downsampler is returning the wrong number of reads"); - - Assert.assertSame(batchedReads.get(0), reads.get(0), "Downsampler read 1 is incorrect"); - Assert.assertSame(batchedReads.get(1), reads.get(1), "Downsampler read 2 is incorrect"); - Assert.assertSame(batchedReads.get(2), reads.get(2), "Downsampler read 3 is incorrect"); - } - - @Test - public void testPoolFilledExactly() { - List reads = new ArrayList(); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,76)); - LegacyReservoirDownsampler downsampler = new LegacyReservoirDownsampler(5); - downsampler.addAll(reads); - - Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be"); - List batchedReads = new ArrayList(downsampler.getDownsampledContents()); - Assert.assertEquals(batchedReads.size(), 5, "Downsampler is returning the wrong number of reads"); - Assert.assertSame(batchedReads.iterator().next(), reads.get(0), "Downsampler is returning an incorrect read"); - - Assert.assertSame(batchedReads.get(0), reads.get(0), "Downsampler read 1 is incorrect"); - Assert.assertSame(batchedReads.get(1), reads.get(1), "Downsampler read 2 is incorrect"); - Assert.assertSame(batchedReads.get(2), reads.get(2), "Downsampler read 3 is incorrect"); - Assert.assertSame(batchedReads.get(3), reads.get(3), "Downsampler read 4 is incorrect"); - Assert.assertSame(batchedReads.get(4), reads.get(4), "Downsampler read 5 is incorrect"); - } - - @Test - public void testLargerPileWithZeroElementPool() { - List reads = new ArrayList(); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,76)); - LegacyReservoirDownsampler downsampler = new LegacyReservoirDownsampler(0); - downsampler.addAll(reads); - - Assert.assertTrue(downsampler.isEmpty(),"Downsampler isn't empty but should be"); - List batchedReads = new ArrayList(downsampler.getDownsampledContents()); - Assert.assertEquals(batchedReads.size(), 0, "Downsampler is returning the wrong number of reads"); - } - - @Test - public void testLargerPileWithSingleElementPool() { - List reads = new ArrayList(); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,76)); - LegacyReservoirDownsampler downsampler = new LegacyReservoirDownsampler(1); - downsampler.addAll(reads); - - Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be"); - List batchedReads = new ArrayList(downsampler.getDownsampledContents()); - Assert.assertEquals(batchedReads.size(), 1, "Downsampler is returning the wrong number of reads"); - Assert.assertTrue(reads.contains(batchedReads.get(0)),"Downsampler is returning a bad read."); - } - - @Test - public void testFillingAcrossLoci() { - List reads = new ArrayList(); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,76)); - LegacyReservoirDownsampler downsampler = new LegacyReservoirDownsampler(5); - downsampler.addAll(reads); - - Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be"); - List batchedReads = new ArrayList(downsampler.getDownsampledContents()); - Assert.assertEquals(batchedReads.size(), 1, "Downsampler is returning the wrong number of reads"); - Assert.assertEquals(batchedReads.get(0), reads.get(0), "Downsampler is returning an incorrect read."); - - reads.clear(); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read2",0,2,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read3",0,2,76)); - - downsampler.clear(); - downsampler.addAll(reads); - - Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be"); - batchedReads = new ArrayList(downsampler.getDownsampledContents()); - Assert.assertEquals(batchedReads.size(), 2, "Downsampler is returning the wrong number of reads"); - Assert.assertEquals(batchedReads.get(0), reads.get(0), "Downsampler is returning an incorrect read."); - Assert.assertEquals(batchedReads.get(1), reads.get(1), "Downsampler is returning an incorrect read."); - - reads.clear(); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read4",0,3,76)); - reads.add(ArtificialSAMUtils.createArtificialRead(header,"read5",0,3,76)); - - downsampler.clear(); - downsampler.addAll(reads); - - Assert.assertFalse(downsampler.isEmpty(),"Downsampler is empty but shouldn't be"); - batchedReads = new ArrayList(downsampler.getDownsampledContents()); - Assert.assertEquals(batchedReads.size(), 2, "Downsampler is returning the wrong number of reads"); - Assert.assertEquals(batchedReads.get(0), reads.get(0), "Downsampler is returning an incorrect read."); - Assert.assertEquals(batchedReads.get(1), reads.get(1), "Downsampler is returning an incorrect read."); - } - -} diff --git a/public/java/test/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java new file mode 100644 index 000000000..7a5fcf0c2 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java @@ -0,0 +1,97 @@ +/* + * Copyright (c) 2012 The Broad Institute + * + * 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.sting.utils; + + +import net.sf.picard.reference.ReferenceSequenceFile; +import net.sf.samtools.SAMFileHeader; +import net.sf.samtools.SAMSequenceDictionary; +import net.sf.samtools.SAMSequenceRecord; +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.LinkedList; +import java.util.List; + +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertTrue; + +public class MRUCachingSAMSequencingDictionaryUnitTest extends BaseTest { + private static ReferenceSequenceFile seq; + private static SAMSequenceDictionary dict; + + @BeforeClass + public void init() throws FileNotFoundException { + // sequence + seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + dict = seq.getSequenceDictionary(); + } + + @Test + public void testBasic() { + final MRUCachingSAMSequenceDictionary caching = new MRUCachingSAMSequenceDictionary(dict); + + Assert.assertEquals(caching.getDictionary(), dict, "Dictionary not the one I expected"); + + for ( final SAMSequenceRecord rec : dict.getSequences() ) { + Assert.assertFalse(caching.isCached(rec.getSequenceIndex()), "Expected index to not be cached"); + Assert.assertFalse(caching.isCached(rec.getSequenceName()), "Expected contig to not be cached"); + + Assert.assertEquals(caching.getSequence(rec.getSequenceName()), rec, "Couldn't query for sequence"); + Assert.assertEquals(caching.getSequence(rec.getSequenceIndex()), rec, "Couldn't query for sequence index"); + Assert.assertEquals(caching.hasContig(rec.getSequenceName()), true, "hasContig query for sequence"); + Assert.assertEquals(caching.hasContigIndex(rec.getSequenceIndex()), true, "hasContigIndex query for sequence"); + Assert.assertEquals(caching.getSequenceIndex(rec.getSequenceName()), rec.getSequenceIndex(), "Couldn't query for sequence"); + + Assert.assertEquals(caching.hasContig(rec.getSequenceName() + "asdfadsfa"), false, "hasContig query for unknown sequence"); + Assert.assertEquals(caching.hasContigIndex(dict.getSequences().size()), false, "hasContigIndex query for unknown index"); + + Assert.assertTrue(caching.isCached(rec.getSequenceIndex()), "Expected index to be cached"); + Assert.assertTrue(caching.isCached(rec.getSequenceName()), "Expected contig to be cached"); + } + } + + @Test(expectedExceptions = ReviewedStingException.class) + public void testBadGetSequence() { + final MRUCachingSAMSequenceDictionary caching = new MRUCachingSAMSequenceDictionary(dict); + caching.getSequence("notInDictionary"); + } + + @Test(expectedExceptions = ReviewedStingException.class) + public void testBadGetSequenceIndex() { + final MRUCachingSAMSequenceDictionary caching = new MRUCachingSAMSequenceDictionary(dict); + caching.getSequence(dict.getSequences().size()); + } +} \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/utils/MWUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/MWUnitTest.java index c81043f90..9d4c562c7 100644 --- a/public/java/test/org/broadinstitute/sting/utils/MWUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/MWUnitTest.java @@ -25,11 +25,9 @@ package org.broadinstitute.sting.utils; -import cern.jet.math.Arithmetic; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.collections.Pair; -import org.jgrapht.alg.StrongConnectivityInspector; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; import org.testng.Assert; diff --git a/public/java/test/org/broadinstitute/sting/utils/UtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/UtilsUnitTest.java index fc10f1102..29c643153 100644 --- a/public/java/test/org/broadinstitute/sting/utils/UtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/UtilsUnitTest.java @@ -25,12 +25,14 @@ package org.broadinstitute.sting.utils; +import org.apache.commons.io.FileUtils; +import org.broadinstitute.sting.utils.io.IOUtils; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.testng.annotations.Test; -import java.util.LinkedHashMap; -import java.util.Map; +import java.io.File; +import java.util.*; /** * Testing framework for general purpose utilities class. @@ -40,6 +42,25 @@ import java.util.Map; */ public class UtilsUnitTest extends BaseTest { + @Test + public void testAppend() { + for ( int leftSize : Arrays.asList(0, 1, 2, 3) ) { + for ( final int rightSize : Arrays.asList(0, 1, 2) ) { + final List left = new LinkedList(); + for ( int i = 0; i < leftSize; i++ ) left.add(i); + final List total = new LinkedList(); + for ( int i = 0; i < leftSize + rightSize; i++ ) total.add(i); + + if ( rightSize == 0 ) + Assert.assertEquals(Utils.append(left), total); + if ( rightSize == 1 ) + Assert.assertEquals(Utils.append(left, leftSize), total); + if ( rightSize == 2 ) + Assert.assertEquals(Utils.append(left, leftSize, leftSize + 1), total); + } + } + + } @Test public void testDupStringNoChars() { @@ -135,4 +156,16 @@ public class UtilsUnitTest extends BaseTest { actual = Utils.escapeExpressions(" one two 'three four' "); Assert.assertEquals(actual, expected); } + + @Test + public void testCalcMD5() throws Exception { + final File source = new File(publicTestDir + "exampleFASTA.fasta"); + final String sourceMD5 = "36880691cf9e4178216f7b52e8d85fbe"; + + final byte[] sourceBytes = IOUtils.readFileIntoByteArray(source); + Assert.assertEquals(Utils.calcMD5(sourceBytes), sourceMD5); + + final String sourceString = FileUtils.readFileToString(source); + Assert.assertEquals(Utils.calcMD5(sourceString), sourceMD5); + } } diff --git a/public/java/test/org/broadinstitute/sting/utils/activeregion/ActiveRegionUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActiveRegionUnitTest.java new file mode 100644 index 000000000..d2ea5d11b --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActiveRegionUnitTest.java @@ -0,0 +1,223 @@ +/* + * Copyright (c) 2012 The Broad Institute + * + * 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.sting.utils.activeregion; + + +// the imports for unit testing. + + +import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.samtools.SAMFileHeader; +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.broadinstitute.sting.utils.sam.GATKSAMRecord; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.*; + + +public class ActiveRegionUnitTest extends BaseTest { + private GenomeLocParser genomeLocParser; + private IndexedFastaSequenceFile seq; + private String contig; + private int contigLength; + + @BeforeClass + public void init() throws FileNotFoundException { + // sequence + seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + genomeLocParser = new GenomeLocParser(seq); + contig = "1"; + contigLength = genomeLocParser.getContigInfo(contig).getSequenceLength(); + } + + @DataProvider(name = "ActionRegionCreationTest") + public Object[][] makePollingData() { + List tests = new ArrayList(); + for ( final int start : Arrays.asList(1, 10, 100, contigLength - 10, contigLength - 1) ) { + for ( final int size : Arrays.asList(1, 10, 100, 1000) ) { + for ( final int ext : Arrays.asList(0, 1, 10, 100) ) { + for ( final boolean isActive : Arrays.asList(true, false) ) { + for ( final boolean addStates : Arrays.asList(true, false) ) { + List states = null; + if ( addStates ) { + states = new LinkedList(); + for ( int i = start; i < start + size; i++ ) { + states.add(new ActivityProfileState(genomeLocParser.createGenomeLoc(contig, i + start), isActive ? 1.0 : 0.0)); + } + } + final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, start, start + size - 1); + tests.add(new Object[]{loc, states, isActive, ext}); + } + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test(enabled = true, dataProvider = "ActionRegionCreationTest") + public void testCreatingActiveRegions(final GenomeLoc loc, final List supportingStates, final boolean isActive, final int extension) { + final ActiveRegion region = new ActiveRegion(loc, supportingStates, isActive, genomeLocParser, extension); + Assert.assertEquals(region.getLocation(), loc); + Assert.assertEquals(region.getExtendedLoc().getStart(), Math.max(loc.getStart() - extension, 1)); + Assert.assertEquals(region.getExtendedLoc().getStop(), Math.min(loc.getStop() + extension, contigLength)); + Assert.assertEquals(region.getReadSpanLoc().getStart(), Math.max(loc.getStart() - extension, 1)); + Assert.assertEquals(region.getReadSpanLoc().getStop(), Math.min(loc.getStop() + extension, contigLength)); + Assert.assertEquals(region.isActive(), isActive); + Assert.assertEquals(region.getExtension(), extension); + Assert.assertEquals(region.getReads(), Collections.emptyList()); + Assert.assertEquals(region.size(), 0); + Assert.assertEquals(region.getSupportingStates(), supportingStates == null ? Collections.emptyList() : supportingStates); + Assert.assertNotNull(region.toString()); + + assertGoodReferenceGetter(region.getActiveRegionReference(seq), region.getExtendedLoc(), 0); + assertGoodReferenceGetter(region.getActiveRegionReference(seq, 10), region.getExtendedLoc(), 10); + assertGoodReferenceGetter(region.getFullReference(seq), region.getReadSpanLoc(), 0); + assertGoodReferenceGetter(region.getFullReference(seq, 10), region.getReadSpanLoc(), 10); + } + + private void assertGoodReferenceGetter(final byte[] actualBytes, final GenomeLoc span, final int padding) { + final int expectedStart = Math.max(span.getStart() - padding, 1); + final int expectedStop = Math.min(span.getStop() + padding, contigLength); + final byte[] expectedBytes = seq.getSubsequenceAt(span.getContig(), expectedStart, expectedStop).getBases(); + Assert.assertEquals(actualBytes, expectedBytes); + } + + @DataProvider(name = "ActiveRegionReads") + public Object[][] makeActiveRegionReads() { + List tests = new ArrayList(); + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); + for ( final int start : Arrays.asList(1, 10, 100, contigLength - 10, contigLength - 1) ) { + for ( final int readStartOffset : Arrays.asList(-100, -10, 0, 10, 100) ) { + for ( final int readSize : Arrays.asList(10, 100, 1000) ) { + final GenomeLoc loc = genomeLocParser.createGenomeLocOnContig(contig, start, start + 10); + + final int readStart = Math.max(start + readStartOffset, 1); + final int readStop = Math.min(readStart + readSize, contigLength); + final int readLength = readStop - readStart + 1; + if ( readLength > 0 ) { + GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, readStart, readLength); + final GenomeLoc readLoc = genomeLocParser.createGenomeLoc(read); + if ( readLoc.overlapsP(loc) ) + tests.add(new Object[]{loc, read}); + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "ActiveRegionReads") + public void testActiveRegionReads(final GenomeLoc loc, final GATKSAMRecord read) { + final GenomeLoc expectedSpan = loc.union(genomeLocParser.createGenomeLoc(read)); + + final ActiveRegion region = new ActiveRegion(loc, null, true, genomeLocParser, 0); + final ActiveRegion region2 = new ActiveRegion(loc, null, true, genomeLocParser, 0); + Assert.assertEquals(region.getReads(), Collections.emptyList()); + Assert.assertEquals(region.size(), 0); + Assert.assertEquals(region.getExtendedLoc(), loc); + Assert.assertEquals(region.getReadSpanLoc(), loc); + Assert.assertTrue(region.equalExceptReads(region2)); + + region.add(read); + Assert.assertEquals(region.getReads(), Collections.singletonList(read)); + Assert.assertEquals(region.size(), 1); + Assert.assertEquals(region.getExtendedLoc(), loc); + Assert.assertEquals(region.getReadSpanLoc(), expectedSpan); + Assert.assertTrue(region.equalExceptReads(region2)); + + region.clearReads(); + Assert.assertEquals(region.getReads(), Collections.emptyList()); + Assert.assertEquals(region.size(), 0); + Assert.assertEquals(region.getExtendedLoc(), loc); + Assert.assertEquals(region.getReadSpanLoc(), loc); + Assert.assertTrue(region.equalExceptReads(region2)); + + region.addAll(Collections.singleton(read)); + Assert.assertEquals(region.getReads(), Collections.singletonList(read)); + Assert.assertEquals(region.size(), 1); + Assert.assertEquals(region.getExtendedLoc(), loc); + Assert.assertEquals(region.getReadSpanLoc(), expectedSpan); + Assert.assertTrue(region.equalExceptReads(region2)); + + region.removeAll(Collections.emptyList()); + Assert.assertEquals(region.getReads(), Collections.singletonList(read)); + Assert.assertEquals(region.size(), 1); + Assert.assertEquals(region.getExtendedLoc(), loc); + Assert.assertEquals(region.getReadSpanLoc(), expectedSpan); + Assert.assertTrue(region.equalExceptReads(region2)); + + region.removeAll(Collections.singletonList(read)); + Assert.assertEquals(region.getReads(), Collections.emptyList()); + Assert.assertEquals(region.size(), 0); + Assert.assertEquals(region.getExtendedLoc(), loc); + Assert.assertEquals(region.getReadSpanLoc(), loc); + Assert.assertTrue(region.equalExceptReads(region2)); + + region.add(read); + region.hardClipToActiveRegion(); + Assert.assertEquals(region.size(), 1); + Assert.assertEquals(region.getExtendedLoc(), loc); + Assert.assertEquals(region.getReadSpanLoc(), loc); + Assert.assertTrue(region.getReads().get(0).getAlignmentStart() >= region.getExtendedLoc().getStart()); + Assert.assertTrue(region.getReads().get(0).getAlignmentEnd() <= region.getExtendedLoc().getStop()); + } + + @DataProvider(name = "BadReadsTest") + public Object[][] makeBadReadsTest() { + List tests = new ArrayList(); + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); + tests.add(new Object[]{ + ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, 10), + ArtificialSAMUtils.createArtificialRead(header, "read2", 0, 9, 10)}); + tests.add(new Object[]{ + ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, 10), + ArtificialSAMUtils.createArtificialRead(header, "read2", 1, 9, 10)}); + tests.add(new Object[]{ + ArtificialSAMUtils.createArtificialRead(header, "read1", 1, 10, 10), + ArtificialSAMUtils.createArtificialRead(header, "read2", 0, 9, 10)}); + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "BadReadsTest", expectedExceptions = IllegalArgumentException.class) + public void testBadReads(final GATKSAMRecord read1, final GATKSAMRecord read2) { + final GenomeLoc loc = genomeLocParser.createGenomeLoc(read1); + final ActiveRegion region = new ActiveRegion(loc, null, true, genomeLocParser, 0); + region.add(read1); + region.add(read2); + } +} \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileStateUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileStateUnitTest.java new file mode 100644 index 000000000..f199a0d82 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileStateUnitTest.java @@ -0,0 +1,92 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.activeregion; + +import net.sf.samtools.SAMFileHeader; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.FileNotFoundException; +import java.util.Arrays; +import java.util.LinkedList; +import java.util.List; + +/** + * Created with IntelliJ IDEA. + * User: depristo + * Date: 1/17/13 + * Time: 2:30 PM + * To change this template use File | Settings | File Templates. + */ +public class ActivityProfileStateUnitTest { + private GenomeLocParser genomeLocParser; + + @BeforeClass + public void init() throws FileNotFoundException { + // sequence + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 100); + genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); + } + + @DataProvider(name = "ActiveProfileResultProvider") + public Object[][] makeActiveProfileResultProvider() { + final List tests = new LinkedList(); + + final String chr = genomeLocParser.getContigs().getSequence(0).getSequenceName(); + for ( final GenomeLoc loc : Arrays.asList( + genomeLocParser.createGenomeLoc(chr, 10, 10), + genomeLocParser.createGenomeLoc(chr, 100, 100) )) { + for ( final double prob : Arrays.asList(0.0, 0.5, 1.0) ) { + for ( final ActivityProfileState.Type state : ActivityProfileState.Type.values() ) { + for ( final Number value : Arrays.asList(1, 2, 4) ) { + tests.add(new Object[]{ loc, prob, state, value}); + } + } + tests.add(new Object[]{ loc, prob, null, null}); + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "ActiveProfileResultProvider") + public void testActiveProfileResultProvider(GenomeLoc loc, final double prob, ActivityProfileState.Type maybeState, final Number maybeNumber) { + final ActivityProfileState apr = maybeState == null + ? new ActivityProfileState(loc, prob) + : new ActivityProfileState(loc, prob, maybeState, maybeNumber); + + Assert.assertEquals(apr.getLoc(), loc); + Assert.assertNotNull(apr.toString()); + Assert.assertEquals(apr.isActiveProb, prob); + Assert.assertEquals(apr.resultState, maybeState == null ? ActivityProfileState.Type.NONE : maybeState); + Assert.assertEquals(apr.resultValue, maybeState == null ? null : maybeNumber); + } +} diff --git a/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java index ff27037d3..b9fdb3afe 100644 --- a/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java @@ -33,6 +33,7 @@ import net.sf.picard.reference.ReferenceSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.testng.Assert; @@ -42,12 +43,11 @@ import org.testng.annotations.Test; import java.io.File; import java.io.FileNotFoundException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; +import java.util.*; public class ActivityProfileUnitTest extends BaseTest { + private final static boolean DEBUG = false; private GenomeLocParser genomeLocParser; private GenomeLoc startLoc; @@ -70,23 +70,28 @@ public class ActivityProfileUnitTest extends BaseTest { List expectedRegions; int extension = 0; GenomeLoc regionStart = startLoc; + final ProfileType type; - public BasicActivityProfileTestProvider(final List probs, final List expectedRegions) { - super(BasicActivityProfileTestProvider.class); - this.probs = probs; - this.expectedRegions = expectedRegions; - setName(getName()); - } - - public BasicActivityProfileTestProvider(final List probs, boolean startActive, int ... startsAndStops) { + public BasicActivityProfileTestProvider(final ProfileType type, final List probs, boolean startActive, int ... startsAndStops) { super(BasicActivityProfileTestProvider.class); + this.type = type; this.probs = probs; this.expectedRegions = toRegions(startActive, startsAndStops); setName(getName()); } private String getName() { - return String.format("probs=%s expectedRegions=%s", Utils.join(",", probs), Utils.join(",", expectedRegions)); + return String.format("type=%s probs=%s expectedRegions=%s", type, Utils.join(",", probs), Utils.join(",", expectedRegions)); + } + + public ActivityProfile makeProfile() { + switch ( type ) { + case Base: return new ActivityProfile(genomeLocParser); + case BandPass: + // zero size => equivalent to ActivityProfile + return new BandPassActivityProfile(genomeLocParser, 0, 0.01, false); + default: throw new IllegalStateException(type.toString()); + } } private List toRegions(boolean isActive, int[] startsAndStops) { @@ -95,7 +100,7 @@ public class ActivityProfileUnitTest extends BaseTest { int start = regionStart.getStart() + startsAndStops[i]; int end = regionStart.getStart() + startsAndStops[i+1] - 1; GenomeLoc activeLoc = genomeLocParser.createGenomeLoc(regionStart.getContig(), start, end); - ActiveRegion r = new ActiveRegion(activeLoc, isActive, genomeLocParser, extension); + ActiveRegion r = new ActiveRegion(activeLoc, Collections.emptyList(), isActive, genomeLocParser, extension); l.add(r); isActive = ! isActive; } @@ -103,34 +108,44 @@ public class ActivityProfileUnitTest extends BaseTest { } } + private enum ProfileType { + Base, BandPass + } + @DataProvider(name = "BasicActivityProfileTestProvider") public Object[][] makeQualIntervalTestProvider() { - new BasicActivityProfileTestProvider(Arrays.asList(1.0), true, 0, 1); - new BasicActivityProfileTestProvider(Arrays.asList(1.0, 0.0), true, 0, 1, 2); - new BasicActivityProfileTestProvider(Arrays.asList(0.0, 1.0), false, 0, 1, 2); - new BasicActivityProfileTestProvider(Arrays.asList(1.0, 0.0, 1.0), true, 0, 1, 2, 3); - new BasicActivityProfileTestProvider(Arrays.asList(1.0, 1.0, 1.0), true, 0, 3); + for ( final ProfileType type : ProfileType.values() ) { + new BasicActivityProfileTestProvider(type, Arrays.asList(1.0), true, 0, 1); + new BasicActivityProfileTestProvider(type, Arrays.asList(1.0, 0.0), true, 0, 1, 2); + new BasicActivityProfileTestProvider(type, Arrays.asList(0.0, 1.0), false, 0, 1, 2); + new BasicActivityProfileTestProvider(type, Arrays.asList(1.0, 0.0, 1.0), true, 0, 1, 2, 3); + new BasicActivityProfileTestProvider(type, Arrays.asList(1.0, 1.0, 1.0), true, 0, 3); + } return BasicActivityProfileTestProvider.getTests(BasicActivityProfileTestProvider.class); } - @Test(dataProvider = "BasicActivityProfileTestProvider") + @Test(enabled = ! DEBUG, dataProvider = "BasicActivityProfileTestProvider") public void testBasicActivityProfile(BasicActivityProfileTestProvider cfg) { - ActivityProfile profile = new ActivityProfile(genomeLocParser, false); + ActivityProfile profile = cfg.makeProfile(); + + Assert.assertTrue(profile.isEmpty()); Assert.assertEquals(profile.parser, genomeLocParser); for ( int i = 0; i < cfg.probs.size(); i++ ) { double p = cfg.probs.get(i); GenomeLoc loc = genomeLocParser.createGenomeLoc(cfg.regionStart.getContig(), cfg.regionStart.getStart() + i, cfg.regionStart.getStart() + i); - profile.add(new ActivityProfileResult(loc, p)); + profile.add(new ActivityProfileState(loc, p)); + Assert.assertFalse(profile.isEmpty(), "Profile shouldn't be empty after adding a state"); } - Assert.assertEquals(profile.regionStartLoc, genomeLocParser.createGenomeLoc(cfg.regionStart.getContig(), cfg.regionStart.getStart(), cfg.regionStart.getStart() )); + Assert.assertEquals(profile.regionStartLoc, genomeLocParser.createGenomeLoc(cfg.regionStart.getContig(), cfg.regionStart.getStart(), cfg.regionStart.getStart() ), "Start loc should be the start of the region"); - Assert.assertEquals(profile.size(), cfg.probs.size()); - assertProbsAreEqual(profile.isActiveList, cfg.probs); + Assert.assertEquals(profile.size(), cfg.probs.size(), "Should have exactly the number of states we expected to add"); + assertProbsAreEqual(profile.stateList, cfg.probs); - assertRegionsAreEqual(profile.createActiveRegions(0, 100), cfg.expectedRegions); + // TODO -- reanble tests + //assertRegionsAreEqual(profile.createActiveRegions(0, 100), cfg.expectedRegions); } private void assertRegionsAreEqual(List actual, List expected) { @@ -140,12 +155,334 @@ public class ActivityProfileUnitTest extends BaseTest { } } - private void assertProbsAreEqual(List actual, List expected) { + private void assertProbsAreEqual(List actual, List expected) { Assert.assertEquals(actual.size(), expected.size()); for ( int i = 0; i < actual.size(); i++ ) { Assert.assertEquals(actual.get(i).isActiveProb, expected.get(i)); } } - // todo -- test extensions + // ------------------------------------------------------------------------------------- + // + // Hardcore tests for adding to the profile and constructing active regions + // + // ------------------------------------------------------------------------------------- + + private static class SizeToStringList extends ArrayList { + @Override public String toString() { return "List[" + size() + "]"; } + } + + @DataProvider(name = "RegionCreationTests") + public Object[][] makeRegionCreationTests() { + final List tests = new LinkedList(); + + final int contigLength = genomeLocParser.getContigs().getSequences().get(0).getSequenceLength(); + for ( int start : Arrays.asList(1, 10, 100, contigLength - 100, contigLength - 10) ) { + for ( int regionSize : Arrays.asList(1, 10, 100, 1000, 10000) ) { + for ( int maxRegionSize : Arrays.asList(10, 50, 200) ) { + for ( final boolean waitUntilEnd : Arrays.asList(false, true) ) { + for ( final boolean forceConversion : Arrays.asList(false, true) ) { + // what do I really want to test here? I'd like to test a few cases: + // -- region is all active (1.0) + // -- region is all inactive (0.0) + // -- cut the interval into 1, 2, 3, 4, 5 ... 10 regions, each with alternating activity values + for ( final boolean startWithActive : Arrays.asList(true, false) ) { + for ( int nParts : Arrays.asList(1, 2, 3, 4, 5, 7, 10, 11, 13) ) { + +// for ( int start : Arrays.asList(1) ) { +// for ( int regionSize : Arrays.asList(100) ) { +// for ( int maxRegionSize : Arrays.asList(10) ) { +// for ( final boolean waitUntilEnd : Arrays.asList(true) ) { +// for ( final boolean forceConversion : Arrays.asList(false) ) { +// for ( final boolean startWithActive : Arrays.asList(true) ) { +// for ( int nParts : Arrays.asList(3) ) { + regionSize = Math.min(regionSize, contigLength - start); + final List regions = makeRegions(regionSize, startWithActive, nParts); + tests.add(new Object[]{ start, regions, maxRegionSize, nParts, forceConversion, waitUntilEnd }); + } + } + } + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + private List makeRegions(final int totalRegionSize, + final boolean startWithActive, + final int nParts) { + final List regions = new SizeToStringList(); + + boolean isActive = startWithActive; + final int activeRegionSize = Math.max(totalRegionSize / nParts, 1); + for ( int i = 0; i < totalRegionSize; i += activeRegionSize ) { + for ( int j = 0; j < activeRegionSize && j + i < totalRegionSize; j++ ) { + regions.add(isActive); + } + isActive = ! isActive; + } + + return regions; + } + + + @Test(enabled = !DEBUG, dataProvider = "RegionCreationTests") + public void testRegionCreation(final int start, final List probs, int maxRegionSize, final int nParts, final boolean forceConversion, final boolean waitUntilEnd) { + final ActivityProfile profile = new ActivityProfile(genomeLocParser); + Assert.assertNotNull(profile.toString()); + + final String contig = genomeLocParser.getContigs().getSequences().get(0).getSequenceName(); + final List seenSites = new ArrayList(Collections.nCopies(probs.size(), false)); + ActiveRegion lastRegion = null; + for ( int i = 0; i < probs.size(); i++ ) { + final boolean isActive = probs.get(i); + final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, i + start); + final ActivityProfileState state = new ActivityProfileState(loc, isActive ? 1.0 : 0.0); + profile.add(state); + Assert.assertNotNull(profile.toString()); + + if ( ! waitUntilEnd ) { + final List regions = profile.popReadyActiveRegions(0, 1, maxRegionSize, false); + lastRegion = assertGoodRegions(start, regions, maxRegionSize, lastRegion, probs, seenSites); + } + } + + if ( waitUntilEnd || forceConversion ) { + final List regions = profile.popReadyActiveRegions(0, 1, maxRegionSize, forceConversion); + lastRegion = assertGoodRegions(start, regions, maxRegionSize, lastRegion, probs, seenSites); + } + + for ( int i = 0; i < probs.size(); i++ ) { + if ( forceConversion || (i + maxRegionSize + profile.getMaxProbPropagationDistance() < probs.size())) + // only require a site to be seen if we are forcing conversion or the site is more than maxRegionSize from the end + Assert.assertTrue(seenSites.get(i), "Missed site " + i); + } + + Assert.assertNotNull(profile.toString()); + } + + private ActiveRegion assertGoodRegions(final int start, final List regions, final int maxRegionSize, ActiveRegion lastRegion, final List probs, final List seenSites) { + for ( final ActiveRegion region : regions ) { + Assert.assertTrue(region.getLocation().size() > 0, "Region " + region + " has a bad size"); + Assert.assertTrue(region.getLocation().size() <= maxRegionSize, "Region " + region + " has a bad size: it's big than the max region size " + maxRegionSize); + if ( lastRegion != null ) { + Assert.assertTrue(region.getLocation().getStart() == lastRegion.getLocation().getStop() + 1, "Region " + region + " doesn't start immediately after previous region" + lastRegion); + } + + // check that all active bases are actually active + final int regionOffset = region.getLocation().getStart() - start; + Assert.assertTrue(regionOffset >= 0 && regionOffset < probs.size(), "Region " + region + " has a bad offset w.r.t. start"); + for ( int j = 0; j < region.getLocation().size(); j++ ) { + final int siteOffset = j + regionOffset; + Assert.assertEquals(region.isActive(), probs.get(siteOffset).booleanValue()); + Assert.assertFalse(seenSites.get(siteOffset), "Site " + j + " in " + region + " was seen already"); + seenSites.set(siteOffset, true); + } + + lastRegion = region; + } + + return lastRegion; + } + + // ------------------------------------------------------------------------------------- + // + // Hardcore tests for adding to the profile and constructing active regions + // + // ------------------------------------------------------------------------------------- + + @DataProvider(name = "SoftClipsTest") + public Object[][] makeSoftClipsTest() { + final List tests = new LinkedList(); + + final int contigLength = genomeLocParser.getContigs().getSequences().get(0).getSequenceLength(); + for ( int start : Arrays.asList(1, 10, 100, contigLength - 100, contigLength - 10, contigLength - 1) ) { + for ( int precedingSites: Arrays.asList(0, 1, 10) ) { + if ( precedingSites + start < contigLength ) { + for ( int softClipSize : Arrays.asList(1, 2, 10, 100) ) { +// for ( int start : Arrays.asList(10) ) { +// for ( int precedingSites: Arrays.asList(10) ) { +// for ( int softClipSize : Arrays.asList(1) ) { + tests.add(new Object[]{ start, precedingSites, softClipSize }); + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test(enabled = ! DEBUG, dataProvider = "SoftClipsTest") + public void testSoftClips(final int start, int nPrecedingSites, final int softClipSize) { + final ActivityProfile profile = new ActivityProfile(genomeLocParser); + + final int contigLength = genomeLocParser.getContigs().getSequences().get(0).getSequenceLength(); + final String contig = genomeLocParser.getContigs().getSequences().get(0).getSequenceName(); + for ( int i = 0; i < nPrecedingSites; i++ ) { + final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, i + start); + final ActivityProfileState state = new ActivityProfileState(loc, 0.0); + profile.add(state); + } + + final GenomeLoc softClipLoc = genomeLocParser.createGenomeLoc(contig, nPrecedingSites + start); + profile.add(new ActivityProfileState(softClipLoc, 1.0, ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS, softClipSize)); + + final int actualNumOfSoftClips = Math.min(softClipSize, profile.getMaxProbPropagationDistance()); + if ( nPrecedingSites == 0 ) { + final int profileSize = Math.min(start + actualNumOfSoftClips, contigLength) - start + 1; + Assert.assertEquals(profile.size(), profileSize, "Wrong number of states in the profile"); + } + + for ( int i = 0; i < profile.size(); i++ ) { + final ActivityProfileState state = profile.getStateList().get(i); + final boolean withinSCRange = state.getLoc().distance(softClipLoc) <= actualNumOfSoftClips; + if ( withinSCRange ) { + Assert.assertTrue(state.isActiveProb > 0.0, "active prob should be changed within soft clip size"); + } else { + Assert.assertEquals(state.isActiveProb, 0.0, "active prob shouldn't be changed outside of clip size"); + } + } + } + + // ------------------------------------------------------------------------------------- + // + // Tests to ensure we cut large active regions in the right place + // + // ------------------------------------------------------------------------------------- + + private void addProb(final List l, final double v) { + l.add(v); + } + + @DataProvider(name = "ActiveRegionCutTests") + public Object[][] makeActiveRegionCutTests() { + final List tests = new LinkedList(); + +// for ( final int activeRegionSize : Arrays.asList(30) ) { +// for ( final int minRegionSize : Arrays.asList(5) ) { + for ( final int activeRegionSize : Arrays.asList(10, 12, 20, 30, 40) ) { + for ( final int minRegionSize : Arrays.asList(1, 5, 10) ) { + final int maxRegionSize = activeRegionSize * 2 / 3; + if ( minRegionSize >= maxRegionSize ) continue; + { // test flat activity profile + final List probs = Collections.nCopies(activeRegionSize, 1.0); + tests.add(new Object[]{minRegionSize, maxRegionSize, maxRegionSize, probs}); + } + + { // test point profile is properly handled + for ( int end = 1; end < activeRegionSize; end++ ) { + final List probs = Collections.nCopies(end, 1.0); + tests.add(new Object[]{minRegionSize, maxRegionSize, Math.min(end, maxRegionSize), probs}); + } + } + + { // test increasing activity profile + final List probs = new ArrayList(activeRegionSize); + for ( int i = 0; i < activeRegionSize; i++ ) { + addProb(probs, (1.0*(i+1))/ activeRegionSize); + } + tests.add(new Object[]{minRegionSize, maxRegionSize, maxRegionSize, probs}); + } + + { // test decreasing activity profile + final List probs = new ArrayList(activeRegionSize); + for ( int i = 0; i < activeRegionSize; i++ ) { + addProb(probs, 1 - (1.0*(i+1))/ activeRegionSize); + } + tests.add(new Object[]{minRegionSize, maxRegionSize, maxRegionSize, probs}); + } + + { // test two peaks +// for ( final double rootSigma : Arrays.asList(2.0) ) { +// int maxPeak1 = 9; { +// int maxPeak2 = 16; { + for ( final double rootSigma : Arrays.asList(1.0, 2.0, 3.0) ) { + for ( int maxPeak1 = 0; maxPeak1 < activeRegionSize / 2; maxPeak1++ ) { + for ( int maxPeak2 = activeRegionSize / 2 + 1; maxPeak2 < activeRegionSize; maxPeak2++ ) { + final double[] gauss1 = makeGaussian(maxPeak1, activeRegionSize, rootSigma); + final double[] gauss2 = makeGaussian(maxPeak2, activeRegionSize, rootSigma+1); + final List probs = new ArrayList(activeRegionSize); + for ( int i = 0; i < activeRegionSize; i++ ) { + addProb(probs, gauss1[i] + gauss2[i]); + } + final int cutSite = findCutSiteForTwoMaxPeaks(probs, minRegionSize); + if ( cutSite != -1 && cutSite < maxRegionSize ) + tests.add(new Object[]{minRegionSize, maxRegionSize, Math.max(cutSite, minRegionSize), probs}); + } + } + } + } + + { // test that the lowest of two minima is taken + // looks like a bunch of 1s, 0.5, some 1.0s, 0.75, some more 1s +// int firstMin = 0; { +// int secondMin = 4; { + for ( int firstMin = 1; firstMin < activeRegionSize; firstMin++ ) { + for ( int secondMin = firstMin + 1; secondMin < activeRegionSize; secondMin++ ) { + final List probs = new ArrayList(Collections.nCopies(activeRegionSize, 1.0)); + probs.set(firstMin, 0.5); + probs.set(secondMin, 0.75); + final int expectedCut; + if ( firstMin + 1 < minRegionSize ) { + if ( firstMin == secondMin - 1 ) // edge case for non-min at minRegionSize + expectedCut = maxRegionSize; + else + expectedCut = secondMin + 1 > maxRegionSize ? maxRegionSize : ( secondMin + 1 < minRegionSize ? maxRegionSize : secondMin + 1); + } else if ( firstMin + 1 > maxRegionSize ) + expectedCut = maxRegionSize; + else { + expectedCut = firstMin + 1; + } + + Math.min(firstMin + 1, maxRegionSize); + tests.add(new Object[]{minRegionSize, maxRegionSize, expectedCut, probs}); + } + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + private double[] makeGaussian(final int mean, final int range, final double sigma) { + final double[] gauss = new double[range]; + for( int iii = 0; iii < range; iii++ ) { + gauss[iii] = MathUtils.NormalDistribution(mean, sigma, iii) + ActivityProfile.ACTIVE_PROB_THRESHOLD; + } + return gauss; + } + + private int findCutSiteForTwoMaxPeaks(final List probs, final int minRegionSize) { + for ( int i = probs.size() - 2; i > minRegionSize; i-- ) { + double prev = probs.get(i - 1); + double next = probs.get(i + 1); + double cur = probs.get(i); + if ( cur < next && cur < prev ) + return i + 1; + } + + return -1; + } + + @Test(dataProvider = "ActiveRegionCutTests") + public void testActiveRegionCutTests(final int minRegionSize, final int maxRegionSize, final int expectedRegionSize, final List probs) { + final ActivityProfile profile = new ActivityProfile(genomeLocParser); + + final String contig = genomeLocParser.getContigs().getSequences().get(0).getSequenceName(); + for ( int i = 0; i <= maxRegionSize + profile.getMaxProbPropagationDistance(); i++ ) { + final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, i + 1); + final double prob = i < probs.size() ? probs.get(i) : 0.0; + final ActivityProfileState state = new ActivityProfileState(loc, prob); + profile.add(state); + } + + final List regions = profile.popReadyActiveRegions(0, minRegionSize, maxRegionSize, false); + Assert.assertTrue(regions.size() >= 1, "Should only be one regions for this test"); + final ActiveRegion region = regions.get(0); + Assert.assertEquals(region.getLocation().getStart(), 1, "Region should start at 1"); + Assert.assertEquals(region.getLocation().size(), expectedRegionSize, "Incorrect region size; cut must have been incorrect"); + } } \ No newline at end of file diff --git a/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java new file mode 100644 index 000000000..cb2a6bfb2 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java @@ -0,0 +1,319 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.activeregion; + + +// the imports for unit testing. + + +import net.sf.picard.reference.ReferenceSequenceFile; +import org.apache.commons.lang.ArrayUtils; +import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextTestProvider; +import org.broadinstitute.variant.vcf.VCFCodec; +import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.io.FileNotFoundException; +import java.util.*; + + +public class BandPassActivityProfileUnitTest extends BaseTest { + private final static boolean DEBUG = false; + private GenomeLocParser genomeLocParser; + + @BeforeClass + public void init() throws FileNotFoundException { + // sequence + ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + genomeLocParser = new GenomeLocParser(seq); + } + + @DataProvider(name = "BandPassBasicTest") + public Object[][] makeBandPassTest() { + final List tests = new LinkedList(); + + for ( int start : Arrays.asList(1, 10, 100, 1000) ) { + for ( boolean precedingIsActive : Arrays.asList(true, false) ) { + for ( int precedingSites: Arrays.asList(0, 1, 10, 100) ) { + for ( int bandPassSize : Arrays.asList(0, 1, 10, 100) ) { + for ( double sigma : Arrays.asList(1.0, 2.0, BandPassActivityProfile.DEFAULT_SIGMA) ) { +// for ( int start : Arrays.asList(10) ) { +// for ( boolean precedingIsActive : Arrays.asList(false) ) { +// for ( int precedingSites: Arrays.asList(0) ) { +// for ( int bandPassSize : Arrays.asList(1) ) { + tests.add(new Object[]{ start, precedingIsActive, precedingSites, bandPassSize, sigma }); + } + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test(enabled = ! DEBUG, dataProvider = "BandPassBasicTest") + public void testBandPass(final int start, final boolean precedingIsActive, final int nPrecedingSites, final int bandPassSize, final double sigma) { + final BandPassActivityProfile profile = new BandPassActivityProfile(genomeLocParser, bandPassSize, sigma, false); + + final int expectedBandSize = bandPassSize * 2 + 1; + Assert.assertEquals(profile.getFilteredSize(), bandPassSize, "Wrong filter size"); + Assert.assertEquals(profile.getSigma(), sigma, "Wrong sigma"); + Assert.assertEquals(profile.getBandSize(), expectedBandSize, "Wrong expected band size"); + + final String contig = genomeLocParser.getContigs().getSequences().get(0).getSequenceName(); + final double precedingProb = precedingIsActive ? 1.0 : 0.0; + for ( int i = 0; i < nPrecedingSites; i++ ) { + final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, i + start); + final ActivityProfileState state = new ActivityProfileState(loc, precedingProb); + profile.add(state); + } + + final GenomeLoc nextLoc = genomeLocParser.createGenomeLoc(contig, nPrecedingSites + start); + profile.add(new ActivityProfileState(nextLoc, 1.0)); + + if ( precedingIsActive == false && nPrecedingSites >= bandPassSize && bandPassSize < start ) { + // we have enough space that all probs fall on the genome + final double[] probs = profile.getProbabilitiesAsArray(); + Assert.assertEquals(MathUtils.sum(probs), 1.0 * (nPrecedingSites * precedingProb + 1), 1e-3, "Activity profile doesn't sum to number of non-zero prob states"); + } + } + + private double[] bandPassInOnePass(final BandPassActivityProfile profile, final double[] activeProbArray) { + final double[] bandPassProbArray = new double[activeProbArray.length]; + + // apply the band pass filter for activeProbArray into filteredProbArray + final double[] GaussianKernel = profile.getKernel(); + for( int iii = 0; iii < activeProbArray.length; iii++ ) { + final double[] kernel = ArrayUtils.subarray(GaussianKernel, Math.max(profile.getFilteredSize() - iii, 0), Math.min(GaussianKernel.length, profile.getFilteredSize() + activeProbArray.length - iii)); + final double[] activeProbSubArray = ArrayUtils.subarray(activeProbArray, Math.max(0,iii - profile.getFilteredSize()), Math.min(activeProbArray.length,iii + profile.getFilteredSize() + 1)); + bandPassProbArray[iii] = MathUtils.dotProduct(activeProbSubArray, kernel); + } + + return bandPassProbArray; + } + + @DataProvider(name = "BandPassComposition") + public Object[][] makeBandPassComposition() { + final List tests = new LinkedList(); + + for ( int bandPassSize : Arrays.asList(0, 1, 10, 100, BandPassActivityProfile.MAX_FILTER_SIZE) ) { + for ( int integrationLength : Arrays.asList(1, 10, 100, 1000) ) { + tests.add(new Object[]{ bandPassSize, integrationLength }); + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test( enabled = ! DEBUG, dataProvider = "BandPassComposition") + public void testBandPassComposition(final int bandPassSize, final int integrationLength) { + final int start = 1; + final BandPassActivityProfile profile = new BandPassActivityProfile(genomeLocParser, bandPassSize, BandPassActivityProfile.DEFAULT_SIGMA); + final double[] rawActiveProbs = new double[integrationLength + bandPassSize * 2]; + + // add a buffer so that we can get all of the band pass values + final String contig = genomeLocParser.getContigs().getSequences().get(0).getSequenceName(); + int pos = start; + int rawProbsOffset = 0; + for ( int i = 0; i < bandPassSize; i++ ) { + final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, pos++); + final ActivityProfileState state = new ActivityProfileState(loc, 0.0); + profile.add(state); + rawActiveProbs[rawProbsOffset++] = 0.0; + rawActiveProbs[rawActiveProbs.length - rawProbsOffset] = 0.0; + } + + for ( int i = 0; i < integrationLength; i++ ) { + final GenomeLoc nextLoc = genomeLocParser.createGenomeLoc(contig, pos++); + profile.add(new ActivityProfileState(nextLoc, 1.0)); + rawActiveProbs[rawProbsOffset++] = 1.0; + + for ( int j = 0; j < profile.size(); j++ ) { + Assert.assertTrue(profile.getStateList().get(j).isActiveProb >= 0.0, "State probability < 0 at " + j); + Assert.assertTrue(profile.getStateList().get(j).isActiveProb <= 1.0 + 1e-3, "State probability > 1 at " + j); + } + } + + final double[] expectedProbs = bandPassInOnePass(profile, rawActiveProbs); + for ( int j = 0; j < profile.size(); j++ ) { + Assert.assertEquals(profile.getStateList().get(j).isActiveProb, expectedProbs[j], "State probability not expected at " + j); + } + } + + // ------------------------------------------------------------------------------------ + // + // Code to test the creation of the kernels + // + // ------------------------------------------------------------------------------------ + + /** + + kernel <- function(sd, pThres) { + raw = dnorm(-80:81, mean=0, sd=sd) + norm = raw / sum(raw) + bad = norm < pThres + paste(norm[! bad], collapse=", ") + } + + print(kernel(0.01, 1e-5)) + print(kernel(1, 1e-5)) + print(kernel(5, 1e-5)) + print(kernel(17, 1e-5)) + + * @return + */ + + @DataProvider(name = "KernelCreation") + public Object[][] makeKernelCreation() { + final List tests = new LinkedList(); + + tests.add(new Object[]{ 0.01, 1000, new double[]{1.0}}); + tests.add(new Object[]{ 1.0, 1000, new double[]{0.0001338302, 0.004431848, 0.053990966, 0.241970723, 0.398942278, 0.241970723, 0.053990966, 0.004431848, 0.0001338302}}); + tests.add(new Object[]{ 1.0, 0, new double[]{1.0}}); + tests.add(new Object[]{ 1.0, 1, new double[]{0.2740686, 0.4518628, 0.2740686}}); + tests.add(new Object[]{ 1.0, 2, new double[]{0.05448868, 0.24420134, 0.40261995, 0.24420134, 0.05448868}}); + tests.add(new Object[]{ 1.0, 1000, new double[]{0.0001338302, 0.004431848, 0.053990966, 0.241970723, 0.398942278, 0.241970723, 0.053990966, 0.004431848, 0.0001338302}}); + tests.add(new Object[]{ 5.0, 1000, new double[]{1.1788613551308e-05, 2.67660451529771e-05, 5.83893851582921e-05, 0.000122380386022754, 0.000246443833694604, 0.000476817640292968, 0.000886369682387602, 0.00158309031659599, 0.00271659384673712, 0.00447890605896858, 0.00709491856924629, 0.0107981933026376, 0.0157900316601788, 0.0221841669358911, 0.029945493127149, 0.0388372109966426, 0.0483941449038287, 0.0579383105522965, 0.0666449205783599, 0.0736540280606647, 0.0782085387950912, 0.0797884560802865, 0.0782085387950912, 0.0736540280606647, 0.0666449205783599, 0.0579383105522965, 0.0483941449038287, 0.0388372109966426, 0.029945493127149, 0.0221841669358911, 0.0157900316601788, 0.0107981933026376, 0.00709491856924629, 0.00447890605896858, 0.00271659384673712, 0.00158309031659599, 0.000886369682387602, 0.000476817640292968, 0.000246443833694604, 0.000122380386022754, 5.83893851582921e-05, 2.67660451529771e-05, 1.1788613551308e-05}}); + tests.add(new Object[]{17.0, 1000, new double[]{1.25162575710745e-05, 1.57001772728555e-05, 1.96260034693739e-05, 2.44487374842009e-05, 3.03513668801384e-05, 3.75489089511911e-05, 4.62928204154855e-05, 5.68757597480354e-05, 6.96366758708924e-05, 8.49661819944029e-05, 0.000103312156275406, 0.000125185491708561, 0.000151165896477646, 0.000181907623161359, 0.000218144981137171, 0.000260697461819069, 0.000310474281706066, 0.000368478124457557, 0.000435807841336874, 0.00051365985048857, 0.000603327960854364, 0.000706201337376934, 0.000823760321812988, 0.000957569829285965, 0.00110927005589186, 0.00128056425833231, 0.00147320340358764, 0.00168896753568649, 0.00192964376796036, 0.00219700088266432, 0.00249276060490197, 0.00281856571330067, 0.00317594525418154, 0.00356627723683793, 0.00399074930220799, 0.00445031797242299, 0.00494566720070898, 0.00547716704583487, 0.00604483338842317, 0.00664828968356621, 0.00728673180099395, 0.00795889703644795, 0.00866303838230695, 0.00939690511889675, 0.0101577307281371, 0.010942229037054, 0.0117465993701676, 0.0125665413280325, 0.0133972796167302, 0.0142335991336574, 0.0150698902735454, 0.0159002041614507, 0.0167183172536454, 0.0175178044808441, 0.0182921198494897, 0.0190346831745763, 0.0197389714002676, 0.020398612780527, 0.0210074820484496, 0.0215597946062309, 0.0220501977225941, 0.022473856734247, 0.0228265343139947, 0.0231046609899767, 0.0233053952756892, 0.0234266719946158, 0.0234672376502799, 0.0234266719946158, 0.0233053952756892, 0.0231046609899767, 0.0228265343139947, 0.022473856734247, 0.0220501977225941, 0.0215597946062309, 0.0210074820484496, 0.020398612780527, 0.0197389714002676, 0.0190346831745763, 0.0182921198494897, 0.0175178044808441, 0.0167183172536454, 0.0159002041614507, 0.0150698902735454, 0.0142335991336574, 0.0133972796167302, 0.0125665413280325, 0.0117465993701676, 0.010942229037054, 0.0101577307281371, 0.00939690511889675, 0.00866303838230695, 0.00795889703644795, 0.00728673180099395, 0.00664828968356621, 0.00604483338842317, 0.00547716704583487, 0.00494566720070898, 0.00445031797242299, 0.00399074930220799, 0.00356627723683793, 0.00317594525418154, 0.00281856571330067, 0.00249276060490197, 0.00219700088266432, 0.00192964376796036, 0.00168896753568649, 0.00147320340358764, 0.00128056425833231, 0.00110927005589186, 0.000957569829285965, 0.000823760321812988, 0.000706201337376934, 0.000603327960854364, 0.00051365985048857, 0.000435807841336874, 0.000368478124457557, 0.000310474281706066, 0.000260697461819069, 0.000218144981137171, 0.000181907623161359, 0.000151165896477646, 0.000125185491708561, 0.000103312156275406, 8.49661819944029e-05, 6.96366758708924e-05, 5.68757597480354e-05, 4.62928204154855e-05, 3.75489089511911e-05, 3.03513668801384e-05, 2.44487374842009e-05, 1.96260034693739e-05, 1.57001772728555e-05, 1.25162575710745e-05}}); + + return tests.toArray(new Object[][]{}); + } + + @Test( enabled = ! DEBUG, dataProvider = "KernelCreation") + public void testKernelCreation(final double sigma, final int maxSize, final double[] expectedKernel) { + final BandPassActivityProfile profile = new BandPassActivityProfile(genomeLocParser, maxSize, sigma, true); + + final double[] kernel = profile.getKernel(); + Assert.assertEquals(kernel.length, expectedKernel.length); + for ( int i = 0; i < kernel.length; i++ ) + Assert.assertEquals(kernel[i], expectedKernel[i], 1e-3, "Kernels not equal at " + i); + } + + // ------------------------------------------------------------------------------------ + // + // Large-scale test, reading in 1000G Phase I chr20 calls and making sure that + // the regions returned are the same if you run on the entire profile vs. doing it + // incremental + // + // ------------------------------------------------------------------------------------ + + @DataProvider(name = "VCFProfile") + public Object[][] makeVCFProfile() { + final List tests = new LinkedList(); + + //tests.add(new Object[]{ privateTestDir + "ALL.chr20.phase1_release_v3.20101123.snps_indels_svs.sites.vcf", "20", 60470, 61000}); + //tests.add(new Object[]{ privateTestDir + "ALL.chr20.phase1_release_v3.20101123.snps_indels_svs.sites.vcf", "20", 60470, 100000}); + //tests.add(new Object[]{ privateTestDir + "ALL.chr20.phase1_release_v3.20101123.snps_indels_svs.sites.vcf", "20", 60470, 1000000}); + tests.add(new Object[]{ privateTestDir + "ALL.chr20.phase1_release_v3.20101123.snps_indels_svs.sites.vcf", "20", 60470, 1000000}); + tests.add(new Object[]{ privateTestDir + "NA12878.WGS.b37.chr20.firstMB.vcf", "20", 1, 1000000}); + + return tests.toArray(new Object[][]{}); + } + + @Test( dataProvider = "VCFProfile") + public void testVCFProfile(final String path, final String contig, final int start, final int end) throws Exception { + final int extension = 50; + final int minRegionSize = 50; + final int maxRegionSize = 300; + + final File file = new File(path); + final VCFCodec codec = new VCFCodec(); + final VariantContextTestProvider.VariantContextContainer reader = VariantContextTestProvider.readAllVCs(file, codec); + + final List incRegions = new ArrayList(); + final BandPassActivityProfile incProfile = new BandPassActivityProfile(genomeLocParser); + final BandPassActivityProfile fullProfile = new BandPassActivityProfile(genomeLocParser); + int pos = start; + for ( final VariantContext vc : reader.getVCs() ) { + if ( vc == null ) continue; + while ( pos < vc.getStart() ) { + final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, pos); + //logger.warn("Adding 0.0 at " + loc + " because vc.getStart is " + vc.getStart()); + incProfile.add(new ActivityProfileState(loc, 0.0)); + fullProfile.add(new ActivityProfileState(loc, 0.0)); + pos++; + } + if ( vc.getStart() >= start && vc.getEnd() <= end ) { + final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, pos); + //logger.warn("Adding 1.0 at " + loc); + ActivityProfileState.Type type = ActivityProfileState.Type.NONE; + Number value = null; + if ( vc.isBiallelic() && vc.isIndel() ) { + type = ActivityProfileState.Type.HIGH_QUALITY_SOFT_CLIPS; + value = Math.abs(vc.getIndelLengths().get(0)); + } + final ActivityProfileState state = new ActivityProfileState(loc, 1.0, type, value); + incProfile.add(state); + fullProfile.add(state); + pos++; + } + + incRegions.addAll(incProfile.popReadyActiveRegions(extension, minRegionSize, maxRegionSize, false)); + + if ( vc.getStart() > end ) + break; + } + + incRegions.addAll(incProfile.popReadyActiveRegions(extension, minRegionSize, maxRegionSize, true)); + + final List fullRegions = fullProfile.popReadyActiveRegions(extension, minRegionSize, maxRegionSize, true); + assertGoodRegions(fullRegions, start, end, maxRegionSize); + assertGoodRegions(incRegions, start, end, maxRegionSize); + + Assert.assertEquals(incRegions.size(), fullRegions.size(), "incremental and full region sizes aren't the same"); + for ( int i = 0; i < fullRegions.size(); i++ ) { + final ActiveRegion incRegion = incRegions.get(i); + final ActiveRegion fullRegion = fullRegions.get(i); + Assert.assertTrue(incRegion.equalExceptReads(fullRegion), "Full and incremental regions are not equal: full = " + fullRegion + " inc = " + incRegion); + } + } + + private void assertGoodRegions(final List regions, final int start, final int end, final int maxRegionSize) { + int lastPosSeen = start - 1; + for ( int regionI = 0; regionI < regions.size(); regionI++ ) { + final ActiveRegion region = regions.get(regionI); + Assert.assertEquals(region.getLocation().getStart(), lastPosSeen + 1, "discontinuous with previous region. lastPosSeen " + lastPosSeen + " but region is " + region); + Assert.assertTrue(region.getLocation().size() <= maxRegionSize, "Region is too big: " + region); + lastPosSeen = region.getLocation().getStop(); + + for ( final ActivityProfileState state : region.getSupportingStates() ) { + Assert.assertEquals(state.isActiveProb > ActivityProfile.ACTIVE_PROB_THRESHOLD, region.isActive(), + "Region is active=" + region.isActive() + " but contains a state " + state + " with prob " + + state.isActiveProb + " not within expected values given threshold for activity of " + + ActivityProfile.ACTIVE_PROB_THRESHOLD); + } + } + } +} diff --git a/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java index 1e3386426..da82e9de5 100644 --- a/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java @@ -203,6 +203,23 @@ public class BAQUnitTest extends BaseTest { Assert.assertTrue(baq.calcEpsilon( ref, alt, (byte)i) >= 0.0, "Failed to get baq epsilon range"); } + @Test(enabled = true) + public void testBAQOverwritesExistingTagWithNull() { + + // create a read with a single base off the end of the contig, which cannot be BAQed + final SAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, fasta.getSequenceDictionary().getSequence("chr1").getSequenceLength() + 1, 1); + read.setReadBases(new byte[] {(byte) 'A'}); + read.setBaseQualities(new byte[] {(byte) 20}); + read.setCigarString("1M"); + read.setAttribute("BQ", "A"); + + // try to BAQ and tell it to RECALCULATE AND ADD_TAG + BAQ baq = new BAQ(1e-3, 0.1, 7, (byte)4, false); + baq.baqRead(read, fasta, BAQ.CalculationMode.RECALCULATE, BAQ.QualityMode.ADD_TAG); + + // did we remove the existing tag? + Assert.assertTrue(read.getAttribute("BQ") == null); + } public void testBAQ(BAQTest test, boolean lookupWithFasta) { BAQ baqHMM = new BAQ(1e-3, 0.1, 7, (byte)4, false); // matches current samtools parameters diff --git a/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java index 7421767c7..9c9248669 100644 --- a/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java @@ -38,7 +38,7 @@ public class GATKKeyIntegrationTest extends WalkerTest { public static final String BASE_COMMAND = String.format("-T PrintReads -R %s -I %s -o %%s", publicTestDir + "exampleFASTA.fasta", publicTestDir + "exampleBAM.bam"); - public static final String MD5_UPON_SUCCESSFUL_RUN = "b9dc5bf6753ca2819e70b056eaf61258"; + public static final String MD5_UPON_SUCCESSFUL_RUN = "e7b4a5b62f9d4badef1cd07040011b2b"; private void runGATKKeyTest ( String testName, String etArg, String keyArg, Class expectedException, String md5 ) { diff --git a/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java index c67e52f2e..0c1b5b069 100644 --- a/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java @@ -32,8 +32,10 @@ package org.broadinstitute.sting.utils.fasta; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.ReferenceSequence; import net.sf.samtools.SAMSequenceRecord; +import org.apache.commons.lang.StringUtils; import org.apache.log4j.Priority; import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @@ -49,7 +51,7 @@ import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; /** - * Basic unit test for GenomeLoc + * Basic unit test for CachingIndexedFastaSequenceFile */ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest { private File simpleFasta = new File(publicTestDir + "/exampleFASTA.fasta"); @@ -80,7 +82,7 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest { @Test(dataProvider = "fastas", enabled = true && ! DEBUG) public void testCachingIndexedFastaReaderSequential1(File fasta, int cacheSize, int querySize) throws FileNotFoundException { - final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true); + final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false); SAMSequenceRecord contig = caching.getSequenceDictionary().getSequence(0); logger.warn(String.format("Checking contig %s length %d with cache size %d and query size %d", @@ -122,7 +124,7 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest { @Test(dataProvider = "fastas", enabled = true && ! DEBUG) public void testCachingIndexedFastaReaderTwoStage(File fasta, int cacheSize, int querySize) throws FileNotFoundException { final IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta); - final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true); + final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false); SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0); @@ -167,7 +169,7 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest { @Test(dataProvider = "ParallelFastaTest", enabled = true && ! DEBUG, timeOut = 60000) public void testCachingIndexedFastaReaderParallel(final File fasta, final int cacheSize, final int querySize, final int nt) throws FileNotFoundException, InterruptedException { - final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true); + final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false); logger.warn(String.format("Parallel caching index fasta reader test cacheSize %d querySize %d nt %d", caching.getCacheSize(), querySize, nt)); for ( int iterations = 0; iterations < 1; iterations++ ) { @@ -230,4 +232,33 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest { else return new String(reader.getSubsequenceAt(contig, start, stop).getBases()); } + + @Test(enabled = true) + public void testIupacChanges() throws FileNotFoundException, InterruptedException { + final String testFasta = privateTestDir + "iupacFASTA.fasta"; + final CachingIndexedFastaSequenceFile iupacPreserving = new CachingIndexedFastaSequenceFile(new File(testFasta), CachingIndexedFastaSequenceFile.DEFAULT_CACHE_SIZE, false, true); + final CachingIndexedFastaSequenceFile makeNs = new CachingIndexedFastaSequenceFile(new File(testFasta)); + + int preservingNs = 0; + int changingNs = 0; + for ( SAMSequenceRecord contig : iupacPreserving.getSequenceDictionary().getSequences() ) { + final String sPreserving = fetchBaseString(iupacPreserving, contig.getSequenceName(), 0, 15000); + preservingNs += StringUtils.countMatches(sPreserving, "N"); + + final String sChanging = fetchBaseString(makeNs, contig.getSequenceName(), 0, 15000); + changingNs += StringUtils.countMatches(sChanging, "N"); + } + + Assert.assertEquals(changingNs, preservingNs + 4); + } + + @Test(enabled = true, expectedExceptions = {UserException.class}) + public void testFailOnBadBase() throws FileNotFoundException, InterruptedException { + final String testFasta = privateTestDir + "problematicFASTA.fasta"; + final CachingIndexedFastaSequenceFile fasta = new CachingIndexedFastaSequenceFile(new File(testFasta)); + + for ( SAMSequenceRecord contig : fasta.getSequenceDictionary().getSequences() ) { + fetchBaseString(fasta, contig.getSequenceName(), -1, -1); + } + } } diff --git a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java index dc8a31945..98ecd0f43 100644 --- a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java @@ -78,7 +78,7 @@ public class IntervalIntegrationTest extends WalkerTest { // our base file File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam"); spec.setOutputFileLocation(baseOutputFile); - spec.addAuxFile("748a38ed5eb0a043dfc7b82f0d1e8063",createTempFileFromBase(baseOutputFile.getAbsolutePath())); + spec.addAuxFile("95e98192e5b90cf80eaa87a4ace263da",createTempFileFromBase(baseOutputFile.getAbsolutePath())); spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai")); executeTest("testUnmappedReadInclusion",spec); @@ -99,7 +99,7 @@ public class IntervalIntegrationTest extends WalkerTest { // our base file File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam"); spec.setOutputFileLocation(baseOutputFile); - spec.addAuxFile("083ef1e9ded868e0d12c05a1354c0319",createTempFileFromBase(baseOutputFile.getAbsolutePath())); + spec.addAuxFile("3944b5a6bfc06277ed3afb928a20d588",createTempFileFromBase(baseOutputFile.getAbsolutePath())); spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai")); executeTest("testUnmappedReadInclusion",spec); diff --git a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java index 35f9d4137..2be2745de 100644 --- a/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java @@ -1068,7 +1068,7 @@ public class IntervalUtilsUnitTest extends BaseTest { List> intervalArgs = new ArrayList>(1); intervalArgs.add(new IntervalBinding(picardIntervalFile.getAbsolutePath())); - IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalSetRule, argCollection.intervalMerging, argCollection.intervalPadding, genomeLocParser); + IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalArguments.intervalSetRule, argCollection.intervalArguments.intervalMerging, argCollection.intervalArguments.intervalPadding, genomeLocParser); } @Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData") @@ -1081,7 +1081,7 @@ public class IntervalUtilsUnitTest extends BaseTest { List> intervalArgs = new ArrayList>(1); intervalArgs.add(new IntervalBinding(gatkIntervalFile.getAbsolutePath())); - IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalSetRule, argCollection.intervalMerging, argCollection.intervalPadding, genomeLocParser); + IntervalUtils.loadIntervals(intervalArgs, argCollection.intervalArguments.intervalSetRule, argCollection.intervalArguments.intervalMerging, argCollection.intervalArguments.intervalPadding, genomeLocParser); } private File createTempFile( String tempFilePrefix, String tempFileExtension, String... lines ) throws Exception { diff --git a/public/java/test/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachineUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachineUnitTest.java index 2f1e95a1f..7cb148b61 100644 --- a/public/java/test/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachineUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachineUnitTest.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; diff --git a/public/java/test/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java b/public/java/test/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java index 31be5a25a..d856805f8 100644 --- a/public/java/test/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java +++ b/public/java/test/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; diff --git a/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java b/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java index c0938676e..e52cd46cc 100644 --- a/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java +++ b/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; diff --git a/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java b/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java index 7c8c6108c..1a51440ad 100644 --- a/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; diff --git a/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java index 47e386ab5..eb7e61ed8 100644 --- a/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.locusiterator; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.downsampling.DownsampleType; @@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.sam.ArtificialBAMBuilder; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -50,9 +51,35 @@ import java.util.*; * testing of the new (non-legacy) version of LocusIteratorByState */ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { - private static final boolean DEBUG = false; + private static final boolean DEBUG = true; protected LocusIteratorByState li; + @Test(enabled = true) + public void testUnmappedAndAllIReadsPassThrough() { + final int readLength = 10; + GATKSAMRecord mapped1 = ArtificialSAMUtils.createArtificialRead(header,"mapped1",0,1,readLength); + GATKSAMRecord mapped2 = ArtificialSAMUtils.createArtificialRead(header,"mapped2",0,1,readLength); + GATKSAMRecord unmapped = ArtificialSAMUtils.createArtificialRead(header,"unmapped",0,1,readLength); + GATKSAMRecord allI = ArtificialSAMUtils.createArtificialRead(header,"allI",0,1,readLength); + + unmapped.setReadUnmappedFlag(true); + unmapped.setCigarString("*"); + allI.setCigarString(readLength + "I"); + + List reads = Arrays.asList(mapped1, unmapped, allI, mapped2); + + // create the iterator by state with the fake reads and fake records + li = makeLTBS(reads,createTestReadProperties(DownsamplingMethod.NONE, true)); + + Assert.assertTrue(li.hasNext()); + AlignmentContext context = li.next(); + ReadBackedPileup pileup = context.getBasePileup(); + Assert.assertEquals(pileup.depthOfCoverage(), 2, "Should see only 2 reads in pileup, even with unmapped and all I reads"); + + final List rawReads = li.transferReadsFromAllPreviousPileups(); + Assert.assertEquals(rawReads, reads, "Input and transferred read lists should be the same, and include the unmapped and all I reads"); + } + @Test(enabled = true && ! DEBUG) public void testXandEQOperators() { final byte[] bases1 = new byte[] {'A','A','A','A','A','A','A','A','A','A'}; @@ -350,7 +377,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { // Arrays.asList(3)); } - @Test(enabled = true, dataProvider = "LIBSTest") + @Test(enabled = true && ! DEBUG, dataProvider = "LIBSTest") public void testLIBS(LIBSTest params) { // create the iterator by state with the fake reads and fake records final GATKSAMRecord read = params.makeRead(); @@ -406,22 +433,25 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { // // ------------------------------------------------------------ - @DataProvider(name = "LIBSKeepSubmittedReads") - public Object[][] makeLIBSKeepSubmittedReads() { + @DataProvider(name = "LIBS_ComplexPileupTests") + public Object[][] makeLIBS_ComplexPileupTests() { final List tests = new LinkedList(); - for ( final boolean doSampling : Arrays.asList(true, false) ) { - for ( final int nReadsPerLocus : Arrays.asList(1, 10) ) { + for ( final int downsampleTo : Arrays.asList(-1, 1, 2, 5, 10, 30)) { + for ( final int nReadsPerLocus : Arrays.asList(1, 10, 60) ) { for ( final int nLoci : Arrays.asList(1, 10, 25) ) { for ( final int nSamples : Arrays.asList(1, 2, 10) ) { for ( final boolean keepReads : Arrays.asList(true, false) ) { for ( final boolean grabReadsAfterEachCycle : Arrays.asList(true, false) ) { -// for ( final int nReadsPerLocus : Arrays.asList(1) ) { -// for ( final int nLoci : Arrays.asList(1) ) { -// for ( final int nSamples : Arrays.asList(1) ) { -// for ( final boolean keepReads : Arrays.asList(true) ) { -// for ( final boolean grabReadsAfterEachCycle : Arrays.asList(true) ) { - tests.add(new Object[]{nReadsPerLocus, nLoci, nSamples, keepReads, grabReadsAfterEachCycle, doSampling}); +// for ( final int downsampleTo : Arrays.asList(1)) { +// for ( final int nReadsPerLocus : Arrays.asList(1) ) { +// for ( final int nLoci : Arrays.asList(1) ) { +// for ( final int nSamples : Arrays.asList(1) ) { +// for ( final boolean keepReads : Arrays.asList(true) ) { +// for ( final boolean grabReadsAfterEachCycle : Arrays.asList(true) ) { + tests.add(new Object[]{nReadsPerLocus, nLoci, nSamples, + keepReads, grabReadsAfterEachCycle, + downsampleTo}); } } } @@ -432,37 +462,29 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { return tests.toArray(new Object[][]{}); } - @Test(enabled = true && ! DEBUG, dataProvider = "LIBSKeepSubmittedReads") - public void testLIBSKeepSubmittedReads(final int nReadsPerLocus, - final int nLoci, - final int nSamples, - final boolean keepReads, - final boolean grabReadsAfterEachCycle, - final boolean downsample) { - logger.warn(String.format("testLIBSKeepSubmittedReads %d %d %d %b %b %b", nReadsPerLocus, nLoci, nSamples, keepReads, grabReadsAfterEachCycle, downsample)); + @Test(enabled = true && ! DEBUG, dataProvider = "LIBS_ComplexPileupTests") + public void testLIBS_ComplexPileupTests(final int nReadsPerLocus, + final int nLoci, + final int nSamples, + final boolean keepReads, + final boolean grabReadsAfterEachCycle, + final int downsampleTo) { + //logger.warn(String.format("testLIBSKeepSubmittedReads %d %d %d %b %b %b", nReadsPerLocus, nLoci, nSamples, keepReads, grabReadsAfterEachCycle, downsample)); final int readLength = 10; - final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 100000); - final List samples = new ArrayList(nSamples); - for ( int i = 0; i < nSamples; i++ ) { - final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("rg" + i); - final String sample = "sample" + i; - samples.add(sample); - rg.setSample(sample); - rg.setPlatform(NGSPlatform.ILLUMINA.getDefaultPlatform()); - header.addReadGroup(rg); - } - - final int maxCoveragePerSampleAtLocus = nReadsPerLocus * readLength / 2; - final int maxDownsampledCoverage = Math.max(maxCoveragePerSampleAtLocus / 2, 1); + final boolean downsample = downsampleTo != -1; final DownsamplingMethod downsampler = downsample - ? new DownsamplingMethod(DownsampleType.BY_SAMPLE, maxDownsampledCoverage, null, false) - : new DownsamplingMethod(DownsampleType.NONE, null, null, false); - final List reads = ArtificialSAMUtils.createReadStream(nReadsPerLocus, nLoci, header, 1, readLength); + ? new DownsamplingMethod(DownsampleType.BY_SAMPLE, downsampleTo, null) + : new DownsamplingMethod(DownsampleType.NONE, null, null); + + final ArtificialBAMBuilder bamBuilder = new ArtificialBAMBuilder(header.getSequenceDictionary(), nReadsPerLocus, nLoci); + bamBuilder.createAndSetHeader(nSamples).setReadLength(readLength).setAlignmentStart(1); + + final List reads = bamBuilder.makeReads(); li = new LocusIteratorByState(new FakeCloseableIterator(reads.iterator()), createTestReadProperties(downsampler, keepReads), genomeLocParser, - samples); + bamBuilder.getSamples()); final Set seenSoFar = new HashSet(); final Set keptReads = new HashSet(); @@ -472,6 +494,8 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { final AlignmentContext alignmentContext = li.next(); final ReadBackedPileup p = alignmentContext.getBasePileup(); + AssertWellOrderedPileup(p); + if ( downsample ) { // just not a safe test //Assert.assertTrue(p.getNumberOfElements() <= maxDownsampledCoverage * nSamples, "Too many reads at locus after downsampling"); @@ -480,22 +504,29 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { Assert.assertTrue(p.getNumberOfElements() >= minPileupSize); } + // the number of reads starting here + int nReadsStartingHere = 0; + for ( final GATKSAMRecord read : p.getReads() ) + if ( read.getAlignmentStart() == alignmentContext.getPosition() ) + nReadsStartingHere++; + + // we can have no more than maxDownsampledCoverage per sample + final int maxCoveragePerLocus = downsample ? downsampleTo : nReadsPerLocus; + Assert.assertTrue(nReadsStartingHere <= maxCoveragePerLocus * nSamples); + seenSoFar.addAll(p.getReads()); if ( keepReads && grabReadsAfterEachCycle ) { final List locusReads = li.transferReadsFromAllPreviousPileups(); - // the number of reads starting here - int nReadsStartingHere = 0; - for ( final GATKSAMRecord read : p.getReads() ) - if ( read.getAlignmentStart() == alignmentContext.getPosition() ) - nReadsStartingHere++; - if ( downsample ) + if ( downsample ) { // with downsampling we might have some reads here that were downsampled away - // in the pileup + // in the pileup. We want to ensure that no more than the max coverage per sample is added Assert.assertTrue(locusReads.size() >= nReadsStartingHere); - else + Assert.assertTrue(locusReads.size() <= maxCoveragePerLocus * nSamples); + } else { Assert.assertEquals(locusReads.size(), nReadsStartingHere); + } keptReads.addAll(locusReads); // check that all reads we've seen so far are in our keptReads @@ -543,6 +574,196 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { for ( final GATKSAMRecord read : seenSoFar ) { Assert.assertTrue(keptReads.contains(read), "A read that appeared in a pileup wasn't found in the kept reads: " + read); } + + if ( ! downsample ) { + // check that every read in the list of keep reads occurred at least once in one of the pileups + for ( final GATKSAMRecord keptRead : keptReads ) { + Assert.assertTrue(seenSoFar.contains(keptRead), "There's a read " + keptRead + " in our keptReads list that never appeared in any pileup"); + } + } } } + + private void AssertWellOrderedPileup(final ReadBackedPileup pileup) { + if ( ! pileup.isEmpty() ) { + int leftMostPos = -1; + + for ( final PileupElement pe : pileup ) { + Assert.assertTrue(pileup.getLocation().getContig().equals(pe.getRead().getReferenceName()), "ReadBackedPileup contains an element " + pe + " that's on a different contig than the pileup itself"); + Assert.assertTrue(pe.getRead().getAlignmentStart() >= leftMostPos, + "ReadBackedPileup contains an element " + pe + " whose read's alignment start " + pe.getRead().getAlignmentStart() + + " occurs before the leftmost position we've seen previously " + leftMostPos); + } + } + } + + // --------------------------------------------------------------------------- + // make sure that downsampling isn't holding onto a bazillion reads + // + @DataProvider(name = "LIBS_NotHoldingTooManyReads") + public Object[][] makeLIBS_NotHoldingTooManyReads() { + final List tests = new LinkedList(); + + for ( final int downsampleTo : Arrays.asList(1, 10)) { + for ( final int nReadsPerLocus : Arrays.asList(100, 1000, 10000, 100000) ) { + for ( final int payloadInBytes : Arrays.asList(0, 1024, 1024*1024) ) { + tests.add(new Object[]{nReadsPerLocus, downsampleTo, payloadInBytes}); + } + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test(enabled = true && ! DEBUG, dataProvider = "LIBS_NotHoldingTooManyReads") +// @Test(enabled = true, dataProvider = "LIBS_NotHoldingTooManyReads", timeOut = 100000) + public void testLIBS_NotHoldingTooManyReads(final int nReadsPerLocus, final int downsampleTo, final int payloadInBytes) { + logger.warn(String.format("testLIBS_NotHoldingTooManyReads %d %d %d", nReadsPerLocus, downsampleTo, payloadInBytes)); + final int readLength = 10; + + final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 100000); + final int nSamples = 1; + final List samples = new ArrayList(nSamples); + for ( int i = 0; i < nSamples; i++ ) { + final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("rg" + i); + final String sample = "sample" + i; + samples.add(sample); + rg.setSample(sample); + rg.setPlatform(NGSPlatform.ILLUMINA.getDefaultPlatform()); + header.addReadGroup(rg); + } + + final boolean downsample = downsampleTo != -1; + final DownsamplingMethod downsampler = downsample + ? new DownsamplingMethod(DownsampleType.BY_SAMPLE, downsampleTo, null) + : new DownsamplingMethod(DownsampleType.NONE, null, null); + + // final List reads = ArtificialSAMUtils.createReadStream(nReadsPerLocus, nLoci, header, 1, readLength); + + final WeakReadTrackingIterator iterator = new WeakReadTrackingIterator(nReadsPerLocus, readLength, payloadInBytes, header); + + li = new LocusIteratorByState(iterator, + createTestReadProperties(downsampler, false), + genomeLocParser, + samples); + + while ( li.hasNext() ) { + final AlignmentContext next = li.next(); + Assert.assertTrue(next.getBasePileup().getNumberOfElements() <= downsampleTo, "Too many elements in pileup " + next); + // TODO -- assert that there are <= X reads in memory after GC for some X + } + } + + private static class WeakReadTrackingIterator implements Iterator { + final int nReads, readLength, payloadInBytes; + int readI = 0; + final SAMFileHeader header; + + private WeakReadTrackingIterator(int nReads, int readLength, final int payloadInBytes, final SAMFileHeader header) { + this.nReads = nReads; + this.readLength = readLength; + this.header = header; + this.payloadInBytes = payloadInBytes; + } + + @Override public boolean hasNext() { return readI < nReads; } + @Override public void remove() { throw new UnsupportedOperationException("no remove"); } + + @Override + public GATKSAMRecord next() { + readI++; + return makeRead(); + } + + private GATKSAMRecord makeRead() { + final SAMReadGroupRecord rg = header.getReadGroups().get(0); + final String readName = String.format("%s.%d.%s", "read", readI, rg.getId()); + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, readName, 0, 1, readLength); + read.setReadGroup(new GATKSAMReadGroupRecord(rg)); + if ( payloadInBytes > 0 ) + // add a payload byte array to push memory use per read even higher + read.setAttribute("PL", new byte[payloadInBytes]); + return read; + } + } + + // --------------------------------------------------------------------------- + // + // make sure that adapter clipping is working properly in LIBS + // + // --------------------------------------------------------------------------- + @DataProvider(name = "AdapterClippingTest") + public Object[][] makeAdapterClippingTest() { + final List tests = new LinkedList(); + + final int start = 10; +// for ( final int goodBases : Arrays.asList(10) ) { +// for ( final int nClipsOnTheRight : Arrays.asList(0)) { + for ( final int goodBases : Arrays.asList(10, 20, 30) ) { + for ( final int nClips : Arrays.asList(0, 1, 2, 10)) { + for ( final boolean onLeft : Arrays.asList(true, false) ) { + final int readLength = nClips + goodBases; + GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1" , 0, start, readLength); + read.setReadBases(Utils.dupBytes((byte) 'A', readLength)); + read.setBaseQualities(Utils.dupBytes((byte) '@', readLength)); + read.setCigarString(readLength + "M"); + + if ( onLeft ) { + read.setReadNegativeStrandFlag(true); + read.setMateAlignmentStart(start + nClips); + read.setInferredInsertSize(readLength); + tests.add(new Object[]{nClips, goodBases, 0, read}); + } else { + read.setReadNegativeStrandFlag(false); + read.setMateAlignmentStart(start - 1); + read.setInferredInsertSize(goodBases - 1); + tests.add(new Object[]{0, goodBases, nClips, read}); + } + } + } + } + +// for ( final int nClipsOnTheLeft : Arrays.asList(0, 1, 2, 10)) { +// final int readLength = nClipsOnTheLeft + goodBases; +// GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1" , 0, start, readLength); +// read.setReadBases(Utils.dupBytes((byte) 'A', readLength)); +// read.setBaseQualities(Utils.dupBytes((byte) '@', readLength)); +// read.setCigarString(readLength + "M"); +// read.setReadNegativeStrandFlag(true); +// +// read.setMateAlignmentStart(start + nClipsOnTheLeft); +// read.setInferredInsertSize(readLength); +// +// tests.add(new Object[]{nClipsOnTheLeft, goodBases, 0, read}); +// } +// } + + return tests.toArray(new Object[][]{}); + } + + @Test(enabled = true, dataProvider = "AdapterClippingTest") +// @Test(enabled = true, dataProvider = "LIBS_NotHoldingTooManyReads", timeOut = 100000) + public void testAdapterClipping(final int nClipsOnLeft, final int nReadContainingPileups, final int nClipsOnRight, final GATKSAMRecord read) { + + li = new LocusIteratorByState(new FakeCloseableIterator(Collections.singletonList(read).iterator()), + createTestReadProperties(DownsamplingMethod.NONE, false), + genomeLocParser, + LocusIteratorByState.sampleListForSAMWithoutReadGroups()); + + int expectedPos = read.getAlignmentStart() + nClipsOnLeft; + int nPileups = 0; + while ( li.hasNext() ) { + final AlignmentContext next = li.next(); + Assert.assertEquals(next.getLocation().getStart(), expectedPos); +// if ( nPileups < nClipsOnLeft || nPileups > (nClipsOnLeft + nReadContainingPileups) ) +// Assert.assertEquals(next.getBasePileup().getNumberOfElements(), 0, "Expected empty pileups when the read is in the adapter clipping zone at " + nPileups); +// else +// Assert.assertEquals(next.getBasePileup().getNumberOfElements(), 1, "Expected a pileups with 1 element when the read is within the good part of the read at " + nPileups); + nPileups++; + expectedPos++; + } + + final int nExpectedPileups = nReadContainingPileups; + Assert.assertEquals(nPileups, nExpectedPileups, "Wrong number of pileups seen"); + } } diff --git a/public/java/test/org/broadinstitute/sting/utils/locusiterator/ReadStateManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java similarity index 79% rename from public/java/test/org/broadinstitute/sting/utils/locusiterator/ReadStateManagerUnitTest.java rename to public/java/test/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java index 1db0605c7..77dd29e60 100644 --- a/public/java/test/org/broadinstitute/sting/utils/locusiterator/ReadStateManagerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.locusiterator; @@ -38,11 +38,7 @@ import java.util.*; /** * testing of the new (non-legacy) version of LocusIteratorByState */ -public class ReadStateManagerUnitTest extends LocusIteratorByStateBaseTest { - /////////////////////////////////////// - // Read State Manager Tests // - /////////////////////////////////////// - +public class PerSampleReadStateManagerUnitTest extends LocusIteratorByStateBaseTest { private class PerSampleReadStateManagerTest extends TestDataProvider { private List readCountsPerAlignmentStart; private List reads; @@ -63,15 +59,12 @@ public class ReadStateManagerUnitTest extends LocusIteratorByStateBaseTest { } public void run() { - final List samples = LocusIteratorByState.sampleListForSAMWithoutReadGroups(); - final Iterator iterator = new LinkedList().iterator(); - ReadStateManager readStateManager = new ReadStateManager(iterator, samples, LIBSDownsamplingInfo.NO_DOWNSAMPLING, false); - ReadStateManager.PerSampleReadStateManager perSampleReadStateManager = readStateManager.new PerSampleReadStateManager(LIBSDownsamplingInfo.NO_DOWNSAMPLING); + PerSampleReadStateManager perSampleReadStateManager = new PerSampleReadStateManager(LIBSDownsamplingInfo.NO_DOWNSAMPLING); makeReads(); for ( ArrayList stackRecordStates : recordStatesByAlignmentStart ) { - perSampleReadStateManager.addStatesAtNextAlignmentStart(stackRecordStates); + perSampleReadStateManager.addStatesAtNextAlignmentStart(new LinkedList(stackRecordStates)); } // read state manager should have the right number of reads diff --git a/public/java/test/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java index a760833f5..888ab7f7f 100644 --- a/public/java/test/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java @@ -1,27 +1,27 @@ /* - * Copyright (c) 2012 The Broad Institute - * - * 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. - */ +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.pileup; diff --git a/public/java/test/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemonUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemonUnitTest.java index 4de24bc15..c33c1976b 100644 --- a/public/java/test/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemonUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/progressmeter/ProgressMeterDaemonUnitTest.java @@ -84,7 +84,7 @@ public class ProgressMeterDaemonUnitTest extends BaseTest { } @Test(dataProvider = "PollingData", invocationCount = 10, successPercentage = 90) - public void testMe(final long poll, final int ticks) throws InterruptedException { + public void testProgressMeterDaemon(final long poll, final int ticks) throws InterruptedException { final TestingProgressMeter meter = new TestingProgressMeter(poll); final ProgressMeterDaemon daemon = meter.getProgressMeterDaemon(); Assert.assertTrue(daemon.isDaemon()); @@ -96,6 +96,9 @@ public class ProgressMeterDaemonUnitTest extends BaseTest { daemon.done(); Assert.assertTrue(daemon.isDone()); + // wait for the thread to actually finish + daemon.join(); + Assert.assertTrue(meter.progressCalls.size() >= 1, "Expected at least one progress update call from daemon thread, but only got " + meter.progressCalls.size() + " with exact calls " + meter.progressCalls); diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java index f088574d7..d9f514593 100644 --- a/public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java @@ -25,13 +25,16 @@ package org.broadinstitute.sting.utils.sam; -import junit.framework.Assert; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import net.sf.samtools.*; +import org.apache.commons.lang.ArrayUtils; +import org.broadinstitute.sting.utils.Utils; +import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import java.util.*; + public class AlignmentUtilsUnitTest { private SAMFileHeader header; @@ -121,4 +124,205 @@ public class AlignmentUtilsUnitTest { start, ArtificialSAMUtils.DEFAULT_READ_LENGTH); } + + private final List> makeCigarElementCombinations() { + // this functionality can be adapted to provide input data for whatever you might want in your data + final List cigarElements = new LinkedList(); + for ( final int size : Arrays.asList(0, 10) ) { + for ( final CigarOperator op : CigarOperator.values() ) { + cigarElements.add(new CigarElement(size, op)); + } + } + + final List> combinations = new LinkedList>(); + for ( final int nElements : Arrays.asList(1, 2, 3) ) { + combinations.addAll(Utils.makePermutations(cigarElements, nElements, true)); + } + + return combinations; + } + + + @DataProvider(name = "NumAlignedBasesCountingSoftClips") + public Object[][] makeNumAlignedBasesCountingSoftClips() { + List tests = new ArrayList(); + + final EnumSet alignedToGenome = EnumSet.of(CigarOperator.M, CigarOperator.EQ, CigarOperator.X, CigarOperator.S); + for ( final List elements : makeCigarElementCombinations() ) { + int n = 0; + for ( final CigarElement elt : elements ) n += alignedToGenome.contains(elt.getOperator()) ? elt.getLength() : 0; + tests.add(new Object[]{new Cigar(elements), n}); + } + + tests.add(new Object[]{null, 0}); + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "NumAlignedBasesCountingSoftClips") + public void testNumAlignedBasesCountingSoftClips(final Cigar cigar, final int expected) { + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, cigar == null ? 10 : cigar.getReadLength()); + read.setCigar(cigar); + Assert.assertEquals(AlignmentUtils.getNumAlignedBasesCountingSoftClips(read), expected, "Cigar " + cigar + " failed NumAlignedBasesCountingSoftClips"); + } + + @DataProvider(name = "CigarHasZeroElement") + public Object[][] makeCigarHasZeroElement() { + List tests = new ArrayList(); + + for ( final List elements : makeCigarElementCombinations() ) { + boolean hasZero = false; + for ( final CigarElement elt : elements ) hasZero = hasZero || elt.getLength() == 0; + tests.add(new Object[]{new Cigar(elements), hasZero}); + } + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "CigarHasZeroElement") + public void testCigarHasZeroSize(final Cigar cigar, final boolean hasZero) { + Assert.assertEquals(AlignmentUtils.cigarHasZeroSizeElement(cigar), hasZero, "Cigar " + cigar.toString() + " failed cigarHasZeroSizeElement"); + } + + @DataProvider(name = "NumHardClipped") + public Object[][] makeNumHardClipped() { + List tests = new ArrayList(); + + for ( final List elements : makeCigarElementCombinations() ) { + int n = 0; + for ( final CigarElement elt : elements ) n += elt.getOperator() == CigarOperator.H ? elt.getLength() : 0; + tests.add(new Object[]{new Cigar(elements), n}); + } + + tests.add(new Object[]{null, 0}); + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "NumHardClipped") + public void testNumHardClipped(final Cigar cigar, final int expected) { + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, cigar == null ? 10 : cigar.getReadLength()); + read.setCigar(cigar); + Assert.assertEquals(AlignmentUtils.getNumHardClippedBases(read), expected, "Cigar " + cigar + " failed num hard clips"); + } + + @DataProvider(name = "NumAlignedBlocks") + public Object[][] makeNumAlignedBlocks() { + List tests = new ArrayList(); + + for ( final List elements : makeCigarElementCombinations() ) { + int n = 0; + for ( final CigarElement elt : elements ) { + switch ( elt.getOperator() ) { + case M:case X:case EQ: n++; break; + default: break; + } + } + tests.add(new Object[]{new Cigar(elements), n}); + } + + tests.add(new Object[]{null, 0}); + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "NumAlignedBlocks") + public void testNumAlignedBlocks(final Cigar cigar, final int expected) { + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, cigar == null ? 10 : cigar.getReadLength()); + read.setCigar(cigar); + Assert.assertEquals(AlignmentUtils.getNumAlignmentBlocks(read), expected, "Cigar " + cigar + " failed NumAlignedBlocks"); + } + + @Test + public void testConsolidateCigar() { + { + //1M1M1M1D2M1M --> 3M1D3M + List list = new ArrayList(); + list.add( new CigarElement(1, CigarOperator.M)); + list.add( new CigarElement(1, CigarOperator.M)); + list.add( new CigarElement(1, CigarOperator.M)); + list.add( new CigarElement(1, CigarOperator.D)); + list.add( new CigarElement(2, CigarOperator.M)); + list.add( new CigarElement(1, CigarOperator.M)); + Cigar unconsolidatedCigar = new Cigar(list); + + list.clear(); + list.add( new CigarElement(3, CigarOperator.M)); + list.add( new CigarElement(1, CigarOperator.D)); + list.add( new CigarElement(3, CigarOperator.M)); + Cigar consolidatedCigar = new Cigar(list); + + Assert.assertEquals(consolidatedCigar.toString(), AlignmentUtils.consolidateCigar(unconsolidatedCigar).toString()); + } + + { + //6M6M6M --> 18M + List list = new ArrayList(); + list.add( new CigarElement(6, CigarOperator.M)); + list.add( new CigarElement(6, CigarOperator.M)); + list.add( new CigarElement(6, CigarOperator.M)); + Cigar unconsolidatedCigar = new Cigar(list); + + list.clear(); + list.add( new CigarElement(18, CigarOperator.M)); + Cigar consolidatedCigar = new Cigar(list); + + Assert.assertEquals(consolidatedCigar.toString(), AlignmentUtils.consolidateCigar(unconsolidatedCigar).toString()); + } + } + + @DataProvider(name = "SoftClipsDataProvider") + public Object[][] makeSoftClipsDataProvider() { + List tests = new ArrayList(); + + // this functionality can be adapted to provide input data for whatever you might want in your data + for ( final int lengthOfLeftClip : Arrays.asList(0, 1, 10) ) { + for ( final int lengthOfRightClip : Arrays.asList(0, 1, 10) ) { + for ( final int qualThres : Arrays.asList(10, 20, 30) ) { + for ( final String middleOp : Arrays.asList("M", "D") ) { + for ( final int matchSize : Arrays.asList(0, 1, 10) ) { + final byte[] left = makeQualArray(lengthOfLeftClip, qualThres); + final byte[] right = makeQualArray(lengthOfRightClip, qualThres); + int n = 0; + for ( int i = 0; i < left.length; i++ ) n += left[i] > qualThres ? 1 : 0; + for ( int i = 0; i < right.length; i++ ) n += right[i] > qualThres ? 1 : 0; + tests.add(new Object[]{left, matchSize, middleOp, right, qualThres, n}); + } + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + private byte[] makeQualArray(final int length, final int qualThreshold) { + final byte[] array = new byte[length]; + for ( int i = 0; i < array.length; i++ ) + array[i] = (byte)(qualThreshold + ( i % 2 == 0 ? 1 : - 1 )); + return array; + } + + @Test(dataProvider = "SoftClipsDataProvider") + public void testSoftClipsData(final byte[] qualsOfSoftClipsOnLeft, final int middleSize, final String middleOp, final byte[] qualOfSoftClipsOnRight, final int qualThreshold, final int numExpected) { + final int readLength = (middleOp.equals("D") ? 0 : middleSize) + qualOfSoftClipsOnRight.length + qualsOfSoftClipsOnLeft.length; + final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, readLength); + final byte[] bases = Utils.dupBytes((byte) 'A', readLength); + final byte[] matchBytes = middleOp.equals("D") ? new byte[]{} : Utils.dupBytes((byte)30, middleSize); + final byte[] quals = ArrayUtils.addAll(ArrayUtils.addAll(qualsOfSoftClipsOnLeft, matchBytes), qualOfSoftClipsOnRight); + + // set the read's bases and quals + read.setReadBases(bases); + read.setBaseQualities(quals); + + final StringBuilder cigar = new StringBuilder(); + if (qualsOfSoftClipsOnLeft.length > 0 ) cigar.append(qualsOfSoftClipsOnLeft.length + "S"); + if (middleSize > 0 ) cigar.append(middleSize + middleOp); + if (qualOfSoftClipsOnRight.length > 0 ) cigar.append(qualOfSoftClipsOnRight.length + "S"); + + read.setCigarString(cigar.toString()); + + final int actual = AlignmentUtils.calcNumHighQualitySoftClips(read, (byte) qualThreshold); + Assert.assertEquals(actual, numExpected, "Wrong number of soft clips detected for read " + read.getSAMString()); + } } diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java new file mode 100644 index 000000000..a2aec1b1e --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java @@ -0,0 +1,122 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.sting.utils.sam; + +import net.sf.samtools.SAMFileReader; +import net.sf.samtools.SAMRecord; +import org.apache.commons.collections.IteratorUtils; +import org.broadinstitute.sting.BaseTest; +import org.testng.Assert; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import java.io.File; +import java.util.Arrays; +import java.util.Iterator; +import java.util.LinkedList; +import java.util.List; + +/** + * Created with IntelliJ IDEA. + * User: depristo + * Date: 1/15/13 + * Time: 3:49 PM + * To change this template use File | Settings | File Templates. + */ +public class ArtificialBAMBuilderUnitTest extends BaseTest { + @DataProvider(name = "ArtificialBAMBuilderUnitTestProvider") + public Object[][] makeArtificialBAMBuilderUnitTestProvider() { + final List tests = new LinkedList(); + + final List starts = Arrays.asList( + 1, // very start of the chromosome + ArtificialBAMBuilder.BAM_SHARD_SIZE - 100, // right before the shard boundary + ArtificialBAMBuilder.BAM_SHARD_SIZE + 100 // right after the shard boundary + ); + + for ( final int readLength : Arrays.asList(10, 20) ) { + for ( final int skips : Arrays.asList(0, 1, 10) ) { + for ( final int start : starts ) { + for ( final int nSamples : Arrays.asList(1, 2) ) { + for ( final int nReadsPerLocus : Arrays.asList(1, 10) ) { + for ( final int nLoci : Arrays.asList(10, 100, 1000) ) { + final ArtificialBAMBuilder bamBuilder = new ArtificialBAMBuilder(nReadsPerLocus, nLoci); + bamBuilder.setReadLength(readLength); + bamBuilder.setSkipNLoci(skips); + bamBuilder.setAlignmentStart(start); + bamBuilder.createAndSetHeader(nSamples); + tests.add(new Object[]{bamBuilder, readLength, skips, start, nSamples, nReadsPerLocus, nLoci}); + } + } + } + } + } + } + + return tests.toArray(new Object[][]{}); + } + + @Test(dataProvider = "ArtificialBAMBuilderUnitTestProvider") + public void testBamProvider(final ArtificialBAMBuilder bamBuilder, int readLength, int skips, int start, int nSamples, int nReadsPerLocus, int nLoci) { + Assert.assertEquals(bamBuilder.getReadLength(), readLength); + Assert.assertEquals(bamBuilder.getSkipNLoci(), skips); + Assert.assertEquals(bamBuilder.getAlignmentStart(), start); + Assert.assertEquals(bamBuilder.getNSamples(), nSamples); + Assert.assertEquals(bamBuilder.getnReadsPerLocus(), nReadsPerLocus); + Assert.assertEquals(bamBuilder.getnLoci(), nLoci); + + final List reads = bamBuilder.makeReads(); + Assert.assertEquals(reads.size(), bamBuilder.expectedNumberOfReads()); + for ( final GATKSAMRecord read : reads ) { + assertGoodRead(read, bamBuilder); + } + + final File bam = bamBuilder.makeTemporarilyBAMFile(); + final SAMFileReader reader = new SAMFileReader(bam); + Assert.assertTrue(reader.hasIndex()); + final Iterator bamIt = reader.iterator(); + int nReadsFromBam = 0; + int lastStart = -1; + while ( bamIt.hasNext() ) { + final SAMRecord read = bamIt.next(); + assertGoodRead(read, bamBuilder); + nReadsFromBam++; + Assert.assertTrue(read.getAlignmentStart() >= lastStart); + lastStart = read.getAlignmentStart(); + } + Assert.assertEquals(nReadsFromBam, bamBuilder.expectedNumberOfReads()); + } + + private void assertGoodRead(final SAMRecord read, final ArtificialBAMBuilder bamBuilder) { + Assert.assertEquals(read.getReadLength(), bamBuilder.getReadLength()); + Assert.assertEquals(read.getReadBases().length, bamBuilder.getReadLength()); + Assert.assertEquals(read.getBaseQualities().length, bamBuilder.getReadLength()); + Assert.assertTrue(read.getAlignmentStart() >= bamBuilder.getAlignmentStart()); + Assert.assertNotNull(read.getReadGroup()); + } +} + + diff --git a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java index 71c7d1bb0..b01c53e77 100644 --- a/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java @@ -26,87 +26,143 @@ package org.broadinstitute.sting.utils.sam; import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.utils.BaseUtils; import org.testng.Assert; +import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import java.util.LinkedList; +import java.util.List; +import java.util.Random; + public class ReadUtilsUnitTest extends BaseTest { - @Test - public void testGetAdaptorBoundary() { + private interface GetAdaptorFunc { + public int getAdaptor(final GATKSAMRecord record); + } + + @DataProvider(name = "AdaptorGetter") + public Object[][] makeActiveRegionCutTests() { + final List tests = new LinkedList(); + + tests.add( new Object[]{ new GetAdaptorFunc() { + @Override public int getAdaptor(final GATKSAMRecord record) { return ReadUtils.getAdaptorBoundary(record); } + }}); + + tests.add( new Object[]{ new GetAdaptorFunc() { + @Override public int getAdaptor(final GATKSAMRecord record) { return record.getAdaptorBoundary(); } + }}); + + return tests.toArray(new Object[][]{}); + } + + private GATKSAMRecord makeRead(final int fragmentSize, final int mateStart) { final byte[] bases = {'A', 'C', 'G', 'T', 'A', 'C', 'G', 'T'}; final byte[] quals = {30, 30, 30, 30, 30, 30, 30, 30}; final String cigar = "8M"; + GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, cigar); + read.setMateAlignmentStart(mateStart); + read.setInferredInsertSize(fragmentSize); + return read; + } + + @Test(dataProvider = "AdaptorGetter") + public void testGetAdaptorBoundary(final GetAdaptorFunc get) { final int fragmentSize = 10; final int mateStart = 1000; final int BEFORE = mateStart - 2; final int AFTER = mateStart + 2; - Integer myStart, boundary; - - GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, cigar); - read.setMateAlignmentStart(mateStart); - read.setInferredInsertSize(fragmentSize); + int myStart, boundary; + GATKSAMRecord read; // Test case 1: positive strand, first read + read = makeRead(fragmentSize, mateStart); myStart = BEFORE; read.setAlignmentStart(myStart); read.setReadNegativeStrandFlag(false); - boundary = ReadUtils.getAdaptorBoundary(read); - Assert.assertEquals(boundary.intValue(), myStart + fragmentSize + 1); + boundary = get.getAdaptor(read); + Assert.assertEquals(boundary, myStart + fragmentSize + 1); // Test case 2: positive strand, second read + read = makeRead(fragmentSize, mateStart); myStart = AFTER; read.setAlignmentStart(myStart); read.setReadNegativeStrandFlag(false); - boundary = ReadUtils.getAdaptorBoundary(read); - Assert.assertEquals(boundary.intValue(), myStart + fragmentSize + 1); + boundary = get.getAdaptor(read); + Assert.assertEquals(boundary, myStart + fragmentSize + 1); // Test case 3: negative strand, second read + read = makeRead(fragmentSize, mateStart); myStart = AFTER; read.setAlignmentStart(myStart); read.setReadNegativeStrandFlag(true); - boundary = ReadUtils.getAdaptorBoundary(read); - Assert.assertEquals(boundary.intValue(), mateStart - 1); + boundary = get.getAdaptor(read); + Assert.assertEquals(boundary, mateStart - 1); // Test case 4: negative strand, first read + read = makeRead(fragmentSize, mateStart); myStart = BEFORE; read.setAlignmentStart(myStart); read.setReadNegativeStrandFlag(true); - boundary = ReadUtils.getAdaptorBoundary(read); - Assert.assertEquals(boundary.intValue(), mateStart - 1); + boundary = get.getAdaptor(read); + Assert.assertEquals(boundary, mateStart - 1); // Test case 5: mate is mapped to another chromosome (test both strands) + read = makeRead(fragmentSize, mateStart); read.setInferredInsertSize(0); read.setReadNegativeStrandFlag(true); - boundary = ReadUtils.getAdaptorBoundary(read); - Assert.assertNull(boundary); + boundary = get.getAdaptor(read); + Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY); read.setReadNegativeStrandFlag(false); - boundary = ReadUtils.getAdaptorBoundary(read); - Assert.assertNull(boundary); + boundary = get.getAdaptor(read); + Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY); read.setInferredInsertSize(10); // Test case 6: read is unmapped + read = makeRead(fragmentSize, mateStart); read.setReadUnmappedFlag(true); - boundary = ReadUtils.getAdaptorBoundary(read); - Assert.assertNull(boundary); + boundary = get.getAdaptor(read); + Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY); read.setReadUnmappedFlag(false); // Test case 7: reads don't overlap and look like this: // <--------| // |------> // first read: + read = makeRead(fragmentSize, mateStart); myStart = 980; read.setAlignmentStart(myStart); read.setInferredInsertSize(20); read.setReadNegativeStrandFlag(true); - boundary = ReadUtils.getAdaptorBoundary(read); - Assert.assertNull(boundary); + boundary = get.getAdaptor(read); + Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY); // second read: + read = makeRead(fragmentSize, mateStart); myStart = 1000; read.setAlignmentStart(myStart); + read.setInferredInsertSize(20); read.setMateAlignmentStart(980); read.setReadNegativeStrandFlag(false); - boundary = ReadUtils.getAdaptorBoundary(read); - Assert.assertNull(boundary); + boundary = get.getAdaptor(read); + Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY); + } + + @Test (enabled = true) + public void testGetBasesReverseComplement() { + int iterations = 1000; + Random random = GenomeAnalysisEngine.getRandomGenerator(); + while(iterations-- > 0) { + final int l = random.nextInt(1000); + GATKSAMRecord read = GATKSAMRecord.createRandomRead(l); + byte [] original = read.getReadBases(); + byte [] reconverted = new byte[l]; + String revComp = ReadUtils.getBasesReverseComplement(read); + for (int i=0; i priority = vcs2priority(inputs); - final VariantContext merged = VariantContextUtils.simpleMerge( + final VariantContext merged = GATKVariantContextUtils.simpleMerge( inputs, priority, - VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, - VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false); + GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, + GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false); Assert.assertEquals(merged.getAlleles(), cfg.expected); } @@ -250,10 +236,10 @@ public class VariantContextUtilsUnitTest extends BaseTest { inputs.add(new VariantContextBuilder(snpVC1).id(id).make()); } - final VariantContext merged = VariantContextUtils.simpleMerge( + final VariantContext merged = GATKVariantContextUtils.simpleMerge( inputs, null, - VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, - VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, "set", false, false); + GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, + GATKVariantContextUtils.GenotypeMergeType.UNSORTED, false, false, "set", false, false); Assert.assertEquals(merged.getID(), cfg.expected); } @@ -267,14 +253,14 @@ public class VariantContextUtilsUnitTest extends BaseTest { List inputs; VariantContext expected; String setExpected; - VariantContextUtils.FilteredRecordMergeType type; + GATKVariantContextUtils.FilteredRecordMergeType type; private MergeFilteredTest(String name, VariantContext input1, VariantContext input2, VariantContext expected, String setExpected) { - this(name, input1, input2, expected, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, setExpected); + this(name, input1, input2, expected, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, setExpected); } - private MergeFilteredTest(String name, VariantContext input1, VariantContext input2, VariantContext expected, VariantContextUtils.FilteredRecordMergeType type, String setExpected) { + private MergeFilteredTest(String name, VariantContext input1, VariantContext input2, VariantContext expected, GATKVariantContextUtils.FilteredRecordMergeType type, String setExpected) { super(MergeFilteredTest.class, name); LinkedList all = new LinkedList(Arrays.asList(input1, input2)); this.expected = expected; @@ -294,66 +280,66 @@ public class VariantContextUtilsUnitTest extends BaseTest { makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), - VariantContextUtils.MERGE_INTERSECTION); + GATKVariantContextUtils.MERGE_INTERSECTION); new MergeFilteredTest("noFilters", makeVC("1", Arrays.asList(Aref, T), "."), makeVC("2", Arrays.asList(Aref, T), "."), makeVC("3", Arrays.asList(Aref, T), "."), - VariantContextUtils.MERGE_INTERSECTION); + GATKVariantContextUtils.MERGE_INTERSECTION); new MergeFilteredTest("oneFiltered", makeVC("1", Arrays.asList(Aref, T), "."), makeVC("2", Arrays.asList(Aref, T), "FAIL"), makeVC("3", Arrays.asList(Aref, T), "."), - String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX)); + String.format("1-%s2", GATKVariantContextUtils.MERGE_FILTER_PREFIX)); new MergeFilteredTest("onePassOneFail", makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), makeVC("2", Arrays.asList(Aref, T), "FAIL"), makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), - String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX)); + String.format("1-%s2", GATKVariantContextUtils.MERGE_FILTER_PREFIX)); new MergeFilteredTest("AllFiltered", makeVC("1", Arrays.asList(Aref, T), "FAIL"), makeVC("2", Arrays.asList(Aref, T), "FAIL"), makeVC("3", Arrays.asList(Aref, T), "FAIL"), - VariantContextUtils.MERGE_FILTER_IN_ALL); + GATKVariantContextUtils.MERGE_FILTER_IN_ALL); // test ALL vs. ANY new MergeFilteredTest("FailOneUnfiltered", makeVC("1", Arrays.asList(Aref, T), "FAIL"), makeVC("2", Arrays.asList(Aref, T), "."), makeVC("3", Arrays.asList(Aref, T), "."), - VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, - String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX)); + GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, + String.format("%s1-2", GATKVariantContextUtils.MERGE_FILTER_PREFIX)); new MergeFilteredTest("OneFailAllUnfilteredArg", makeVC("1", Arrays.asList(Aref, T), "FAIL"), makeVC("2", Arrays.asList(Aref, T), "."), makeVC("3", Arrays.asList(Aref, T), "FAIL"), - VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ALL_UNFILTERED, - String.format("%s1-2", VariantContextUtils.MERGE_FILTER_PREFIX)); + GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ALL_UNFILTERED, + String.format("%s1-2", GATKVariantContextUtils.MERGE_FILTER_PREFIX)); // test excluding allele in filtered record new MergeFilteredTest("DontIncludeAlleleOfFilteredRecords", makeVC("1", Arrays.asList(Aref, T), "."), makeVC("2", Arrays.asList(Aref, T), "FAIL"), makeVC("3", Arrays.asList(Aref, T), "."), - String.format("1-%s2", VariantContextUtils.MERGE_FILTER_PREFIX)); + String.format("1-%s2", GATKVariantContextUtils.MERGE_FILTER_PREFIX)); // promotion of site from unfiltered to PASSES new MergeFilteredTest("UnfilteredPlusPassIsPass", makeVC("1", Arrays.asList(Aref, T), "."), makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), makeVC("3", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS), - VariantContextUtils.MERGE_INTERSECTION); + GATKVariantContextUtils.MERGE_INTERSECTION); new MergeFilteredTest("RefInAll", makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS), makeVC("2", Arrays.asList(Aref), VariantContext.PASSES_FILTERS), makeVC("3", Arrays.asList(Aref), VariantContext.PASSES_FILTERS), - VariantContextUtils.MERGE_REF_IN_ALL); + GATKVariantContextUtils.MERGE_REF_IN_ALL); new MergeFilteredTest("RefInOne", makeVC("1", Arrays.asList(Aref), VariantContext.PASSES_FILTERS), @@ -367,8 +353,8 @@ public class VariantContextUtilsUnitTest extends BaseTest { @Test(dataProvider = "mergeFiltered") public void testMergeFiltered(MergeFilteredTest cfg) { final List priority = vcs2priority(cfg.inputs); - final VariantContext merged = VariantContextUtils.simpleMerge( - cfg.inputs, priority, cfg.type, VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false); + final VariantContext merged = GATKVariantContextUtils.simpleMerge( + cfg.inputs, priority, cfg.type, GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false); // test alleles are equal Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles()); @@ -493,9 +479,9 @@ public class VariantContextUtilsUnitTest extends BaseTest { @Test(dataProvider = "mergeGenotypes") public void testMergeGenotypes(MergeGenotypesTest cfg) { - final VariantContext merged = VariantContextUtils.simpleMerge( - cfg.inputs, cfg.priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, - VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false); + final VariantContext merged = GATKVariantContextUtils.simpleMerge( + cfg.inputs, cfg.priority, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, + GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false); // test alleles are equal Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles()); @@ -534,23 +520,24 @@ public class VariantContextUtilsUnitTest extends BaseTest { final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)); final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2)); - final VariantContext merged = VariantContextUtils.simpleMerge( - Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, - VariantContextUtils.GenotypeMergeType.UNIQUIFY, false, false, "set", false, false); + final VariantContext merged = GATKVariantContextUtils.simpleMerge( + Arrays.asList(vc1, vc2), null, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, + GATKVariantContextUtils.GenotypeMergeType.UNIQUIFY, false, false, "set", false, false); // test genotypes Assert.assertEquals(merged.getSampleNames(), new HashSet(Arrays.asList("s1.1", "s1.2"))); } - @Test(expectedExceptions = IllegalStateException.class) - public void testMergeGenotypesRequireUnique() { - final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)); - final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2)); - - final VariantContext merged = VariantContextUtils.simpleMerge( - Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, - VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE, false, false, "set", false, false); - } +// TODO: remove after testing +// @Test(expectedExceptions = IllegalStateException.class) +// public void testMergeGenotypesRequireUnique() { +// final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)); +// final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2)); +// +// final VariantContext merged = VariantContextUtils.simpleMerge( +// Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, +// VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE, false, false, "set", false, false); +// } // -------------------------------------------------------------------------------- // @@ -566,12 +553,12 @@ public class VariantContextUtilsUnitTest extends BaseTest { VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS); VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS); - final VariantContext merged = VariantContextUtils.simpleMerge( - Arrays.asList(vc1, vc2), priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, - VariantContextUtils.GenotypeMergeType.PRIORITIZE, annotate, false, set, false, false); + final VariantContext merged = GATKVariantContextUtils.simpleMerge( + Arrays.asList(vc1, vc2), priority, GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, + GATKVariantContextUtils.GenotypeMergeType.PRIORITIZE, annotate, false, set, false, false); if ( annotate ) - Assert.assertEquals(merged.getAttribute(set), VariantContextUtils.MERGE_INTERSECTION); + Assert.assertEquals(merged.getAttribute(set), GATKVariantContextUtils.MERGE_INTERSECTION); else Assert.assertFalse(merged.hasAttribute(set)); } @@ -588,78 +575,6 @@ public class VariantContextUtilsUnitTest extends BaseTest { return priority; } - - // -------------------------------------------------------------------------------- - // - // Test repeats - // - // -------------------------------------------------------------------------------- - - private class RepeatDetectorTest extends TestDataProvider { - String ref; - boolean isTrueRepeat; - VariantContext vc; - - private RepeatDetectorTest(boolean isTrueRepeat, String ref, String refAlleleString, String ... altAlleleStrings) { - super(RepeatDetectorTest.class); - this.isTrueRepeat = isTrueRepeat; - this.ref = ref; - - List alleles = new LinkedList(); - final Allele refAllele = Allele.create(refAlleleString, true); - alleles.add(refAllele); - for ( final String altString: altAlleleStrings) { - final Allele alt = Allele.create(altString, false); - alleles.add(alt); - } - - VariantContextBuilder builder = new VariantContextBuilder("test", "chr1", 1, refAllele.length(), alleles); - this.vc = builder.make(); - } - - public String toString() { - return String.format("%s refBases=%s trueRepeat=%b vc=%s", super.toString(), ref, isTrueRepeat, vc); - } - } - - @DataProvider(name = "RepeatDetectorTest") - public Object[][] makeRepeatDetectorTest() { - new RepeatDetectorTest(true, "NAAC", "N", "NA"); - new RepeatDetectorTest(true, "NAAC", "NA", "N"); - new RepeatDetectorTest(false, "NAAC", "NAA", "N"); - new RepeatDetectorTest(false, "NAAC", "N", "NC"); - new RepeatDetectorTest(false, "AAC", "A", "C"); - - // running out of ref bases => false - new RepeatDetectorTest(false, "NAAC", "N", "NCAGTA"); - - // complex repeats - new RepeatDetectorTest(true, "NATATATC", "N", "NAT"); - new RepeatDetectorTest(true, "NATATATC", "N", "NATA"); - new RepeatDetectorTest(true, "NATATATC", "N", "NATAT"); - new RepeatDetectorTest(true, "NATATATC", "NAT", "N"); - new RepeatDetectorTest(false, "NATATATC", "NATA", "N"); - new RepeatDetectorTest(false, "NATATATC", "NATAT", "N"); - - // multi-allelic - new RepeatDetectorTest(true, "NATATATC", "N", "NAT", "NATAT"); - new RepeatDetectorTest(true, "NATATATC", "N", "NAT", "NATA"); - new RepeatDetectorTest(true, "NATATATC", "NAT", "N", "NATAT"); - new RepeatDetectorTest(true, "NATATATC", "NAT", "N", "NATA"); // two As - new RepeatDetectorTest(false, "NATATATC", "NAT", "N", "NATC"); // false - new RepeatDetectorTest(false, "NATATATC", "NAT", "N", "NCC"); // false - new RepeatDetectorTest(false, "NATATATC", "NAT", "NATAT", "NCC"); // false - - return RepeatDetectorTest.getTests(RepeatDetectorTest.class); - } - - @Test(dataProvider = "RepeatDetectorTest") - public void testRepeatDetectorTest(RepeatDetectorTest cfg) { - - // test alleles are equal - Assert.assertEquals(GATKVariantContextUtils.isTandemRepeat(cfg.vc, cfg.ref.getBytes()), cfg.isTrueRepeat); - } - // -------------------------------------------------------------------------------- // // basic allele clipping test @@ -707,6 +622,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { Assert.assertEquals(result, cfg.expectedClip); } + // -------------------------------------------------------------------------------- // // test splitting into bi-allelics @@ -817,4 +733,159 @@ public class VariantContextUtilsUnitTest extends BaseTest { } } } -} \ No newline at end of file + + + // -------------------------------------------------------------------------------- + // + // Test repeats + // + // -------------------------------------------------------------------------------- + + private class RepeatDetectorTest extends TestDataProvider { + String ref; + boolean isTrueRepeat; + VariantContext vc; + + private RepeatDetectorTest(boolean isTrueRepeat, String ref, String refAlleleString, String ... altAlleleStrings) { + super(RepeatDetectorTest.class); + this.isTrueRepeat = isTrueRepeat; + this.ref = ref; + + List alleles = new LinkedList(); + final Allele refAllele = Allele.create(refAlleleString, true); + alleles.add(refAllele); + for ( final String altString: altAlleleStrings) { + final Allele alt = Allele.create(altString, false); + alleles.add(alt); + } + + VariantContextBuilder builder = new VariantContextBuilder("test", "chr1", 1, refAllele.length(), alleles); + this.vc = builder.make(); + } + + public String toString() { + return String.format("%s refBases=%s trueRepeat=%b vc=%s", super.toString(), ref, isTrueRepeat, vc); + } + } + + @DataProvider(name = "RepeatDetectorTest") + public Object[][] makeRepeatDetectorTest() { + new RepeatDetectorTest(true, "NAAC", "N", "NA"); + new RepeatDetectorTest(true, "NAAC", "NA", "N"); + new RepeatDetectorTest(false, "NAAC", "NAA", "N"); + new RepeatDetectorTest(false, "NAAC", "N", "NC"); + new RepeatDetectorTest(false, "AAC", "A", "C"); + + // running out of ref bases => false + new RepeatDetectorTest(false, "NAAC", "N", "NCAGTA"); + + // complex repeats + new RepeatDetectorTest(true, "NATATATC", "N", "NAT"); + new RepeatDetectorTest(true, "NATATATC", "N", "NATA"); + new RepeatDetectorTest(true, "NATATATC", "N", "NATAT"); + new RepeatDetectorTest(true, "NATATATC", "NAT", "N"); + new RepeatDetectorTest(false, "NATATATC", "NATA", "N"); + new RepeatDetectorTest(false, "NATATATC", "NATAT", "N"); + + // multi-allelic + new RepeatDetectorTest(true, "NATATATC", "N", "NAT", "NATAT"); + new RepeatDetectorTest(true, "NATATATC", "N", "NAT", "NATA"); + new RepeatDetectorTest(true, "NATATATC", "NAT", "N", "NATAT"); + new RepeatDetectorTest(true, "NATATATC", "NAT", "N", "NATA"); // two As + new RepeatDetectorTest(false, "NATATATC", "NAT", "N", "NATC"); // false + new RepeatDetectorTest(false, "NATATATC", "NAT", "N", "NCC"); // false + new RepeatDetectorTest(false, "NATATATC", "NAT", "NATAT", "NCC"); // false + + return RepeatDetectorTest.getTests(RepeatDetectorTest.class); + } + + @Test(dataProvider = "RepeatDetectorTest") + public void testRepeatDetectorTest(RepeatDetectorTest cfg) { + + // test alleles are equal + Assert.assertEquals(GATKVariantContextUtils.isTandemRepeat(cfg.vc, cfg.ref.getBytes()), cfg.isTrueRepeat); + } + + @Test + public void testRepeatAllele() { + Allele nullR = Allele.create("A", true); + Allele nullA = Allele.create("A", false); + Allele atc = Allele.create("AATC", false); + Allele atcatc = Allele.create("AATCATC", false); + Allele ccccR = Allele.create("ACCCC", true); + Allele cc = Allele.create("ACC", false); + Allele cccccc = Allele.create("ACCCCCC", false); + Allele gagaR = Allele.create("AGAGA", true); + Allele gagagaga = Allele.create("AGAGAGAGA", false); + + // - / ATC [ref] from 20-22 + String delLoc = "chr1"; + int delLocStart = 20; + int delLocStop = 22; + + // - [ref] / ATC from 20-20 + String insLoc = "chr1"; + int insLocStart = 20; + int insLocStop = 20; + + Pair,byte[]> result; + byte[] refBytes = "TATCATCATCGGA".getBytes(); + + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("ATG".getBytes(), "ATGATGATGATG".getBytes(), true),4); + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("G".getBytes(), "ATGATGATGATG".getBytes(), true),0); + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("T".getBytes(), "T".getBytes(), true),1); + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("AT".getBytes(), "ATGATGATCATG".getBytes(), true),1); + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("CCC".getBytes(), "CCCCCCCC".getBytes(), true),2); + + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("ATG".getBytes()),3); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("AAA".getBytes()),1); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CACACAC".getBytes()),7); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CACACA".getBytes()),2); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CATGCATG".getBytes()),4); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("AATAATA".getBytes()),7); + + + // A*,ATC, context = ATC ATC ATC : (ATC)3 -> (ATC)4 + VariantContext vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStop, Arrays.asList(nullR,atc)).make(); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); + Assert.assertEquals(result.getFirst().toArray()[0],3); + Assert.assertEquals(result.getFirst().toArray()[1],4); + Assert.assertEquals(result.getSecond().length,3); + + // ATC*,A,ATCATC + vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+3, Arrays.asList(Allele.create("AATC", true),nullA,atcatc)).make(); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); + Assert.assertEquals(result.getFirst().toArray()[0],3); + Assert.assertEquals(result.getFirst().toArray()[1],2); + Assert.assertEquals(result.getFirst().toArray()[2],4); + Assert.assertEquals(result.getSecond().length,3); + + // simple non-tandem deletion: CCCC*, - + refBytes = "TCCCCCCCCATG".getBytes(); + vc = new VariantContextBuilder("foo", delLoc, 10, 14, Arrays.asList(ccccR,nullA)).make(); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); + Assert.assertEquals(result.getFirst().toArray()[0],8); + Assert.assertEquals(result.getFirst().toArray()[1],4); + Assert.assertEquals(result.getSecond().length,1); + + // CCCC*,CC,-,CCCCCC, context = CCC: (C)7 -> (C)5,(C)3,(C)9 + refBytes = "TCCCCCCCAGAGAGAG".getBytes(); + vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(ccccR,cc, nullA,cccccc)).make(); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); + Assert.assertEquals(result.getFirst().toArray()[0],7); + Assert.assertEquals(result.getFirst().toArray()[1],5); + Assert.assertEquals(result.getFirst().toArray()[2],3); + Assert.assertEquals(result.getFirst().toArray()[3],9); + Assert.assertEquals(result.getSecond().length,1); + + // GAGA*,-,GAGAGAGA + refBytes = "TGAGAGAGAGATTT".getBytes(); + vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(gagaR, nullA,gagagaga)).make(); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); + Assert.assertEquals(result.getFirst().toArray()[0],5); + Assert.assertEquals(result.getFirst().toArray()[1],3); + Assert.assertEquals(result.getFirst().toArray()[2],7); + Assert.assertEquals(result.getSecond().length,2); + + } +} diff --git a/public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java similarity index 98% rename from public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java rename to public/java/test/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java index 2d36f09c2..f4cef7730 100644 --- a/public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java @@ -23,10 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.variant.vcf; +package org.broadinstitute.sting.utils.variant; import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.annotations.Test; import java.io.File; diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java b/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java similarity index 97% rename from public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java rename to public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java index 34abe372f..51a47d86d 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java +++ b/public/java/test/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java @@ -23,13 +23,13 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.variant.variantcontext; +package org.broadinstitute.sting.utils.variant; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.variant.variantcontext.*; import org.broadinstitute.variant.vcf.VCFCodec; import java.util.ArrayList; @@ -73,8 +73,6 @@ public class VariantContextBenchmark extends SimpleBenchmark { MERGE } - private GenomeLocParser b37GenomeLocParser; - @Override protected void setUp() { // TODO -- update for new tribble interface // try { @@ -233,9 +231,9 @@ public class VariantContextBenchmark extends SimpleBenchmark { toMerge.add(new VariantContextBuilder(vc).genotypes(gc).make()); } - VariantContextUtils.simpleMerge(toMerge, null, - VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, - VariantContextUtils.GenotypeMergeType.UNSORTED, + GATKVariantContextUtils.simpleMerge(toMerge, null, + GATKVariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, + GATKVariantContextUtils.GenotypeMergeType.UNSORTED, true, false, "set", false, true); } }; diff --git a/public/java/test/org/broadinstitute/variant/VariantBaseTest.java b/public/java/test/org/broadinstitute/variant/VariantBaseTest.java new file mode 100644 index 000000000..6cec4d40b --- /dev/null +++ b/public/java/test/org/broadinstitute/variant/VariantBaseTest.java @@ -0,0 +1,166 @@ +/* +* Copyright (c) 2012 The Broad Institute +* +* 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.variant; + +import org.testng.Assert; + +import java.io.File; +import java.io.IOException; +import java.util.*; + +/** + * Base class for test classes within org.broadinstitute.variant + */ +public class VariantBaseTest { + + public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta"; + public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta"; + + // TODO: change this to an appropriate value once the move to the Picard repo takes place + public static final String variantTestDataRoot = new File("private/testdata/").getAbsolutePath() + "/"; + + /** + * Simple generic utility class to creating TestNG data providers: + * + * 1: inherit this class, as in + * + * private class SummarizeDifferenceTest extends TestDataProvider { + * public SummarizeDifferenceTest() { + * super(SummarizeDifferenceTest.class); + * } + * ... + * } + * + * Provide a reference to your class to the TestDataProvider constructor. + * + * 2: Create instances of your subclass. Return from it the call to getTests, providing + * the class type of your test + * + * @DataProvider(name = "summaries" + * public Object[][] createSummaries() { + * new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2"); + * new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1"); + * return SummarizeDifferenceTest.getTests(SummarizeDifferenceTest.class); + * } + * + * This class magically tracks created objects of this + */ + public static class TestDataProvider { + private static final Map> tests = new HashMap>(); + protected String name; + + /** + * Create a new TestDataProvider instance bound to the class variable C + * @param c + */ + public TestDataProvider(Class c, String name) { + if ( ! tests.containsKey(c) ) + tests.put(c, new ArrayList()); + tests.get(c).add(this); + this.name = name; + } + + public TestDataProvider(Class c) { + this(c, ""); + } + + public void setName(final String name) { + this.name = name; + } + + /** + * Return all of the data providers in the form expected by TestNG of type class C + * @param c + * @return + */ + public static Object[][] getTests(Class c) { + List params2 = new ArrayList(); + for ( Object x : tests.get(c) ) params2.add(new Object[]{x}); + return params2.toArray(new Object[][]{}); + } + + @Override + public String toString() { + return "TestDataProvider("+name+")"; + } + } + + /** + * Creates a temp file that will be deleted on exit after tests are complete. + * @param name Prefix of the file. + * @param extension Extension to concat to the end of the file. + * @return A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits. + */ + public static File createTempFile(String name, String extension) { + try { + File file = File.createTempFile(name, extension); + file.deleteOnExit(); + return file; + } catch (IOException ex) { + throw new RuntimeException("Cannot create temp file: " + ex.getMessage(), ex); + } + } + + private static final double DEFAULT_FLOAT_TOLERANCE = 1e-1; + + public static final void assertEqualsDoubleSmart(final Object actual, final Double expected) { + Assert.assertTrue(actual instanceof Double, "Not a double"); + assertEqualsDoubleSmart((double)(Double)actual, (double)expected); + } + + public static final void assertEqualsDoubleSmart(final Object actual, final Double expected, final double tolerance) { + Assert.assertTrue(actual instanceof Double, "Not a double"); + assertEqualsDoubleSmart((double)(Double)actual, (double)expected, tolerance); + } + + public static final void assertEqualsDoubleSmart(final double actual, final double expected) { + assertEqualsDoubleSmart(actual, expected, DEFAULT_FLOAT_TOLERANCE); + } + + public static final void assertEqualsSet(final Set actual, final Set expected, final String info) { + final Set actualSet = new HashSet(actual); + final Set expectedSet = new HashSet(expected); + Assert.assertTrue(actualSet.equals(expectedSet), info); // note this is necessary due to testng bug for set comps + } + + public static void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance) { + assertEqualsDoubleSmart(actual, expected, tolerance, null); + } + + public static void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance, final String message) { + if ( Double.isNaN(expected) ) // NaN == NaN => false unfortunately + Assert.assertTrue(Double.isNaN(actual), "expected is nan, actual is not"); + else if ( Double.isInfinite(expected) ) // NaN == NaN => false unfortunately + Assert.assertTrue(Double.isInfinite(actual), "expected is infinite, actual is not"); + else { + final double delta = Math.abs(actual - expected); + final double ratio = Math.abs(actual / expected - 1.0); + Assert.assertTrue(delta < tolerance || ratio < tolerance, "expected = " + expected + " actual = " + actual + + " not within tolerance " + tolerance + + (message == null ? "" : "message: " + message)); + } + } +} diff --git a/public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java b/public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java index 35c4eacfb..8f3a216b7 100644 --- a/public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java @@ -25,12 +25,9 @@ package org.broadinstitute.variant.bcf2; - // the imports for unit testing. - - import org.apache.commons.lang.ArrayUtils; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.variant.VariantBaseTest; import org.broadinstitute.variant.variantcontext.writer.BCF2Encoder; import org.testng.Assert; import org.testng.annotations.BeforeSuite; @@ -47,7 +44,7 @@ import java.util.Collections; import java.util.List; -public class BCF2EncoderDecoderUnitTest extends BaseTest { +public class BCF2EncoderDecoderUnitTest extends VariantBaseTest { private final double FLOAT_TOLERANCE = 1e-6; final List primitives = new ArrayList(); final List basicTypes = new ArrayList(); @@ -561,7 +558,7 @@ public class BCF2EncoderDecoderUnitTest extends BaseTest { final double valueFloat = (Double)tv.value; final double decodedFloat = (Double)decoded; - BaseTest.assertEqualsDoubleSmart(decodedFloat, valueFloat, FLOAT_TOLERANCE); + VariantBaseTest.assertEqualsDoubleSmart(decodedFloat, valueFloat, FLOAT_TOLERANCE); } else Assert.assertEquals(decoded, tv.value); } diff --git a/public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java b/public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java index 6d854f080..5d01a458b 100644 --- a/public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.variant.bcf2; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.variant.VariantBaseTest; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.vcf.*; import java.util.*; @@ -37,7 +37,7 @@ import org.testng.annotations.Test; /** * Tests for BCF2Utils */ -public final class BCF2UtilsUnitTest extends BaseTest { +public final class BCF2UtilsUnitTest extends VariantBaseTest { @DataProvider(name = "CollapseExpandTest") public Object[][] makeCollapseExpandTest() { List tests = new ArrayList(); @@ -87,7 +87,7 @@ public final class BCF2UtilsUnitTest extends BaseTest { final List empty = Collections.emptyList(); final List> permutations = extrasToTake == 0 ? Collections.singletonList(empty) - : Utils.makePermutations(extraLines, extrasToTake, false); + : GeneralUtils.makePermutations(extraLines, extrasToTake, false); for ( final List permutation : permutations ) { for ( int i = -1; i < inputLines.size(); i++ ) { final List allLines = new ArrayList(inputLines); @@ -113,7 +113,7 @@ public final class BCF2UtilsUnitTest extends BaseTest { final List> permutations = testSamples.isEmpty() ? Collections.singletonList(testSamples) - : Utils.makePermutations(testSamples, testSamples.size(), false); + : GeneralUtils.makePermutations(testSamples, testSamples.size(), false); for ( final List testSamplesPermutation : permutations ) { final VCFHeader testHeaderWithSamples = new VCFHeader(inputHeader.getMetaDataInInputOrder(), testSamplesPermutation); final boolean expectedConsistent = testSamples.equals(inSamples); diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java index f1dff7ab1..7fa652f2f 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java @@ -28,6 +28,7 @@ package org.broadinstitute.variant.variantcontext; // the imports for unit testing. +import org.broadinstitute.variant.VariantBaseTest; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.Test; @@ -44,7 +45,7 @@ import org.testng.annotations.Test; /** * Basic unit test for RecalData */ -public class AlleleUnitTest { +public class AlleleUnitTest extends VariantBaseTest { Allele ARef, A, T, ATIns, ATCIns, NoCall; @BeforeSuite diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java index 49720d1f6..562130101 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java @@ -30,9 +30,8 @@ package org.broadinstitute.variant.variantcontext; import org.broad.tribble.TribbleException; -import org.broadinstitute.variant.utils.BaseUtils; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.variant.VariantBaseTest; +import org.broadinstitute.variant.utils.GeneralUtils; import org.testng.Assert; import org.testng.annotations.Test; @@ -44,7 +43,7 @@ import java.util.List; /** * Basic unit test for Genotype likelihoods objects */ -public class GenotypeLikelihoodsUnitTest { +public class GenotypeLikelihoodsUnitTest extends VariantBaseTest { double [] v = new double[]{-10.5, -1.25, -5.11}; final static String vGLString = "-10.50,-1.25,-5.11"; final static String vPLString = "93,0,39"; @@ -88,7 +87,7 @@ public class GenotypeLikelihoodsUnitTest { //Linear scale glMap = gl.getAsMap(true); - double [] vl = MathUtils.normalizeFromLog10(v); + double [] vl = GeneralUtils.normalizeFromLog10(v); Assert.assertEquals(vl[GenotypeType.HOM_REF.ordinal()-1],glMap.get(GenotypeType.HOM_REF)); Assert.assertEquals(vl[GenotypeType.HET.ordinal()-1],glMap.get(GenotypeType.HET)); Assert.assertEquals(vl[GenotypeType.HOM_VAR.ordinal()-1],glMap.get(GenotypeType.HOM_VAR)); @@ -118,7 +117,7 @@ public class GenotypeLikelihoodsUnitTest { //GQ for the best guess genotype Assert.assertEquals(gl.getLog10GQ(GenotypeType.HET),-3.9); - double[] test = MathUtils.normalizeFromLog10(gl.getAsVector()); + double[] test = GeneralUtils.normalizeFromLog10(gl.getAsVector()); //GQ for the other genotypes Assert.assertEquals(gl.getLog10GQ(GenotypeType.HOM_REF), Math.log10(1.0 - test[GenotypeType.HOM_REF.ordinal()-1])); @@ -154,9 +153,9 @@ public class GenotypeLikelihoodsUnitTest { public void testGetQualFromLikelihoodsMultiAllelic() { GenotypeLikelihoods gl = GenotypeLikelihoods.fromLog10Likelihoods(triAllelic); - Allele ref = Allele.create(BaseUtils.A,true); - Allele alt1 = Allele.create(BaseUtils.C); - Allele alt2 = Allele.create(BaseUtils.T); + Allele ref = Allele.create((byte)'A',true); + Allele alt1 = Allele.create((byte)'C'); + Allele alt2 = Allele.create((byte)'T'); List allAlleles = Arrays.asList(ref,alt1,alt2); List gtAlleles = Arrays.asList(alt1,alt2); GenotypeBuilder gtBuilder = new GenotypeBuilder(); diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java index 2148b555e..8d0d2af90 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java @@ -29,13 +29,13 @@ package org.broadinstitute.variant.variantcontext; // the imports for unit testing. -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.variant.VariantBaseTest; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.Test; -public class GenotypeUnitTest extends BaseTest { +public class GenotypeUnitTest extends VariantBaseTest { Allele A, Aref, T; @BeforeSuite diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java index a7e7fe357..1618ad1f2 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java @@ -30,8 +30,8 @@ package org.broadinstitute.variant.variantcontext; import org.broad.tribble.util.ParsingUtils; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.variant.VariantBaseTest; +import org.broadinstitute.variant.utils.GeneralUtils; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; @@ -40,7 +40,7 @@ import org.testng.annotations.Test; import java.util.*; -public class GenotypesContextUnitTest extends BaseTest { +public class GenotypesContextUnitTest extends VariantBaseTest { Allele Aref, C, T; Genotype AA, AT, TT, AC, CT, CC, MISSING; List allGenotypes; @@ -128,7 +128,7 @@ public class GenotypesContextUnitTest extends BaseTest { // sorted new GenotypesContextProvider(maker, samples); // unsorted - new GenotypesContextProvider(maker, Utils.reverse(samples)); + new GenotypesContextProvider(maker, GeneralUtils.reverse(samples)); } } diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java index 0a2dc384e..4c948e8e2 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java @@ -25,15 +25,13 @@ package org.broadinstitute.variant.variantcontext; -import org.apache.log4j.Logger; import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodecHeader; import org.broad.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.Utils; +import org.broadinstitute.variant.VariantBaseTest; import org.broadinstitute.variant.bcf2.BCF2Codec; +import org.broadinstitute.variant.utils.GeneralUtils; import org.broadinstitute.variant.vcf.*; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.variant.variantcontext.writer.Options; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.testng.Assert; @@ -50,8 +48,6 @@ import java.util.*; * @since Date created */ public class VariantContextTestProvider { - final protected static Logger logger = Logger.getLogger(VariantContextTestProvider.class); - final private static boolean ENABLE_GENOTYPE_TESTS = true; final private static boolean ENABLE_A_AND_G_TESTS = true; final private static boolean ENABLE_VARARRAY_TESTS = true; @@ -68,12 +64,30 @@ public class VariantContextTestProvider { private final static List testSourceVCFs = new ArrayList(); static { - testSourceVCFs.add(new File(BaseTest.privateTestDir + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf")); - testSourceVCFs.add(new File(BaseTest.privateTestDir + "ex2.vcf")); - testSourceVCFs.add(new File(BaseTest.privateTestDir + "dbsnp_135.b37.1000.vcf")); + testSourceVCFs.add(new File(VariantBaseTest.variantTestDataRoot + "ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf")); + testSourceVCFs.add(new File(VariantBaseTest.variantTestDataRoot + "ex2.vcf")); + testSourceVCFs.add(new File(VariantBaseTest.variantTestDataRoot + "dbsnp_135.b37.1000.vcf")); if ( ENABLE_SYMBOLIC_ALLELE_TESTS ) { - testSourceVCFs.add(new File(BaseTest.privateTestDir + "diagnosis_targets_testfile.vcf")); - testSourceVCFs.add(new File(BaseTest.privateTestDir + "VQSR.mixedTest.recal")); + testSourceVCFs.add(new File(VariantBaseTest.variantTestDataRoot + "diagnosis_targets_testfile.vcf")); + testSourceVCFs.add(new File(VariantBaseTest.variantTestDataRoot + "VQSR.mixedTest.recal")); + } + } + + public static class VariantContextContainer { + private VCFHeader header; + private Iterable vcs; + + public VariantContextContainer( VCFHeader header, Iterable vcs ) { + this.header = header; + this.vcs = vcs; + } + + public VCFHeader getHeader() { + return header; + } + + public Iterable getVCs() { + return vcs; } } @@ -153,17 +167,15 @@ public class VariantContextTestProvider { if ( ENABLE_SOURCE_VCF_TESTS ) { for ( final File file : testSourceVCFs ) { VCFCodec codec = new VCFCodec(); - Pair> x = readAllVCs( file, codec ); + VariantContextContainer x = readAllVCs( file, codec ); List fullyDecoded = new ArrayList(); - logger.warn("Reading records from " + file); - for ( final VariantContext raw : x.getSecond() ) { + for ( final VariantContext raw : x.getVCs() ) { if ( raw != null ) - fullyDecoded.add(raw.fullyDecode(x.getFirst(), false)); + fullyDecoded.add(raw.fullyDecode(x.getHeader(), false)); } - logger.warn("Done reading " + file); - TEST_DATAs.add(new VariantContextTestData(x.getFirst(), fullyDecoded)); + TEST_DATAs.add(new VariantContextTestData(x.getHeader(), fullyDecoded)); } } } @@ -621,8 +633,8 @@ public class VariantContextTestProvider { writeVCsToFile(writer, header, data.vcs); // ensure writing of expected == actual - final Pair> p = readAllVCs(tmpFile, tester.makeCodec()); - final Iterable actual = p.getSecond(); + final VariantContextContainer p = readAllVCs(tmpFile, tester.makeCodec()); + final Iterable actual = p.getVCs(); int i = 0; for ( final VariantContext readVC : actual ) { @@ -660,14 +672,14 @@ public class VariantContextTestProvider { writeVCsToFile(writer, header, vcs); // ensure writing of expected == actual - final Pair> p = readAllVCs(tmpFile, tester.makeCodec()); - final Iterable actual = p.getSecond(); + final VariantContextContainer p = readAllVCs(tmpFile, tester.makeCodec()); + final Iterable actual = p.getVCs(); assertEquals(actual, expected); if ( recurse ) { // if we are doing a recursive test, grab a fresh iterator over the written values - final Iterable read = readAllVCs(tmpFile, tester.makeCodec()).getSecond(); - testReaderWriter(tester, p.getFirst(), expected, read, false); + final Iterable read = readAllVCs(tmpFile, tester.makeCodec()).getVCs(); + testReaderWriter(tester, p.getHeader(), expected, read, false); } } @@ -688,7 +700,7 @@ public class VariantContextTestProvider { * @return * @throws IOException */ - private final static Pair> readAllVCs( final File source, final FeatureCodec codec ) throws IOException { + public final static VariantContextContainer readAllVCs( final File source, final FeatureCodec codec ) throws IOException { // read in the features PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source)); FeatureCodecHeader header = codec.readHeader(pbs); @@ -698,10 +710,10 @@ public class VariantContextTestProvider { pbs.skip(header.getHeaderEnd()); final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue(); - return new Pair>(vcfHeader, new VCIterable(pbs, codec, vcfHeader)); + return new VariantContextContainer(vcfHeader, new VCIterable(pbs, codec, vcfHeader)); } - private static class VCIterable implements Iterable, Iterator { + public static class VCIterable implements Iterable, Iterator { final PositionalBufferedStream pbs; final FeatureCodec codec; final VCFHeader header; @@ -743,10 +755,10 @@ public class VariantContextTestProvider { } public static void assertVCFandBCFFilesAreTheSame(final File vcfFile, final File bcfFile) throws IOException { - final Pair> vcfData = readAllVCs(vcfFile, new VCFCodec()); - final Pair> bcfData = readAllVCs(bcfFile, new BCF2Codec()); - assertEquals(bcfData.getFirst(), vcfData.getFirst()); - assertEquals(bcfData.getSecond(), vcfData.getSecond()); + final VariantContextContainer vcfData = readAllVCs(vcfFile, new VCFCodec()); + final VariantContextContainer bcfData = readAllVCs(bcfFile, new BCF2Codec()); + assertEquals(bcfData.getHeader(), vcfData.getHeader()); + assertEquals(bcfData.getVCs(), vcfData.getVCs()); } public static void assertEquals(final Iterable actual, final Iterable expected) { @@ -788,12 +800,12 @@ public class VariantContextTestProvider { assertAttributesEquals(actual.getAttributes(), expected.getAttributes()); Assert.assertEquals(actual.filtersWereApplied(), expected.filtersWereApplied(), "filtersWereApplied"); Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "isFiltered"); - BaseTest.assertEqualsSet(actual.getFilters(), expected.getFilters(), "filters"); - BaseTest.assertEqualsDoubleSmart(actual.getPhredScaledQual(), expected.getPhredScaledQual()); + VariantBaseTest.assertEqualsSet(actual.getFilters(), expected.getFilters(), "filters"); + VariantBaseTest.assertEqualsDoubleSmart(actual.getPhredScaledQual(), expected.getPhredScaledQual()); Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes(), "hasGenotypes"); if ( expected.hasGenotypes() ) { - BaseTest.assertEqualsSet(actual.getSampleNames(), expected.getSampleNames(), "sample names set"); + VariantBaseTest.assertEqualsSet(actual.getSampleNames(), expected.getSampleNames(), "sample names set"); Assert.assertEquals(actual.getSampleNamesOrderedByName(), expected.getSampleNamesOrderedByName(), "sample names"); final Set samples = expected.getSampleNames(); for ( final String sample : samples ) { @@ -879,7 +891,7 @@ public class VariantContextTestProvider { private static void assertAttributeEquals(final String key, final Object actual, final Object expected) { if ( expected instanceof Double ) { // must be very tolerant because doubles are being rounded to 2 sig figs - BaseTest.assertEqualsDoubleSmart(actual, (Double)expected, 1e-2); + VariantBaseTest.assertEqualsDoubleSmart(actual, (Double)expected, 1e-2); } else Assert.assertEquals(actual, expected, "Attribute " + key); } @@ -935,7 +947,7 @@ public class VariantContextTestProvider { } private static List> makeAllGenotypes(final List alleles, final int highestPloidy) { - return Utils.makePermutations(alleles, highestPloidy, true); + return GeneralUtils.makePermutations(alleles, highestPloidy, true); } public static void assertEquals(final VCFHeader actual, final VCFHeader expected) { diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java index d34e6396d..103c8ab3b 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java @@ -28,10 +28,7 @@ package org.broadinstitute.variant.variantcontext; // the imports for unit testing. - -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.VariantBaseTest; import org.testng.annotations.BeforeSuite; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; @@ -41,7 +38,7 @@ import org.testng.Assert; import java.util.*; -public class VariantContextUnitTest extends BaseTest { +public class VariantContextUnitTest extends VariantBaseTest { Allele A, Aref, C, T, Tref; Allele del, delRef, ATC, ATCref; @@ -485,78 +482,6 @@ public class VariantContextUnitTest extends BaseTest { Assert.assertNotNull(vc.getFiltersMaybeNull()); } - @Test - public void testRepeatAllele() { - Allele nullR = Allele.create("A", true); - Allele nullA = Allele.create("A", false); - Allele atc = Allele.create("AATC", false); - Allele atcatc = Allele.create("AATCATC", false); - Allele ccccR = Allele.create("ACCCC", true); - Allele cc = Allele.create("ACC", false); - Allele cccccc = Allele.create("ACCCCCC", false); - Allele gagaR = Allele.create("AGAGA", true); - Allele gagagaga = Allele.create("AGAGAGAGA", false); - - Pair,byte[]> result; - byte[] refBytes = "TATCATCATCGGA".getBytes(); - - Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("ATG".getBytes(), "ATGATGATGATG".getBytes()),4); - Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("G".getBytes(), "ATGATGATGATG".getBytes()),0); - Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("T".getBytes(), "T".getBytes()),1); - Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("AT".getBytes(), "ATGATGATCATG".getBytes()),1); - Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("CCC".getBytes(), "CCCCCCCC".getBytes()),2); - - Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("ATG".getBytes()),3); - Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("AAA".getBytes()),1); - Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CACACAC".getBytes()),7); - Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CACACA".getBytes()),2); - Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CATGCATG".getBytes()),4); - Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("AATAATA".getBytes()),7); - - - // A*,ATC, context = ATC ATC ATC : (ATC)3 -> (ATC)4 - VariantContext vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStop, Arrays.asList(nullR,atc)).make(); - result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); - Assert.assertEquals(result.getFirst().toArray()[0],3); - Assert.assertEquals(result.getFirst().toArray()[1],4); - Assert.assertEquals(result.getSecond().length,3); - - // ATC*,A,ATCATC - vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+3, Arrays.asList(Allele.create("AATC", true),nullA,atcatc)).make(); - result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); - Assert.assertEquals(result.getFirst().toArray()[0],3); - Assert.assertEquals(result.getFirst().toArray()[1],2); - Assert.assertEquals(result.getFirst().toArray()[2],4); - Assert.assertEquals(result.getSecond().length,3); - - // simple non-tandem deletion: CCCC*, - - refBytes = "TCCCCCCCCATG".getBytes(); - vc = new VariantContextBuilder("foo", delLoc, 10, 14, Arrays.asList(ccccR,nullA)).make(); - result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); - Assert.assertEquals(result.getFirst().toArray()[0],8); - Assert.assertEquals(result.getFirst().toArray()[1],4); - Assert.assertEquals(result.getSecond().length,1); - - // CCCC*,CC,-,CCCCCC, context = CCC: (C)7 -> (C)5,(C)3,(C)9 - refBytes = "TCCCCCCCAGAGAGAG".getBytes(); - vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(ccccR,cc, nullA,cccccc)).make(); - result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); - Assert.assertEquals(result.getFirst().toArray()[0],7); - Assert.assertEquals(result.getFirst().toArray()[1],5); - Assert.assertEquals(result.getFirst().toArray()[2],3); - Assert.assertEquals(result.getFirst().toArray()[3],9); - Assert.assertEquals(result.getSecond().length,1); - - // GAGA*,-,GAGAGAGA - refBytes = "TGAGAGAGAGATTT".getBytes(); - vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(gagaR, nullA,gagagaga)).make(); - result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); - Assert.assertEquals(result.getFirst().toArray()[0],5); - Assert.assertEquals(result.getFirst().toArray()[1],3); - Assert.assertEquals(result.getFirst().toArray()[2],7); - Assert.assertEquals(result.getSecond().length,2); - - } @Test public void testGetGenotypeCounts() { List alleles = Arrays.asList(Aref, T); diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java index f2213e088..8d2569771 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java @@ -25,13 +25,8 @@ package org.broadinstitute.variant.variantcontext; -import net.sf.samtools.SAMFileHeader; +import org.broadinstitute.variant.VariantBaseTest; import org.testng.Assert; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; - import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; @@ -49,8 +44,7 @@ import java.util.Map; * * Test out parts of the VariantJEXLContext */ -public class VariantJEXLContextUnitTest extends BaseTest { - +public class VariantJEXLContextUnitTest extends VariantBaseTest { private static String expression = "QUAL > 500.0"; private static VariantContextUtils.JexlVCMatchExp exp; @@ -60,27 +54,15 @@ public class VariantJEXLContextUnitTest extends BaseTest { Allele ATC, ATCref; // A [ref] / T at 10 - GenomeLoc snpLoc; // - / ATC [ref] from 20-23 - private static int startingChr = 1; - private static int endingChr = 2; - private static int readCount = 100; - private static int DEFAULT_READ_LENGTH = ArtificialSAMUtils.DEFAULT_READ_LENGTH; - static SAMFileHeader header; - - private static GenomeLocParser genomeLocParser; - @BeforeClass public void beforeClass() { - header = ArtificialSAMUtils.createArtificialSamHeader(( endingChr - startingChr ) + 1, startingChr, readCount + DEFAULT_READ_LENGTH); - genomeLocParser = new GenomeLocParser(header.getSequenceDictionary()); try { exp = new VariantContextUtils.JexlVCMatchExp("name", VariantContextUtils.engine.createExpression(expression)); } catch (Exception e) { Assert.fail("Unable to create expression" + e.getMessage()); } - snpLoc = genomeLocParser.createGenomeLoc("chr1", 10, 10, true); } @BeforeMethod @@ -142,9 +124,7 @@ public class VariantJEXLContextUnitTest extends BaseTest { private JEXLMap getVarContext() { List alleles = Arrays.asList(Aref, T); - VariantContext vc = new VariantContextBuilder("test", snpLoc.getContig(), snpLoc.getStart(), snpLoc.getStop(), alleles).make(); + VariantContext vc = new VariantContextBuilder("test", "chr1", 10, 10, alleles).make(); return new JEXLMap(Arrays.asList(exp),vc); } - - } diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java index 79258e844..bbfac11cb 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java @@ -29,16 +29,11 @@ import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broad.tribble.AbstractFeatureReader; import org.broad.tribble.FeatureReader; import org.broad.tribble.Tribble; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.variant.VariantBaseTest; import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.variant.vcf.VCFHeaderLine; import org.broadinstitute.variant.vcf.VCFHeaderVersion; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeClass; @@ -58,22 +53,20 @@ import java.util.*; *

* This class tests out the ability of the VCF writer to correctly write VCF files */ -public class VCFWriterUnitTest extends BaseTest { +public class VCFWriterUnitTest extends VariantBaseTest { private Set metaData = new HashSet(); private Set additionalColumns = new HashSet(); private File fakeVCFFile = new File("FAKEVCFFILEFORTESTING.vcf"); - private GenomeLocParser genomeLocParser; private IndexedFastaSequenceFile seq; @BeforeClass public void beforeTests() { - File referenceFile = new File(hg18Reference); + File referenceFile = new File(hg19Reference); try { - seq = new CachingIndexedFastaSequenceFile(referenceFile); - genomeLocParser = new GenomeLocParser(seq); + seq = new IndexedFastaSequenceFile(referenceFile); } catch(FileNotFoundException ex) { - throw new UserException.CouldNotReadInputFile(referenceFile,ex); + throw new RuntimeException(referenceFile.getAbsolutePath(), ex); } } @@ -108,7 +101,7 @@ public class VCFWriterUnitTest extends BaseTest { fakeVCFFile.delete(); } catch (IOException e ) { - throw new ReviewedStingException(e.getMessage()); + throw new RuntimeException(e.getMessage()); } } @@ -133,8 +126,6 @@ public class VCFWriterUnitTest extends BaseTest { * @return a VCFRecord */ private VariantContext createVC(VCFHeader header) { - - GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1",1); List alleles = new ArrayList(); Set filters = null; Map attributes = new HashMap(); @@ -148,7 +139,7 @@ public class VCFWriterUnitTest extends BaseTest { Genotype gt = new GenotypeBuilder(name,alleles.subList(1,2)).GQ(0).attribute("BB", "1").phased(true).make(); genotypes.add(gt); } - return new VariantContextBuilder("RANDOM", loc.getContig(), loc.getStart(), loc.getStop(), alleles) + return new VariantContextBuilder("RANDOM", "chr1", 1, 1, alleles) .genotypes(genotypes).attributes(attributes).make(); } diff --git a/public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java index 023f48928..9e6541bfa 100644 --- a/public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java @@ -32,11 +32,10 @@ package org.broadinstitute.variant.variantcontext.writer; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.SAMSequenceDictionary; import org.broad.tribble.FeatureCodec; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.variant.VariantBaseTest; import org.broadinstitute.variant.bcf2.BCF2Codec; import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.variant.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContextTestProvider; import org.testng.annotations.BeforeSuite; @@ -50,15 +49,13 @@ import java.util.EnumSet; import java.util.List; -public class VariantContextWritersUnitTest extends BaseTest { +public class VariantContextWritersUnitTest extends VariantBaseTest { private SAMSequenceDictionary dictionary; @BeforeSuite public void before() throws IOException { final File source = new File(b37KGReference); - //final File source = new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta"); - IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(source); - //IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference)); + IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(source); dictionary = seq.getSequenceDictionary(); VariantContextTestProvider.initializeTests(); } diff --git a/public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java b/public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java index b0b07d148..6292baae3 100644 --- a/public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java @@ -25,15 +25,14 @@ package org.broadinstitute.variant.vcf; +import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.SAMSequenceDictionary; import org.broad.tribble.AbstractFeatureReader; import org.broad.tribble.CloseableTribbleIterator; import org.broad.tribble.Tribble; import org.broad.tribble.index.Index; import org.broad.tribble.index.IndexFactory; -import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.variant.VariantBaseTest; import org.broadinstitute.variant.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.writer.Options; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; @@ -50,10 +49,10 @@ import java.util.EnumSet; /** * tests out the various functions in the index factory class */ -public class IndexFactoryUnitTest extends BaseTest { +public class IndexFactoryUnitTest extends VariantBaseTest { - File inputFile = new File(privateTestDir + "HiSeq.10000.vcf"); - File outputFile = new File(privateTestDir + "onTheFlyOutputTest.vcf"); + File inputFile = new File(variantTestDataRoot + "HiSeq.10000.vcf"); + File outputFile = new File(variantTestDataRoot + "onTheFlyOutputTest.vcf"); File outputFileIndex = Tribble.indexFile(outputFile); private SAMSequenceDictionary dict; @@ -61,10 +60,10 @@ public class IndexFactoryUnitTest extends BaseTest { @BeforeTest public void setup() { try { - dict = new CachingIndexedFastaSequenceFile(new File(b37KGReference)).getSequenceDictionary(); + dict = new IndexedFastaSequenceFile(new File(b37KGReference)).getSequenceDictionary(); } catch(FileNotFoundException ex) { - throw new UserException.CouldNotReadInputFile(b37KGReference,ex); + throw new RuntimeException(b37KGReference,ex); } } diff --git a/public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java b/public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java index d7d3c8d6c..7d6b11953 100644 --- a/public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java @@ -27,9 +27,8 @@ package org.broadinstitute.variant.vcf; import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.VariantBaseTest; import org.testng.Assert; -import org.broadinstitute.sting.BaseTest; import org.testng.annotations.Test; @@ -45,7 +44,7 @@ import java.security.NoSuchAlgorithmException; * Time: 3:32:08 PM * To change this template use File | Settings | File Templates. */ -public class VCFHeaderUnitTest extends BaseTest { +public class VCFHeaderUnitTest extends VariantBaseTest { private VCFHeader createHeader(String headerStr) { VCFCodec codec = new VCFCodec(); @@ -80,13 +79,13 @@ public class VCFHeaderUnitTest extends BaseTest { try { digest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { - throw new ReviewedStingException("Unable to find MD5 digest"); + throw new RuntimeException("Unable to find MD5 digest"); } InputStream is; try { is = new FileInputStream(file); } catch (FileNotFoundException e) { - throw new ReviewedStingException("Unable to open file " + file); + throw new RuntimeException("Unable to open file " + file); } byte[] buffer = new byte[8192]; int read; @@ -100,14 +99,14 @@ public class VCFHeaderUnitTest extends BaseTest { } catch (IOException e) { - throw new ReviewedStingException("Unable to process file for MD5", e); + throw new RuntimeException("Unable to process file for MD5", e); } finally { try { is.close(); } catch (IOException e) { - throw new ReviewedStingException("Unable to close input stream for MD5 calculation", e); + throw new RuntimeException("Unable to close input stream for MD5 calculation", e); } } } diff --git a/public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java b/public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java index b77191051..02090c9cd 100644 --- a/public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.variant.vcf; -import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.variant.VariantBaseTest; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import org.testng.Assert; @@ -41,7 +41,7 @@ import java.util.List; * Time: 3:32:08 PM * To change this template use File | Settings | File Templates. */ -public class VCFStandardHeaderLinesUnitTest extends BaseTest { +public class VCFStandardHeaderLinesUnitTest extends VariantBaseTest { @DataProvider(name = "getStandardLines") public Object[][] makeGetStandardLines() { List tests = new ArrayList(); diff --git a/public/packages/GenomeAnalysisTKLite.xml b/public/packages/GenomeAnalysisTKLite.xml deleted file mode 100644 index b2f73434c..000000000 --- a/public/packages/GenomeAnalysisTKLite.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - - - - - - - - - - - - - - - diff --git a/public/packages/PicardPrivate.xml b/public/packages/PicardPrivate.xml index a800294d6..d898a5d07 100644 --- a/public/packages/PicardPrivate.xml +++ b/public/packages/PicardPrivate.xml @@ -2,26 +2,9 @@ - - - - - - - - - - - - - - - - - diff --git a/public/packages/QueueLite.xml b/public/packages/QueueLite.xml deleted file mode 100644 index 0ead68fb0..000000000 --- a/public/packages/QueueLite.xml +++ /dev/null @@ -1,40 +0,0 @@ - - - - - - - - - - - - - - - - - - diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala index 848554dfc..30fd4c81f 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala @@ -30,11 +30,13 @@ import org.broadinstitute.sting.queue.function.scattergather.GatherFunction /** - * Created with IntelliJ IDEA. - * User: ami - * Date: 12/11/12 - * Time: 2:04 PM - * To change this template use File | Settings | File Templates. + * + * Currently this is the default gather for VCFs. + * One can set a specific gatherer to use by adding @Gather before any output argument. + * For example (used to be part of UG): + * @Gather(className = "org.broadinstitute.sting.queue.extensions.gatk.CatVariantsGatherer") + * @Output(doc="File to which variants should be written",required=true) + * protected VariantContextWriter writer = null; */ class CatVariantsGatherer extends CatVariants with GatherFunction with RetryMemoryLimit{ this.assumeSorted = true @@ -45,6 +47,7 @@ class CatVariantsGatherer extends CatVariants with GatherFunction with RetryMemo this.reference = originalGATK.reference_sequence this.variant = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input"+index) } this.outputFile = this.originalOutput + this.assumeSorted = true super.freezeFieldValues() } diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala index 59a51db96..7567434e2 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala @@ -48,7 +48,7 @@ class MarkDuplicates extends org.broadinstitute.sting.queue.function.JavaCommand @Output(doc="The output bam index", shortName = "out_index", fullName = "output_bam_index_file", required = false) var outputIndex: File = _ - @Output(doc="File to write duplication metrics to", shortName = "out_metrics", fullName = "output_metrics_file", required = false) + @Output(doc="File to write duplication metrics to", shortName = "out_metrics", fullName = "output_metrics_file", required = true) var metrics: File = new File(output + ".metrics") @Argument(doc="If true do not write duplicates to the output file instead of writing them with appropriate flags set.", shortName = "remdup", fullName = "remove_duplicates", required = false) diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala index 1b54231f3..81c76dd29 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala @@ -59,9 +59,17 @@ trait QFunction extends Logging with QJobReport { /** Directory to run the command in. */ var commandDirectory: File = new File(".") - /** Temporary directory to write any files */ + /** Temporary directory to write any files. Must be network accessible. */ var jobTempDir: File = null + /** + * Local path available on all machines to store LOCAL temporary files. Not an @Input, + * nor an @Output. Currently only used for local intermediate files for composite jobs. + * Needs to be an annotated field so that it's mutated during cloning. + */ + @Argument(doc="Local path available on all machines to store LOCAL temporary files.") + var jobLocalDir: File = _ + /** Order the function was added to the graph. */ var addOrder: Seq[Int] = Nil @@ -97,6 +105,7 @@ trait QFunction extends Logging with QJobReport { function.qSettings = this.qSettings function.commandDirectory = this.commandDirectory function.jobTempDir = this.jobTempDir + function.jobLocalDir = this.jobLocalDir function.addOrder = this.addOrder function.jobPriority = this.jobPriority function.jobRestartable = this.jobRestartable @@ -232,6 +241,7 @@ trait QFunction extends Logging with QJobReport { var dirs = Set.empty[File] dirs += commandDirectory dirs += jobTempDir + dirs += jobLocalDir dirs += jobOutputFile.getParentFile if (jobErrorFile != null) dirs += jobErrorFile.getParentFile @@ -370,11 +380,15 @@ trait QFunction extends Logging with QJobReport { if (jobTempDir == null) jobTempDir = qSettings.tempDirectory + if (jobLocalDir == null) + jobLocalDir = jobTempDir + if (jobPriority.isEmpty) jobPriority = qSettings.jobPriority - // Do not set the temp dir relative to the command directory + // Do not set the temp and local dir relative to the command directory jobTempDir = IOUtils.absolute(jobTempDir) + jobLocalDir = IOUtils.absolute(jobLocalDir) absoluteCommandDirectory() } diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala index 66fdf0f8f..67138eb75 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala @@ -109,7 +109,7 @@ trait ScatterGatherableFunction extends CommandLineFunction { this.copySettingsTo(scatterFunction) scatterFunction.originalFunction = this scatterFunction.originalInputs = inputFiles - scatterFunction.commandDirectory = this.scatterGatherTempDir("scatter") + scatterFunction.commandDirectory = this.scatterGatherCommandDir("scatter") scatterFunction.jobOutputFile = new File("scatter.out") scatterFunction.addOrder = this.addOrder :+ 1 scatterFunction.isIntermediate = true @@ -154,7 +154,7 @@ trait ScatterGatherableFunction extends CommandLineFunction { this.copySettingsTo(gatherFunction) gatherFunction.originalFunction = this gatherFunction.originalOutput = gatherOutput - gatherFunction.commandDirectory = this.scatterGatherTempDir("gather-" + gatherField.field.getName) + gatherFunction.commandDirectory = this.scatterGatherCommandDir("gather-" + gatherField.field.getName) gatherFunction.jobOutputFile = new File("gather-" + gatherOutput.getName + ".out") gatherFunction.addOrder = this.addOrder :+ gatherAddOrder @@ -178,10 +178,14 @@ trait ScatterGatherableFunction extends CommandLineFunction { cloneFunction.analysisName = this.analysisName cloneFunction.cloneIndex = i cloneFunction.cloneCount = numClones - cloneFunction.commandDirectory = this.scatterGatherTempDir(dirFormat.format(i)) + cloneFunction.commandDirectory = this.scatterGatherCommandDir(dirFormat.format(i)) cloneFunction.jobOutputFile = if (IOUtils.isSpecialFile(this.jobOutputFile)) this.jobOutputFile else new File(this.jobOutputFile.getName) if (this.jobErrorFile != null) cloneFunction.jobErrorFile = if (IOUtils.isSpecialFile(this.jobErrorFile)) this.jobErrorFile else new File(this.jobErrorFile.getName) + // jic the "local" dir is actually on the network, create different sub local directories for each clone. + // This might be better handled with a hook that allows clones to create unique file names. Right now no hook + // like freezeFieldValues exists for specifying per cloneFunction fields. + cloneFunction.jobLocalDir = this.scatterGatherLocalDir(dirFormat.format(i)) cloneFunction.addOrder = this.addOrder :+ (i+1) cloneFunction.isIntermediate = true @@ -350,7 +354,7 @@ trait ScatterGatherableFunction extends CommandLineFunction { this.copySettingsTo(gatherLogFunction) gatherLogFunction.logs = functions.map(logFile).filter(_ != null) gatherLogFunction.jobOutputFile = logFile(this) - gatherLogFunction.commandDirectory = this.scatterGatherTempDir() + gatherLogFunction.commandDirectory = this.scatterGatherCommandDir() gatherLogFunction.addOrder = this.addOrder :+ addOrder gatherLogFunction.isIntermediate = false gatherLogFunction @@ -361,5 +365,12 @@ trait ScatterGatherableFunction extends CommandLineFunction { * @param subDir directory under the scatter gather directory. * @return temporary directory under this scatter gather directory. */ - private def scatterGatherTempDir(subDir: String = "") = IOUtils.absolute(this.scatterGatherDirectory, this.jobName + "-sg/" + subDir) + private def scatterGatherCommandDir(subDir: String = "") = IOUtils.absolute(this.scatterGatherDirectory, this.jobName + "-sg/" + subDir) + + /** + * Returns a sub directory under this job local directory. + * @param subDir directory under the job local directory. + * @return absolute path to a directory under the original job local directory. + */ + private def scatterGatherLocalDir(subDir: String = "") = IOUtils.absolute(this.jobLocalDir, this.jobName + "-sg/" + subDir) } diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/RemoteFile.scala b/public/scala/src/org/broadinstitute/sting/queue/util/RemoteFile.scala index 28be82136..23a99b586 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/RemoteFile.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/util/RemoteFile.scala @@ -27,6 +27,8 @@ package org.broadinstitute.sting.queue.util import java.io.File import org.broadinstitute.sting.utils.io.FileExtension +import java.util.Date +import java.net.URL /** * An extension of java.io.File that can be pulled from or pushed to a remote location. @@ -35,5 +37,6 @@ trait RemoteFile extends File with FileExtension { def pullToLocal() def pushToRemote() def deleteRemote() + def createUrl(expiration: Date): URL def remoteDescription: String } diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2375.jar b/settings/repository/edu.mit.broad/picard-private-parts-2375.jar deleted file mode 100644 index bfa2f65ad..000000000 Binary files a/settings/repository/edu.mit.broad/picard-private-parts-2375.jar and /dev/null differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2662.jar b/settings/repository/edu.mit.broad/picard-private-parts-2662.jar new file mode 100644 index 000000000..54ef6d5e2 Binary files /dev/null and b/settings/repository/edu.mit.broad/picard-private-parts-2662.jar differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2375.xml b/settings/repository/edu.mit.broad/picard-private-parts-2662.xml similarity index 58% rename from settings/repository/edu.mit.broad/picard-private-parts-2375.xml rename to settings/repository/edu.mit.broad/picard-private-parts-2662.xml index b467f934a..119255e8d 100644 --- a/settings/repository/edu.mit.broad/picard-private-parts-2375.xml +++ b/settings/repository/edu.mit.broad/picard-private-parts-2662.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/picard-1.67.1197.xml b/settings/repository/net.sf/picard-1.67.1197.xml deleted file mode 100644 index 7d9042d6b..000000000 --- a/settings/repository/net.sf/picard-1.67.1197.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/picard-1.67.1197.jar b/settings/repository/net.sf/picard-1.84.1337.jar similarity index 61% rename from settings/repository/net.sf/picard-1.67.1197.jar rename to settings/repository/net.sf/picard-1.84.1337.jar index 9243c02df..68db41848 100644 Binary files a/settings/repository/net.sf/picard-1.67.1197.jar and b/settings/repository/net.sf/picard-1.84.1337.jar differ diff --git a/settings/repository/net.sf/picard-1.84.1337.xml b/settings/repository/net.sf/picard-1.84.1337.xml new file mode 100644 index 000000000..99f746ff6 --- /dev/null +++ b/settings/repository/net.sf/picard-1.84.1337.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/net.sf/sam-1.67.1197.xml b/settings/repository/net.sf/sam-1.67.1197.xml deleted file mode 100644 index d43aba4ed..000000000 --- a/settings/repository/net.sf/sam-1.67.1197.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/sam-1.67.1197.jar b/settings/repository/net.sf/sam-1.84.1337.jar similarity index 67% rename from settings/repository/net.sf/sam-1.67.1197.jar rename to settings/repository/net.sf/sam-1.84.1337.jar index 8a8343cfa..3d28e1928 100644 Binary files a/settings/repository/net.sf/sam-1.67.1197.jar and b/settings/repository/net.sf/sam-1.84.1337.jar differ diff --git a/settings/repository/net.sf/sam-1.84.1337.xml b/settings/repository/net.sf/sam-1.84.1337.xml new file mode 100644 index 000000000..4d31fe250 --- /dev/null +++ b/settings/repository/net.sf/sam-1.84.1337.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/org.broad/tribble-119.jar b/settings/repository/org.broad/tribble-1.84.1337.jar similarity index 51% rename from settings/repository/org.broad/tribble-119.jar rename to settings/repository/org.broad/tribble-1.84.1337.jar index c74bea398..a4c336101 100644 Binary files a/settings/repository/org.broad/tribble-119.jar and b/settings/repository/org.broad/tribble-1.84.1337.jar differ diff --git a/settings/repository/org.broad/tribble-1.84.1337.xml b/settings/repository/org.broad/tribble-1.84.1337.xml new file mode 100644 index 000000000..f14af794e --- /dev/null +++ b/settings/repository/org.broad/tribble-1.84.1337.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/org.broad/tribble-119.xml b/settings/repository/org.broad/tribble-119.xml deleted file mode 100644 index 08037b20e..000000000 --- a/settings/repository/org.broad/tribble-119.xml +++ /dev/null @@ -1,3 +0,0 @@ - - -