From 2ca5fc62a2c9aa7613a1d0fa0b612f6cb9b4fe82 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 19 Jul 2012 16:14:11 -0400 Subject: [PATCH 02/12] Support for MISSING BCF2 type -- Heng wants to use 0x0? to represent any missing type value, which in our implementation was invalid. Updated our codebase to support this construct. Heng said he'll update the BCF2 quick reference. -- Enabled integration test reading Heng's ex2.bcf file -- GATK now only warns in the case where the END info field isn't the same (or +1 due to padding) as the getEnd() function as determined by the GATK. Turns out there's a single record in the 1000G SV call set that doesn't have the right length -- VariantContextTestProvider now tests that X = Y where X -> writing -> reading -> writing -> reading = Y for a variety of variant context inputs X -- Added integration test reading 1000G SV chr1 calls (from Chris) --- .../sting/utils/codecs/bcf2/BCF2Decoder.java | 31 ++++++++-------- .../sting/utils/codecs/bcf2/BCF2Type.java | 12 +++++-- .../sting/utils/codecs/bcf2/BCF2Utils.java | 10 +++--- .../utils/variantcontext/VariantContext.java | 17 +++++++-- .../writer/BCF2FieldEncoder.java | 2 +- .../variantcontext/writer/BCF2Writer.java | 2 +- .../utils/codecs/vcf/VCFIntegrationTest.java | 15 ++++++-- .../VariantContextTestProvider.java | 36 ++++++++++++++----- 8 files changed, 87 insertions(+), 38 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java index 7a6d96131..a13be21c5 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java @@ -139,25 +139,26 @@ public final class BCF2Decoder { return decodeTypedValue(typeDescriptor, size); } + @Requires("size >= 0") public final Object decodeTypedValue(final byte typeDescriptor, final int size) { - final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); - - assert size >= 0; - if ( size == 0 ) { + // missing value => null in java return null; - } else if ( type == BCF2Type.CHAR ) { // special case string decoding for efficiency - return decodeLiteralString(size); - } else if ( size == 1 ) { - return decodeSingleValue(type); } else { - final ArrayList ints = new ArrayList(size); - for ( int i = 0; i < size; i++ ) { - final Object val = decodeSingleValue(type); - if ( val == null ) continue; // auto-pruning. We remove trailing nulls - ints.add(val); + final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); + if ( type == BCF2Type.CHAR ) { // special case string decoding for efficiency + return decodeLiteralString(size); + } else if ( size == 1 ) { + return decodeSingleValue(type); + } else { + final ArrayList ints = new ArrayList(size); + for ( int i = 0; i < size; i++ ) { + final Object val = decodeSingleValue(type); + if ( val == null ) continue; // auto-pruning. We remove trailing nulls + ints.add(val); + } + return ints.isEmpty() ? null : ints; // return null when all of the values are null } - return ints.isEmpty() ? null : ints; // return null when all of the values are null } } @@ -256,7 +257,7 @@ public final class BCF2Decoder { * int elements are still forced to do a fresh allocation as well. * @return see description */ - @Requires({"BCF2Type.INTEGERS.contains(type)", "size >= 0", "type != null"}) + @Requires({"type != null", "type.isIntegerType()", "size >= 0"}) public final int[] decodeIntArray(final int size, final BCF2Type type, int[] maybeDest) { if ( size == 0 ) { return null; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java index f874b14cd..49f375b25 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java @@ -35,6 +35,7 @@ import java.util.EnumSet; * @since 05/12 */ public enum BCF2Type { + MISSING(0, 0, 0x00), INT8 (1, 1, 0xFFFFFF80, -127, 127), // todo -- confirm range INT16(2, 2, 0xFFFF8000, -32767, 32767), INT32(3, 4, 0x80000000, -2147483647, 2147483647), @@ -86,7 +87,7 @@ public enum BCF2Type { * @param v * @return */ - @Requires("INTEGERS.contains(this)") + @Requires("this.isIntegerType()") public final boolean withinRange(final long v) { return v >= minValue && v <= maxValue; } /** @@ -108,7 +109,14 @@ public enum BCF2Type { /** * An enum set of the types that might represent Integer values */ - public final static EnumSet INTEGERS = EnumSet.of(INT8, INT16, INT32); + private final static EnumSet INTEGERS = EnumSet.of(INT8, INT16, INT32); + + /** + * @return true if this BCF2Type corresponds to the magic "MISSING" type (0x00) + */ + public boolean isMissingType() { + return this == MISSING; + } public boolean isIntegerType() { return INTEGERS.contains(this); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java index 143ab52df..43e933948 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java @@ -225,7 +225,7 @@ public final class BCF2Utils { } } - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Ensures("result.isIntegerType()") public final static BCF2Type determineIntegerType(final int value) { for ( final BCF2Type potentialType : INTEGER_TYPES_BY_SIZE) { if ( potentialType.withinRange(value) ) @@ -235,7 +235,7 @@ public final class BCF2Utils { throw new ReviewedStingException("Integer cannot be encoded in allowable range of even INT32: " + value); } - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Ensures("result.isIntegerType()") public final static BCF2Type determineIntegerType(final int[] values) { // literally a copy of the code below, but there's no general way to unify lists and arrays in java BCF2Type maxType = BCF2Type.INT8; @@ -260,8 +260,8 @@ public final class BCF2Utils { * @param t2 * @return */ - @Requires({"BCF2Type.INTEGERS.contains(t1)","BCF2Type.INTEGERS.contains(t2)"}) - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Requires({"t1.isIntegerType()","t2.isIntegerType()"}) + @Ensures("result.isIntegerType()") public final static BCF2Type maxIntegerType(final BCF2Type t1, final BCF2Type t2) { switch ( t1 ) { case INT8: return t2; @@ -271,7 +271,7 @@ public final class BCF2Utils { } } - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Ensures("result.isIntegerType()") public final static BCF2Type determineIntegerType(final List values) { BCF2Type maxType = BCF2Type.INT8; for ( final int value : values ) { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 1f0b2b054..dcdd95d00 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.utils.variantcontext; +import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broad.tribble.TribbleException; import org.broad.tribble.util.ParsingUtils; @@ -176,6 +177,10 @@ import java.util.*; * @author depristo */ public class VariantContext implements Feature { // to enable tribble integration + private final static boolean WARN_ABOUT_BAD_END = true; + 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; @@ -1146,10 +1151,16 @@ public class VariantContext implements Feature { // to enable tribble integratio if ( hasAttribute(VCFConstants.END_KEY) ) { final int end = getAttributeAsInt(VCFConstants.END_KEY, -1); assert end != -1; - if ( end != getEnd() ) - throw new ReviewedStingException("Badly formed variant context at location " + getChr() + ":" + if ( end != getEnd() && end != getEnd() + 1 ) { + // the end is allowed to 1 bigger because of the padding + final String message = "Badly formed variant context at location " + getChr() + ":" + getStart() + "; getEnd() was " + getEnd() - + " but this VariantContext contains an END key with value " + end); + + " but this VariantContext contains an END key with value " + end; + if ( WARN_ABOUT_BAD_END ) + logger.warn(message); + else + throw new ReviewedStingException(message); + } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java index 812e6dd07..ddeb4d284 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java @@ -47,7 +47,7 @@ import java.util.Map; */ @Invariant({ "headerLine != null", - "BCF2Type.INTEGERS.contains(dictionaryOffsetType)", + "dictionaryOffsetType.isIntegerType()", "dictionaryOffset >= 0" }) public abstract class BCF2FieldEncoder { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java index 45610bbf9..c77fe7172 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java @@ -338,7 +338,7 @@ class BCF2Writer extends IndexingVariantContextWriter { } @Requires("! strings.isEmpty()") - @Ensures("BCF2Type.INTEGERS.contains(result)") + @Ensures("result.isIntegerType()") private final BCF2Type encodeStringsByRef(final Collection strings) throws IOException { final List offsets = new ArrayList(strings.size()); diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java index b271d8c84..e9b845d59 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java @@ -39,6 +39,17 @@ public class VCFIntegrationTest extends WalkerTest { executeTest("Test reading and writing breakpoint VCF", spec1); } + @Test(enabled = true) + public void testReadingAndWriting1000GSVs() { + String testVCF = privateTestDir + "1000G_SVs.chr1.vcf"; + + String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; + + String test1 = baseCommand + "-T SelectVariants -V " + testVCF; + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("")); + executeTest("Test reading and writing 1000G Phase I SVs", spec1); + } + @Test public void testReadingAndWritingSamtools() { String testVCF = privateTestDir + "samtools.vcf"; @@ -59,12 +70,12 @@ public class VCFIntegrationTest extends WalkerTest { executeTest("Test writing samtools WEx BCF example", spec1); } - @Test(enabled = false) + @Test(enabled = true) public void testReadingSamtoolsWExBCFExample() { String testVCF = privateTestDir + "ex2.bcf"; String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s "; String test1 = baseCommand + "-T SelectVariants -V " + testVCF; - WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("63a2e0484ae37b0680514f53e0bf0c94")); + WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0439e2b4ccc63bb4ba7c283cd9ab1b25")); executeTest("Test reading samtools WEx BCF example", spec1); } diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java index ca4cdf306..c436a7b45 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java @@ -597,23 +597,41 @@ public class VariantContextTestProvider { } public static void testReaderWriter(final VariantContextIOTest tester, final VariantContextTestData data) throws IOException { + testReaderWriter(tester, data.header, data.vcs, data.vcs, true); + } + + public static void testReaderWriter(final VariantContextIOTest tester, + final VCFHeader header, + final List expected, + final Iterable vcs, + final boolean recurse) throws IOException { final File tmpFile = File.createTempFile("testReaderWriter", tester.getExtension()); tmpFile.deleteOnExit(); - // todo -- test all options - - // write + // write expected to disk final EnumSet options = EnumSet.of(Options.INDEX_ON_THE_FLY); final VariantContextWriter writer = tester.makeWriter(tmpFile, options); - writer.writeHeader(data.header); - final List expected = data.vcs; - for ( VariantContext vc : expected ) - writer.add(vc); - writer.close(); + writeVCsToFile(writer, header, vcs); - final Iterable actual = readAllVCs(tmpFile, tester.makeCodec()).getSecond(); + // ensure writing of expected == actual + final Pair> p = readAllVCs(tmpFile, tester.makeCodec()); + final Iterable actual = p.getSecond(); 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); + } + } + + private static void writeVCsToFile(final VariantContextWriter writer, final VCFHeader header, final Iterable vcs) { + // write + writer.writeHeader(header); + for ( VariantContext vc : vcs ) + if (vc != null) + writer.add(vc); + writer.close(); } /** From af383c30b5e1afeed73f7ccda24a426c1bdb49cd Mon Sep 17 00:00:00 2001 From: Christopher Hartl Date: Thu, 19 Jul 2012 21:24:04 -0400 Subject: [PATCH 03/12] Ensure that the gene summary has a header line --- .../coverage/DepthOfCoverageWalker.java | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index ef52014f3..70f444061 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -507,6 +507,38 @@ public class DepthOfCoverageWalker extends LocusWalker geneStats : statsByGene ) { printTargetSummary(geneSummaryOut,geneStats); From 116885a450a85c7e10dfc22983aff154838baa9a Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 20 Jul 2012 16:33:29 -0400 Subject: [PATCH 05/12] Removed the "Walker" suffix from all walkers that had it. * Did not touch archived walkers... those can be named whatever. * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...) * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats. --- ivy.xml | 3 + ...{CompareBAMWalker.java => CompareBAM.java} | 2 +- .../reducereads/MultiSampleCompressor.java | 2 +- ...educeReadsWalker.java => ReduceReads.java} | 2 +- .../reducereads/SingleSampleCompressor.java | 4 +- .../reducereads/SlidingWindow.java | 4 +- .../haplotypecaller/HaplotypeCaller.java | 22 +- ...onWalker.java => AlignmentValidation.java} | 2 +- ...tsWalker.java => CountBestAlignments.java} | 2 +- .../broadinstitute/sting/gatk/Categorize.java | 38 + .../broadinstitute/sting/gatk/Category.java | 68 ++ .../gatk/executive/LinearMicroScheduler.java | 1 - .../traversals/TraverseActiveRegions.java | 28 +- .../gatk/walkers/ActiveRegionWalker.java | 3 +- .../{ClipReadsWalker.java => ClipReads.java} | 2 +- ...mesWalker.java => FindReadsWithNames.java} | 2 +- .../{FlagStatWalker.java => FlagStat.java} | 6 +- .../{PileupWalker.java => Pileup.java} | 2 +- .../{PrintRODsWalker.java => PrintRODs.java} | 2 +- ...{PrintReadsWalker.java => PrintReads.java} | 2 +- ...itSamFileWalker.java => SplitSamFile.java} | 4 +- .../gatk/walkers/annotator/AlleleBalance.java | 4 +- .../annotator/AlleleBalanceBySample.java | 8 +- .../gatk/walkers/annotator/BaseCounts.java | 4 +- .../walkers/annotator/ChromosomeCounts.java | 13 +- .../walkers/annotator/DepthOfCoverage.java | 4 +- .../annotator/DepthPerAlleleBySample.java | 12 +- .../gatk/walkers/annotator/FisherStrand.java | 4 +- .../gatk/walkers/annotator/GCContent.java | 4 +- .../walkers/annotator/HaplotypeScore.java | 4 +- .../gatk/walkers/annotator/HardyWeinberg.java | 4 +- .../walkers/annotator/HomopolymerRun.java | 5 +- .../walkers/annotator/InbreedingCoeff.java | 6 +- .../gatk/walkers/annotator/IndelType.java | 4 +- .../sting/gatk/walkers/annotator/LowMQ.java | 5 +- .../walkers/annotator/MVLikelihoodRatio.java | 4 +- .../walkers/annotator/MappingQualityZero.java | 4 +- .../annotator/MappingQualityZeroBySample.java | 4 +- .../annotator/MappingQualityZeroFraction.java | 4 +- .../gatk/walkers/annotator/NBaseCount.java | 4 +- .../gatk/walkers/annotator/QualByDepth.java | 4 +- .../walkers/annotator/RMSMappingQuality.java | 4 +- .../gatk/walkers/annotator/RankSumTest.java | 5 +- .../gatk/walkers/annotator/SampleList.java | 4 +- .../sting/gatk/walkers/annotator/SnpEff.java | 6 +- .../walkers/annotator/SpanningDeletions.java | 4 +- .../annotator/TandemRepeatAnnotator.java | 5 +- .../annotator/TechnologyComposition.java | 4 +- .../TransmissionDisequilibriumTest.java | 4 +- .../walkers/annotator/VariantAnnotator.java | 4 +- .../annotator/VariantAnnotatorEngine.java | 6 +- ...leWalker.java => AnnotatorCompatible.java} | 2 +- .../interfaces/GenotypeAnnotation.java | 3 +- .../interfaces/InfoFieldAnnotation.java | 2 +- .../VariantAnnotatorAnnotation.java | 2 +- ...oVCFWalker.java => BeagleOutputToVCF.java} | 6 +- ...putWalker.java => ProduceBeagleInput.java} | 9 +- ...ker.java => VariantsToBeagleUnphased.java} | 6 +- ...ualityScoreRecalibrator.java => BQSR.java} | 4 +- .../bqsr/StandardRecalibrationEngine.java | 2 +- ...lableLociWalker.java => CallableLoci.java} | 2 +- ...ciWalker.java => CompareCallableLoci.java} | 34 +- ...verageWalker.java => DepthOfCoverage.java} | 8 +- ...alWalker.java => GCContentByInterval.java} | 2 +- .../targets/FindCoveredIntervals.java | 3 +- ...iffObjectsWalker.java => DiffObjects.java} | 2 +- ...lker.java => FastaAlternateReference.java} | 2 +- ...ferenceWalker.java => FastaReference.java} | 2 +- ...{FastaStatsWalker.java => FastaStats.java} | 12 +- ...tionWalker.java => VariantFiltration.java} | 8 +- .../walkers/genotyper/UnifiedGenotyper.java | 6 +- ...rWalker.java => SomaticIndelDetector.java} | 5 +- .../gatk/walkers/phasing/PhasingUtils.java | 4 +- ...singWalker.java => ReadBackedPhasing.java} | 4 +- ...{CountBasesWalker.java => CountBases.java} | 2 +- .../{CountLociWalker.java => CountLoci.java} | 2 +- ...{CountMalesWalker.java => CountMales.java} | 2 +- .../{CountRODsWalker.java => CountRODs.java} | 2 +- ...DsByRefWalker.java => CountRODsByRef.java} | 8 +- ...EventsWalker.java => CountReadEvents.java} | 2 +- ...{CountReadsWalker.java => CountReads.java} | 2 +- ...entWalker.java => CountTerminusEvent.java} | 2 +- ...leQualityWalker.java => CycleQuality.java} | 2 +- ...ThrowingWalker.java => ErrorThrowing.java} | 2 +- .../qc/{QCRefWalker.java => QCRef.java} | 11 +- ...tatsWalker.java => ReadClippingStats.java} | 2 +- ...idationWalker.java => ReadValidation.java} | 2 +- ...onWalker.java => RodSystemValidation.java} | 3 +- ...ileupWalker.java => ValidatingPileup.java} | 9 +- ...teWalker.java => GenotypeAndValidate.java} | 4 +- ...alker.java => ValidationSiteSelector.java} | 8 +- ...ariantEvalWalker.java => VariantEval.java} | 3 +- .../MendelianViolationEvaluator.java | 4 +- .../evaluators/VariantEvaluator.java | 10 +- .../evaluators/VariantSummary.java | 4 +- .../stratifications/VariantStratifier.java | 8 +- .../varianteval/util/EvaluationContext.java | 14 +- .../varianteval/util/VariantEvalUtils.java | 10 +- .../sting/utils/help/GATKDocUtils.java | 15 +- .../sting/utils/help/GATKDocWorkUnit.java | 48 +- .../sting/utils/help/GATKDoclet.java | 254 ++++-- .../help/GenericDocumentationHandler.java | 215 +++--- .../gatk/GenomeAnalysisEngineUnitTest.java | 4 +- .../sting/gatk/WalkerManagerUnitTest.java | 7 +- .../reads/GATKWalkerBenchmark.java | 10 +- .../traversals/TraverseReadsUnitTest.java | 15 +- .../gatk/walkers/PrintReadsUnitTest.java | 4 +- .../VariantEvalWalkerUnitTest.java | 4 +- public/packages/GATK-Picard.xml | 12 +- settings/helpTemplates/bootstrap.min.css | 727 ++++++++++++++++++ settings/helpTemplates/bootstrap.min.js | 7 + settings/helpTemplates/common.html | 156 +++- .../helpTemplates/generic.index.template.html | 74 +- settings/helpTemplates/generic.template.html | 227 +++--- settings/helpTemplates/jquery.min.js | 4 + 115 files changed, 1807 insertions(+), 576 deletions(-) rename protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/{CompareBAMWalker.java => CompareBAM.java} (98%) rename protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/{ReduceReadsWalker.java => ReduceReads.java} (99%) rename public/java/src/org/broadinstitute/sting/alignment/{AlignmentValidationWalker.java => AlignmentValidation.java} (98%) rename public/java/src/org/broadinstitute/sting/alignment/{CountBestAlignmentsWalker.java => CountBestAlignments.java} (98%) create mode 100644 public/java/src/org/broadinstitute/sting/gatk/Categorize.java create mode 100644 public/java/src/org/broadinstitute/sting/gatk/Category.java rename public/java/src/org/broadinstitute/sting/gatk/walkers/{ClipReadsWalker.java => ClipReads.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{FindReadsWithNamesWalker.java => FindReadsWithNames.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{FlagStatWalker.java => FlagStat.java} (97%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{PileupWalker.java => Pileup.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{PrintRODsWalker.java => PrintRODs.java} (97%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{PrintReadsWalker.java => PrintReads.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/{SplitSamFileWalker.java => SplitSamFile.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/{AnnotatorCompatibleWalker.java => AnnotatorCompatible.java} (93%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/{BeagleOutputToVCFWalker.java => BeagleOutputToVCF.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/{ProduceBeagleInputWalker.java => ProduceBeagleInput.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/{VariantsToBeagleUnphasedWalker.java => VariantsToBeagleUnphased.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/{BaseQualityScoreRecalibrator.java => BQSR.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/{CallableLociWalker.java => CallableLoci.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/{CompareCallableLociWalker.java => CompareCallableLoci.java} (74%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/{DepthOfCoverageWalker.java => DepthOfCoverage.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/{GCContentByIntervalWalker.java => GCContentByInterval.java} (97%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/{DiffObjectsWalker.java => DiffObjects.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/{FastaAlternateReferenceWalker.java => FastaAlternateReference.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/{FastaReferenceWalker.java => FastaReference.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/{FastaStatsWalker.java => FastaStats.java} (87%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/filters/{VariantFiltrationWalker.java => VariantFiltration.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/indels/{SomaticIndelDetectorWalker.java => SomaticIndelDetector.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/{ReadBackedPhasingWalker.java => ReadBackedPhasing.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountBasesWalker.java => CountBases.java} (95%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountLociWalker.java => CountLoci.java} (94%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountMalesWalker.java => CountMales.java} (95%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountRODsWalker.java => CountRODs.java} (97%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountRODsByRefWalker.java => CountRODsByRef.java} (90%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountReadEventsWalker.java => CountReadEvents.java} (95%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountReadsWalker.java => CountReads.java} (95%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CountTerminusEventWalker.java => CountTerminusEvent.java} (96%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{CycleQualityWalker.java => CycleQuality.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{ErrorThrowingWalker.java => ErrorThrowing.java} (96%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{QCRefWalker.java => QCRef.java} (90%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{ReadClippingStatsWalker.java => ReadClippingStats.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{ReadValidationWalker.java => ReadValidation.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{RodSystemValidationWalker.java => RodSystemValidation.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/qc/{ValidatingPileupWalker.java => ValidatingPileup.java} (94%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/validation/{GenotypeAndValidateWalker.java => GenotypeAndValidate.java} (99%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/{ValidationSiteSelectorWalker.java => ValidationSiteSelector.java} (98%) rename public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/{VariantEvalWalker.java => VariantEval.java} (99%) create mode 100755 settings/helpTemplates/bootstrap.min.css create mode 100644 settings/helpTemplates/bootstrap.min.js create mode 100644 settings/helpTemplates/jquery.min.js diff --git a/ivy.xml b/ivy.xml index 5a8c3986a..a96567889 100644 --- a/ivy.xml +++ b/ivy.xml @@ -100,6 +100,9 @@ + + + diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java similarity index 98% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java index 3e07295e7..f8c9c5396 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAMWalker.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java @@ -40,7 +40,7 @@ import java.util.Map; */ @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class}) -public class CompareBAMWalker extends LocusWalker, CompareBAMWalker.TestResults> { +public class CompareBAM extends LocusWalker, CompareBAM.TestResults> { @Argument(required = true, shortName = "rr", fullName = "reduced_readgroup", doc = "The read group ID corresponding to the compressed BAM being tested") public String reducedReadGroupID; @Argument(required = false, shortName = "teq", fullName = "test_equal_bases", doc = "Test if the bases marked as '=' are indeed ref bases.") public boolean TEST_EQUAL_BASES = false; @Argument(required = false, shortName = "tbc", fullName = "test_base_counts", doc = "Test if the base counts tag in consensus reads are accurate.") public boolean TEST_BASE_COUNTS = false; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java index 0ac9630c2..44971ca38 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java @@ -53,7 +53,7 @@ public class MultiSampleCompressor implements Compressor { final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, final int minBaseQual, - final ReduceReadsWalker.DownsampleStrategy downsampleStrategy) { + final ReduceReads.DownsampleStrategy downsampleStrategy) { for ( String name : SampleUtils.getSAMFileSamples(header) ) { compressorsPerSample.put(name, new SingleSampleCompressor(name, contextSize, downsampleCoverage, diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java similarity index 99% rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java index 1b11cbd4e..d793ae159 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java @@ -83,7 +83,7 @@ import java.util.*; @PartitionBy(PartitionType.INTERVAL) @ReadFilters({UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class, BadCigarFilter.class}) -public class ReduceReadsWalker extends ReadWalker, ReduceReadsStash> { +public class ReduceReads extends ReadWalker, ReduceReadsStash> { @Output protected StingSAMFileWriter out; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java index fd0dfa1ff..6d2c2d215 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java @@ -26,7 +26,7 @@ public class SingleSampleCompressor implements Compressor { protected double minIndelProportionToTriggerVariant; protected int minBaseQual; - protected ReduceReadsWalker.DownsampleStrategy downsampleStrategy; + protected ReduceReads.DownsampleStrategy downsampleStrategy; public SingleSampleCompressor(final String sampleName, final int contextSize, @@ -35,7 +35,7 @@ public class SingleSampleCompressor implements Compressor { final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, final int minBaseQual, - final ReduceReadsWalker.DownsampleStrategy downsampleStrategy) { + final ReduceReads.DownsampleStrategy downsampleStrategy) { this.sampleName = sampleName; this.contextSize = contextSize; this.downsampleCoverage = downsampleCoverage; 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 68dfd041b..60d7096a3 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 @@ -53,7 +53,7 @@ public class SlidingWindow { protected int MIN_BASE_QUAL_TO_COUNT; // qual has to be greater than or equal to this value protected int MIN_MAPPING_QUALITY; - protected ReduceReadsWalker.DownsampleStrategy downsampleStrategy; + protected ReduceReads.DownsampleStrategy downsampleStrategy; private boolean hasIndelQualities; /** @@ -82,7 +82,7 @@ public class SlidingWindow { } - public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader header, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReadsWalker.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities) { + public SlidingWindow(String contig, int contigIndex, int contextSize, SAMFileHeader header, GATKSAMReadGroupRecord readGroupAttribute, int windowNumber, final double minAltProportionToTriggerVariant, final double minIndelProportionToTriggerVariant, int minBaseQual, int minMappingQuality, int downsampleCoverage, final ReduceReads.DownsampleStrategy downsampleStrategy, boolean hasIndelQualities) { this.stopLocation = -1; this.contextSize = contextSize; this.downsampleCoverage = downsampleCoverage; 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 bda94cc8f..546f53002 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -33,20 +33,21 @@ import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; 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.filters.*; +import org.broadinstitute.sting.gatk.filters.BadMateFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.gatk.walkers.ActiveRegionExtension; +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.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; 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.clipping.ReadClipper; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; @@ -56,6 +57,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.FileNotFoundException; import java.io.PrintStream; @@ -90,7 +92,7 @@ import java.util.*; @PartitionBy(PartitionType.LOCUS) @ActiveRegionExtension(extension=65, maxRegion=275) -public class HaplotypeCaller extends ActiveRegionWalker implements AnnotatorCompatibleWalker { +public class HaplotypeCaller extends ActiveRegionWalker implements AnnotatorCompatible { /** * A raw, unfiltered, highly specific callset in VCF format. @@ -361,7 +363,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem //--------------------------------------------------------------------------------------------------------------- @Override - public Integer map( final ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) { + public Integer map( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker metaDataTracker ) { final ArrayList activeAllelesToGenotype = new ArrayList(); @@ -476,7 +478,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem // //--------------------------------------------------------------------------------------------------------------- - private void finalizeActiveRegion( final ActiveRegion activeRegion ) { + private void finalizeActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) { if( DEBUG ) { System.out.println("\nAssembling " + activeRegion.getExtendedLoc() + " with " + activeRegion.size() + " reads:"); } final ArrayList finalizedReadList = new ArrayList(); final FragmentCollection fragmentCollection = FragmentUtils.create( ReadUtils.sortReadsByCoordinate(activeRegion.getReads()) ); @@ -503,7 +505,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem } } - private List filterNonPassingReads( final ActiveRegion activeRegion ) { + private List filterNonPassingReads( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion ) { final ArrayList 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)) ) { @@ -514,7 +516,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem return readsToRemove; } - private GenomeLoc getPaddedLoc( final ActiveRegion activeRegion ) { + 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); diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java rename to public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java index a342cf932..7af83d14b 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java +++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java @@ -46,7 +46,7 @@ import java.util.Iterator; * @author mhanna * @version 0.1 */ -public class AlignmentValidationWalker extends ReadWalker { +public class AlignmentValidation extends ReadWalker { /** * The supporting BWT index generated using BWT. */ diff --git a/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java b/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java rename to public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java index d91b83e7a..b0580fe50 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java +++ b/public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java @@ -48,7 +48,7 @@ import java.util.TreeMap; * @author mhanna * @version 0.1 */ -public class CountBestAlignmentsWalker extends ReadWalker { +public class CountBestAlignments extends ReadWalker { /** * The supporting BWT index generated using BWT. */ diff --git a/public/java/src/org/broadinstitute/sting/gatk/Categorize.java b/public/java/src/org/broadinstitute/sting/gatk/Categorize.java new file mode 100644 index 000000000..b8a222983 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/Categorize.java @@ -0,0 +1,38 @@ +/* + * 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; + +import java.lang.annotation.*; + +/** + * Allows the walker to be tagged, they can have an unlimited number of categories. + */ +@Documented +@Inherited +@Retention(RetentionPolicy.RUNTIME) +@Target(ElementType.TYPE) +public @interface Categorize { + public Category[] value() default {Category.UNCATEGORIZED}; +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/Category.java b/public/java/src/org/broadinstitute/sting/gatk/Category.java new file mode 100644 index 000000000..d1f890f95 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/Category.java @@ -0,0 +1,68 @@ +/* + * 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; + +public enum Category { + + BAM_PROCESSING("Walker", "BAM Processing and Analysis Tools"), + + COMPANION("Walker", "Companion Utilities"), + + CANCER_SPECIFIC("Walker", "Cancer-specific Variant Discovery Tools"), + + QUALITY_CONTROL("Walker", "Quality Control and Simple Analysis Tools"), + + VALIDATION("Walker", "Validation Utilities"), + + VARIANT_DETECTION("ex", "Variant Detection"), + + VARIANT_DISCOVERY("Walker", "Variant Discovery Tools"), + + VARIANT_EVALUATION("Walker", "Variant Evaluation and Manipulation Tools"), + + EXPERIMENTAL("Walker", "Miscellaneous Experimental (and Potentially Unstable) Tools"), + + UNCATEGORIZED("all", "No category"); + + private final String description; + + /** + * Accepted strings are from the GATKDocWorkUnit.group + */ + private final String type; + + private Category(String type, String description) { + this.description = description; + this.type = type; + } + + public String type() { + return type; + } + + public String getDescription() { + return description; + } +} diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java index 16487054b..b35abb775 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java @@ -11,7 +11,6 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.io.DirectOutputTracker; import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions; -import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.SampleUtils; 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 6d0ec0e7c..1b9c12fb0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java @@ -6,10 +6,12 @@ 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.*; +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.GenomeLocSortedSet; -import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.activeregion.ActivityProfile; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -28,7 +30,7 @@ public class TraverseActiveRegions extends TraversalEngine workQueue = new LinkedList(); + private final LinkedList workQueue = new LinkedList(); private final LinkedHashSet myReads = new LinkedHashSet(); @Override @@ -109,18 +111,18 @@ public class TraverseActiveRegions extends TraversalEngine activeRegions = bandPassFiltered.createActiveRegions( activeRegionExtension, maxRegionSize ); + final List activeRegions = bandPassFiltered.createActiveRegions( 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); + final org.broadinstitute.sting.utils.activeregion.ActiveRegion last = workQueue.getLast(); + final org.broadinstitute.sting.utils.activeregion.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.add( new org.broadinstitute.sting.utils.activeregion.ActiveRegion(last.getLocation().union(first.getLocation()), first.isActive, this.engine.getGenomeLocParser(), activeRegionExtension) ); } } workQueue.addAll( activeRegions ); @@ -183,7 +185,7 @@ public class TraverseActiveRegions extends TraversalEngine walker ) { // Just want to output the active regions to a file, not actually process them - for( final ActiveRegion activeRegion : workQueue ) { + for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion : workQueue ) { if( activeRegion.isActive ) { walker.activeRegionOutStream.println( activeRegion.getLocation() ); } @@ -196,7 +198,7 @@ public class TraverseActiveRegions extends TraversalEngine extends TraversalEngine reads, final Queue workQueue, final T sum, final ActiveRegionWalker walker ) { + private T processActiveRegion( final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final LinkedHashSet reads, final Queue workQueue, final T sum, final ActiveRegionWalker walker ) { final ArrayList placedReads = new ArrayList(); for( final GATKSAMRecord read : reads ) { 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 ) { + org.broadinstitute.sting.utils.activeregion.ActiveRegion bestRegion = activeRegion; + for( final org.broadinstitute.sting.utils.activeregion.ActiveRegion otherRegionToTest : workQueue ) { if( otherRegionToTest.getLocation().sizeOfOverlap(readLoc) >= maxOverlap ) { maxOverlap = otherRegionToTest.getLocation().sizeOfOverlap( readLoc ); bestRegion = otherRegionToTest; @@ -227,7 +229,7 @@ public class TraverseActiveRegions extends TraversalEngine extends Walker { +public class ClipReads extends ReadWalker { /** * If provided, ClipReads will write summary statistics about the clipping operations applied * to the reads to this file. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java index 7f9269725..f6f091cfc 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNames.java @@ -49,7 +49,7 @@ import java.util.Set; */ @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) @Requires({DataSource.READS, DataSource.REFERENCE}) -public class FindReadsWithNamesWalker extends ReadWalker { +public class FindReadsWithNames extends ReadWalker { /** an optional argument to dump the reads out to a BAM file */ @Output(doc="Write output to this BAM filename instead of STDOUT") SAMFileWriter out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java index 0777037bf..e5f77018c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java @@ -42,12 +42,12 @@ import java.text.NumberFormat; * @author aaron */ @Requires({DataSource.READS}) -public class FlagStatWalker extends ReadWalker { +public class FlagStat extends ReadWalker { @Output PrintStream out; // what comes out of the flagstat - static class FlagStat { + static class FlagStatus { long readCount = 0L; long QC_failure = 0L; long duplicates = 0L; @@ -117,7 +117,7 @@ public class FlagStatWalker extends ReadWalker { } - private FlagStat myStat = new FlagStat(); + private FlagStatus myStat = new FlagStatus(); public Integer map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) { myStat.readCount++; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java index b3062c546..12b575760 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java @@ -60,7 +60,7 @@ import java.util.List; * Associated command: * samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] */ -public class PileupWalker extends LocusWalker implements TreeReducible { +public class Pileup extends LocusWalker implements TreeReducible { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java index 7960f5c35..cfc096ea2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java @@ -39,7 +39,7 @@ import java.io.PrintStream; * Prints out all of the RODs in the input data set. Data is rendered using the toString() method * of the given ROD. */ -public class PrintRODsWalker extends RodWalker { +public class PrintRODs extends RodWalker { @Input(fullName="input", shortName = "input", doc="The input ROD which should be printed out.", required=true) public RodBinding input; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java index 4159a67b7..6e9960f3a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java @@ -90,7 +90,7 @@ import java.util.TreeSet; */ @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT) @Requires({DataSource.READS, DataSource.REFERENCE}) -public class PrintReadsWalker extends ReadWalker { +public class PrintReads extends ReadWalker { @Output(doc="Write output to this BAM filename instead of STDOUT", required = true) SAMFileWriter out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java index baaaf9e28..e0ee072fe 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java @@ -47,14 +47,14 @@ import java.util.Map; */ @WalkerName("SplitSamFile") @Requires({DataSource.READS}) -public class SplitSamFileWalker extends ReadWalker> { +public class SplitSamFile extends ReadWalker> { @Argument(fullName="outputRoot", doc="output BAM file", required=false) public String outputRoot = null; @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false) public Integer BAMcompression = 5; - private static Logger logger = Logger.getLogger(SplitSamFileWalker.class); + private static Logger logger = Logger.getLogger(SplitSamFile.class); private static String VERSION = "0.0.1"; public void initialize() { 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 index dc589699a..30f81b20c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -28,7 +28,7 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -51,7 +51,7 @@ public class AlleleBalance extends InfoFieldAnnotation { char[] BASES = {'A','C','G','T'}; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; 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 index fd23fb8f6..11c9c3a99 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java @@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker; +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.MathUtils; @@ -14,7 +14,9 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.Arrays; +import java.util.Collection; +import java.util.List; /** @@ -22,7 +24,7 @@ import java.util.*; */ public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation { - public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) { + public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) { Double ratio = annotateSNP(stratifiedContext, vc, g); if (ratio == null) return; 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 index 46aa6d0f3..c3b6de65a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java @@ -34,7 +34,7 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -52,7 +52,7 @@ import java.util.Map; */ public class BaseCounts extends InfoFieldAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 3d07e3a7a..54837baad 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -29,18 +29,17 @@ 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.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; @@ -62,14 +61,14 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn private Set founderIds = new HashSet(); - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( ! vc.hasGenotypes() ) return null; return VariantContextUtils.calculateChromosomeCounts(vc, new HashMap(), true,founderIds); } - public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set headerLines ){ + public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set headerLines ){ //If families were given, get the founders ids founderIds = ((Walker)walker).getSampleDB().getFounderIds(); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index b36de0dac..28ca77f18 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -4,7 +4,7 @@ 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.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; @@ -38,7 +38,7 @@ import java.util.Map; */ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index d56daadea..523aa81b1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -3,10 +3,12 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.Allele; @@ -14,7 +16,9 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; /** @@ -42,7 +46,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa private static final String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time - public void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) { + public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb) { if ( g == null || !g.isCalled() ) return; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 6dc0ba3e1..4669cfef8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -29,7 +29,7 @@ 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.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; @@ -55,7 +55,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat private static final String FS = "FS"; private static final double MIN_PVALUE = 1E-320; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( !vc.isVariant() ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 11a64b49f..263320d1b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker; +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.BaseUtils; @@ -22,7 +22,7 @@ import java.util.Map; */ public class GCContent extends InfoFieldAnnotation implements ExperimentalAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { double content = computeGCContent(ref); Map map = new HashMap(); map.put(getKeyNames().get(0), String.format("%.2f", content)); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index 606de1b88..45444e05d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -28,7 +28,7 @@ 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.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; @@ -60,7 +60,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot private final static int MAX_CONSENSUS_HAPLOTYPES_TO_CONSIDER = 50; private final static char REGEXP_WILDCARD = '.'; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if (stratifiedContexts.size() == 0) // size 0 means that call was made by someone else and we have no data here return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java index 795cdbeb5..6ba85de07 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java @@ -4,7 +4,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation; 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation; import org.broadinstitute.sting.utils.QualityUtils; @@ -29,7 +29,7 @@ public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgress private static final int MIN_GENOTYPE_QUALITY = 10; private static final int MIN_LOG10_PERROR = MIN_GENOTYPE_QUALITY / 10; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { final GenotypesContext genotypes = vc.getGenotypes(); if ( genotypes == null || genotypes.size() < MIN_SAMPLES ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java index 7c4b0b42e..9f20bf375 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java @@ -3,9 +3,8 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; @@ -23,7 +22,7 @@ public class HomopolymerRun extends InfoFieldAnnotation { private boolean ANNOTATE_INDELS = true; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( !vc.isBiallelic() ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java index 0d2b3478d..fa3a7459b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java @@ -3,9 +3,9 @@ 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.Walker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +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.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.MathUtils; @@ -33,7 +33,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno private static final int MIN_SAMPLES = 10; private Set founderIds; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { //If available, get the founder IDs and cache them. the IC will only be computed on founders then. if(founderIds == null) founderIds = ((Walker)walker).getSampleDB().getFounderIds(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java index e0abfcf3c..babaf7ee6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java @@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker; +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.IndelUtils; @@ -18,7 +18,7 @@ import java.util.*; */ public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { int run; if (vc.isMixed()) { 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 index 4651782ef..7f5033adf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java @@ -3,12 +3,11 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.Arrays; @@ -22,7 +21,7 @@ import java.util.Map; */ public class LowMQ extends InfoFieldAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java index 07fbfc3d2..b6f24433e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.samples.Sample; import org.broadinstitute.sting.gatk.samples.SampleDB; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +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.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; @@ -32,7 +32,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment private String fatherId; private String childId; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( mendelianViolation == null ) { if (checkAndSetSamples(((Walker) walker).getSampleDB())) { mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).minGenotypeQualityP ); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java index 780206f30..372d5bc9e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java @@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; @@ -24,7 +24,7 @@ import java.util.Map; */ public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; 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 index c12923be5..b5252f15b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java @@ -28,7 +28,7 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; @@ -47,7 +47,7 @@ import java.util.List; */ public class MappingQualityZeroBySample extends GenotypeAnnotation { public void annotate(RefMetaDataTracker tracker, - AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext context, + AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext context, VariantContext vc, Genotype g, GenotypeBuilder gb) { if ( g == null || !g.isCalled() ) return; 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 index e8490959c..9f542e3bd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java @@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker; +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.codecs.vcf.VCFHeaderLineType; @@ -22,7 +22,7 @@ import java.util.Map; */ public class MappingQualityZeroFraction extends InfoFieldAnnotation implements ExperimentalAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; 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 index 8f0bc876a..ba4303b4a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java @@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -20,7 +20,7 @@ import java.util.Map; * The number of N bases, counting only SOLiD data */ public class NBaseCount extends InfoFieldAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index 5da6492a6..b62cd374b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -4,7 +4,7 @@ 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.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -28,7 +28,7 @@ import java.util.Map; */ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( !vc.hasLog10PError() || stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index fb5767b34..842fde8ad 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -4,7 +4,7 @@ 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.annotator.interfaces.ActiveRegionBasedAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.MathUtils; @@ -29,7 +29,7 @@ import java.util.Map; */ public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index 1955c87b8..bf6adcfac 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -4,9 +4,8 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.utils.MannWhitneyU; import org.broadinstitute.sting.utils.QualityUtils; @@ -32,7 +31,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR static final double INDEL_LIKELIHOOD_THRESH = 0.1; static final boolean DEBUG = false; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if (stratifiedContexts.size() == 0) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java index cbf536e4f..7e4d44cf2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java @@ -28,7 +28,7 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -46,7 +46,7 @@ import java.util.Map; */ public class SampleList extends InfoFieldAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( vc.isMonomorphicInSamples() || !vc.hasGenotypes() ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java index 6c860fce6..4d990e738 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.sting.utils.Utils; @@ -203,7 +203,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio } } - public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set headerLines ) { + public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set headerLines ) { // Make sure that we actually have a valid SnpEff rod binding (just in case the user specified -A SnpEff // without providing a SnpEff rod via --snpEffFile): validateRodBinding(walker.getSnpEffRodBinding()); @@ -225,7 +225,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_COMMAND_LINE_KEY, snpEffCommandLine.getValue())); } - public Map annotate ( RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc ) { + public Map annotate ( RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc ) { RodBinding snpEffRodBinding = walker.getSnpEffRodBinding(); // Get only SnpEff records that start at this locus, not merely span it: diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java index d7529c8ef..af2df8e6a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java @@ -3,7 +3,7 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; @@ -22,7 +22,7 @@ import java.util.Map; */ public class SpanningDeletions extends InfoFieldAnnotation implements StandardAnnotation { - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java index c4d6ea474..eced387b3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java @@ -27,10 +27,9 @@ 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.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; @@ -48,7 +47,7 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa private static final String STR_PRESENT = "STR"; private static final String REPEAT_UNIT_KEY = "RU"; private static final String REPEATS_PER_ALLELE_KEY = "RPA"; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( !vc.isIndel()) return null; 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 index f4feb9aa8..63694d809 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java @@ -4,7 +4,7 @@ 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.AnnotatorCompatibleWalker; +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.codecs.vcf.VCFHeaderLineType; @@ -28,7 +28,7 @@ public class TechnologyComposition extends InfoFieldAnnotation implements Experi private String n454 ="Num454"; private String nSolid = "NumSOLiD"; private String nOther = "NumOther"; - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( stratifiedContexts.size() == 0 ) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java index 1f8ccf652..2e3578dcb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java @@ -4,7 +4,7 @@ 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.samples.Sample; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +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.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; @@ -28,7 +28,7 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen private Set trios = null; private final static int MIN_NUM_VALID_TRIOS = 5; // don't calculate this population-level statistic if there are less than X trios with full genotype likelihood information - public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { + public Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc) { if ( trios == null ) { if ( walker instanceof VariantAnnotator ) { trios = ((VariantAnnotator) walker).getSampleDB().getChildrenWithParents(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 8f7f46c20..d6d2beb91 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -38,8 +38,8 @@ import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.util.*; @@ -79,7 +79,7 @@ import java.util.*; @Allows(value={DataSource.READS, DataSource.REFERENCE}) @Reference(window=@Window(start=-50,stop=50)) @By(DataSource.REFERENCE) -public class VariantAnnotator extends RodWalker implements AnnotatorCompatibleWalker { +public class VariantAnnotator extends RodWalker implements AnnotatorCompatible { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 46212c19c..073faf54e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -46,7 +46,7 @@ public class VariantAnnotatorEngine { private List requestedExpressions = new ArrayList(); private final HashMap, String> dbAnnotations = new HashMap, String>(); - private final AnnotatorCompatibleWalker walker; + private final AnnotatorCompatible walker; private final GenomeAnalysisEngine toolkit; private boolean requireStrictAlleleMatch = false; @@ -75,7 +75,7 @@ public class VariantAnnotatorEngine { } // use this constructor if you want all possible annotations - public VariantAnnotatorEngine(List annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) { + public VariantAnnotatorEngine(List annotationsToExclude, AnnotatorCompatible walker, GenomeAnalysisEngine toolkit) { this.walker = walker; this.toolkit = toolkit; requestedInfoAnnotations = AnnotationInterfaceManager.createAllInfoFieldAnnotations(); @@ -85,7 +85,7 @@ public class VariantAnnotatorEngine { } // use this constructor if you want to select specific annotations (and/or interfaces) - public VariantAnnotatorEngine(List annotationGroupsToUse, List annotationsToUse, List annotationsToExclude, AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit) { + public VariantAnnotatorEngine(List annotationGroupsToUse, List annotationsToUse, List annotationsToExclude, AnnotatorCompatible walker, GenomeAnalysisEngine toolkit) { this.walker = walker; this.toolkit = toolkit; initializeAnnotations(annotationGroupsToUse, annotationsToUse, annotationsToExclude); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java similarity index 93% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java index 1331ad5df..f610a2ba8 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatibleWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java @@ -5,7 +5,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.List; -public interface AnnotatorCompatibleWalker { +public interface AnnotatorCompatible { // getter methods for various used bindings public abstract RodBinding getSnpEffRodBinding(); 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 index c44c834de..bc20f6c97 100755 --- 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 @@ -9,12 +9,11 @@ import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import java.util.List; -import java.util.Map; public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation { // return annotations for the given contexts/genotype split by sample - public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, + public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, GenotypeBuilder gb ); 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 index b94bee31b..1569a605f 100755 --- 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 @@ -11,7 +11,7 @@ import java.util.Map; public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation { // return annotations for the given contexts split by sample - public abstract Map annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, + public abstract Map annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, Map stratifiedContexts, VariantContext vc); // return the descriptions used for the VCF INFO meta field diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java index 521f89016..996d85a67 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java @@ -37,5 +37,5 @@ public abstract class VariantAnnotatorAnnotation { public abstract List getKeyNames(); // initialization method (optional for subclasses, and therefore non-abstract) - public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set headerLines ) { } + 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/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index 31006f4d8..627d561f6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -31,13 +31,13 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; +import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.util.*; @@ -72,7 +72,7 @@ import static java.lang.Math.log10;

Note that Beagle produces some of these files compressed as .gz, so gunzip must be run on them before walker is run in order to decompress them

*/ -public class BeagleOutputToVCFWalker extends RodWalker { +public class BeagleOutputToVCF extends RodWalker { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java index a8e280f43..14e92a066 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java @@ -37,10 +37,13 @@ import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibratio import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFFilterHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.PrintStream; @@ -72,7 +75,7 @@ import java.util.*; * */ -public class ProduceBeagleInputWalker extends RodWalker { +public class ProduceBeagleInput extends RodWalker { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java index d6b19b377..6d83a1d2a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java @@ -38,12 +38,12 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.PrintStream; import java.util.Arrays; @@ -54,7 +54,7 @@ import java.util.Set; * in input variant file. Will additional 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 */ -public class VariantsToBeagleUnphasedWalker extends RodWalker { +public class VariantsToBeagleUnphased extends RodWalker { @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true) public RodBinding variants; @@ -104,7 +104,7 @@ public class VariantsToBeagleUnphasedWalker extends RodWalker GenomeLoc loc = context.getLocation(); VariantContext vc = tracker.getFirstValue(variants, loc); - if ( ProduceBeagleInputWalker.canBeOutputToBeagle(vc) ) { + if ( ProduceBeagleInput.canBeOutputToBeagle(vc) ) { // do we want to hold back this site? boolean makeMissing = dropSite(vc); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java index 8210a11b7..1a03ce1ce 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java @@ -47,7 +47,7 @@ import java.io.File; import java.io.FileNotFoundException; import java.io.PrintStream; import java.lang.reflect.Constructor; -import java.util.*; +import java.util.ArrayList; /** * First pass of the base quality score recalibration -- Generates recalibration table based on various user-specified covariates (such as reported quality score, cycle, and dinucleotide). @@ -106,7 +106,7 @@ import java.util.*; @Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES}) // filter out all reads with zero or unavailable mapping quality @PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta -public class BaseQualityScoreRecalibrator extends LocusWalker implements TreeReducible { +public class BQSR extends LocusWalker implements TreeReducible { @ArgumentCollection private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java index 34d99c018..55c04f1b7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java @@ -105,6 +105,6 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP * @return the covariate keysets for this read */ protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) { - return (ReadCovariates) read.getTemporaryAttribute(BaseQualityScoreRecalibrator.COVARS_ATTRIBUTE); + return (ReadCovariates) read.getTemporaryAttribute(BQSR.COVARS_ATTRIBUTE); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java index 2a8940de0..bc791a5a4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java @@ -120,7 +120,7 @@ import java.io.PrintStream; * @since May 7, 2010 */ @By(DataSource.REFERENCE) -public class CallableLociWalker extends LocusWalker { +public class CallableLoci extends LocusWalker { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java similarity index 74% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java index cd5fdc505..64a51f1b3 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java @@ -41,7 +41,7 @@ import java.util.List; /** * Test routine for new VariantContext object */ -public class CompareCallableLociWalker extends RodWalker, long[][]> { +public class CompareCallableLoci extends RodWalker, long[][]> { @Output protected PrintStream out; @@ -54,8 +54,8 @@ public class CompareCallableLociWalker extends RodWalker map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { + public List map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { if ( tracker != null ) { - CallableLociWalker.CallableBaseState comp1 = getCallableBaseState(tracker, compTrack1); - CallableLociWalker.CallableBaseState comp2 = getCallableBaseState(tracker, compTrack2); + CallableLoci.CallableBaseState comp1 = getCallableBaseState(tracker, compTrack1); + CallableLoci.CallableBaseState comp2 = getCallableBaseState(tracker, compTrack2); if ( printState != null && comp1.getState() == printState1 && comp2.getState() == printState2 ) { out.printf("%s %s %s %s%n", comp1.getLocation(), comp1.getState(), comp2.getLocation(), comp2.getState()); @@ -92,7 +92,7 @@ public class CompareCallableLociWalker extends RodWalker rodBinding) { + private CallableLoci.CallableBaseState getCallableBaseState(RefMetaDataTracker tracker, RodBinding rodBinding) { //System.out.printf("tracker %s%n", tracker); List bindings = tracker.getValues(rodBinding); if ( bindings.size() != 1 ) { @@ -101,8 +101,8 @@ public class CompareCallableLociWalker extends RodWalker comps, long[][] sum) { + public long[][] reduce(List comps, long[][] sum) { if ( comps != null ) { - CallableLociWalker.CallableBaseState comp1 = comps.get(0); - CallableLociWalker.CallableBaseState comp2 = comps.get(1); + CallableLoci.CallableBaseState comp1 = comps.get(0); + CallableLoci.CallableBaseState comp2 = comps.get(1); sum[comp1.getState().ordinal()][comp2.getState().ordinal()]++; } @@ -127,8 +127,8 @@ public class CompareCallableLociWalker extends RodWalker>, CoveragePartitioner> implements TreeReducible { +public class DepthOfCoverage extends LocusWalker>, CoveragePartitioner> implements TreeReducible { @Output @Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"}) Map out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java index 124be2eb4..77d3aa897 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java @@ -63,7 +63,7 @@ import java.util.List; @Allows(value = {DataSource.REFERENCE}) @Requires(value = {DataSource.REFERENCE}) @By(DataSource.REFERENCE) -public class GCContentByIntervalWalker extends LocusWalker { +public class GCContentByInterval extends LocusWalker { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index ac60f5f28..8c4cab877 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -33,7 +33,6 @@ 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.ActiveRegion; import java.io.PrintStream; @@ -56,7 +55,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker { } @Override - public GenomeLoc map(final ActiveRegion activeRegion, final RefMetaDataTracker tracker) { + public GenomeLoc map(final org.broadinstitute.sting.utils.activeregion.ActiveRegion activeRegion, final RefMetaDataTracker tracker) { if (activeRegion.isActive) return activeRegion.getLocation(); else diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java index 2b7a5612b..a04c4f01b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java @@ -131,7 +131,7 @@ import java.util.List; * @author Mark DePristo * @since 7/4/11 */ -public class DiffObjectsWalker extends RodWalker { +public class DiffObjects extends RodWalker { /** * Writes out a file of the DiffEngine format: * diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java index 4e2c17bf6..0d390308e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java @@ -73,7 +73,7 @@ import java.util.List; @WalkerName("FastaAlternateReferenceMaker") @Reference(window=@Window(start=-1,stop=50)) @Requires(value={DataSource.REFERENCE}) -public class FastaAlternateReferenceWalker extends FastaReferenceWalker { +public class FastaAlternateReference extends FastaReference { /** * Variants from these input files are used by this tool to construct an alternate reference. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java index 7ae5c5c75..f1eb6d028 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java @@ -67,7 +67,7 @@ import java.io.PrintStream; * */ @WalkerName("FastaReferenceMaker") -public class FastaReferenceWalker extends RefWalker, GenomeLoc> { +public class FastaReference extends RefWalker, GenomeLoc> { @Output PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java similarity index 87% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java index f5c5f909f..8a1af623e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStatsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java @@ -37,10 +37,10 @@ import java.io.PrintStream; /** * Calculates basic statistics about the reference sequence itself */ -public class FastaStatsWalker extends RefWalker { +public class FastaStats extends RefWalker { @Output PrintStream out; - protected class FastaStats { + protected class FastaStatistics { long nBases = 0, nRegBases = 0; } @@ -50,19 +50,19 @@ public class FastaStatsWalker extends RefWalker { +public class VariantFiltration extends RodWalker { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index d504badab..10c8c0d69 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -35,16 +35,16 @@ import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; -import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.PrintStream; import java.util.*; @@ -121,7 +121,7 @@ import java.util.*; // TODO -- When LocusIteratorByState gets cleaned up, we should enable multiple @By sources: // TODO -- @By( {DataSource.READS, DataSource.REFERENCE_ORDERED_DATA} ) @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250) -public class UnifiedGenotyper extends LocusWalker, UnifiedGenotyper.UGStatistics> implements TreeReducible, AnnotatorCompatibleWalker { +public class UnifiedGenotyper extends LocusWalker, UnifiedGenotyper.UGStatistics> implements TreeReducible, AnnotatorCompatible { @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index 504359f3f..ef0909c2f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -25,7 +25,6 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.*; import org.apache.commons.jexl2.Expression; import org.apache.commons.jexl2.JexlContext; import org.apache.commons.jexl2.JexlEngine; @@ -53,7 +52,6 @@ import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec; import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature; import org.broadinstitute.sting.utils.codecs.refseq.Transcript; import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.collections.CircularArray; import org.broadinstitute.sting.utils.collections.PrimitivePair; import org.broadinstitute.sting.utils.exceptions.StingException; @@ -64,6 +62,7 @@ import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.*; import java.util.*; @@ -127,7 +126,7 @@ import java.util.*; */ @ReadFilters({Platform454Filter.class, MappingQualityZeroFilter.class, PlatformUnitFilter.class}) -public class SomaticIndelDetectorWalker extends ReadWalker { +public class SomaticIndelDetector extends ReadWalker { // @Output // PrintStream out; @Output(doc="File to write variants (indels) in VCF format",required=true) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java index 4bf24cf86..630d99ce9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java @@ -113,7 +113,7 @@ class PhasingUtils { Map mergedGtAttribs = new HashMap(); PhaseAndQuality phaseQual = calcPhaseForMergedGenotypes(gt1, gt2); if (phaseQual.PQ != null) - mergedGtAttribs.put(ReadBackedPhasingWalker.PQ_KEY, phaseQual.PQ); + mergedGtAttribs.put(ReadBackedPhasing.PQ_KEY, phaseQual.PQ); Genotype mergedGt = new GenotypeBuilder(gt1.getSampleName(), mergedAllelesForSample).log10PError(mergedGQ).attributes(mergedGtAttribs).phased(phaseQual.isPhased).make(); mergedGenotypes.add(mergedGt); @@ -373,7 +373,7 @@ class PhasingUtils { public PhaseAndQuality(Genotype gt) { this.isPhased = gt.isPhased(); if (this.isPhased) { - this.PQ = gt.getAttributeAsDouble(ReadBackedPhasingWalker.PQ_KEY, -1); + this.PQ = gt.getAttributeAsDouble(ReadBackedPhasing.PQ_KEY, -1); if ( this.PQ == -1 ) this.PQ = null; } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index 261c51bcc..154c8c789 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -91,7 +91,7 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr // Filter out all reads with zero mapping quality @ReadFilters({MappingQualityZeroFilter.class}) -public class ReadBackedPhasingWalker extends RodWalker { +public class ReadBackedPhasing extends RodWalker { private static final boolean DEBUG = false; /** * The VCF file we are phasing variants from. @@ -255,7 +255,7 @@ public class ReadBackedPhasingWalker extends RodWalker { +public class CountBases extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { return read.getReadLength(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java index 09113704a..11cf0fe39 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java @@ -37,7 +37,7 @@ import java.io.PrintStream; * * */ -public class CountLociWalker extends LocusWalker implements TreeReducible { +public class CountLoci extends LocusWalker implements TreeReducible { @Output(doc="Write count to this file instead of STDOUT") PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java index dbbd8e761..0856fcda0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMalesWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java @@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * --read-filter command line argument). Simplest example of a read-backed analysis. */ @Requires({DataSource.READS, DataSource.REFERENCE}) -public class CountMalesWalker extends ReadWalker { +public class CountMales extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { Sample sample = getSampleDB().getSample(read); return sample.getGender() == Gender.MALE ? 1 : 0; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java index edbd5ff75..67ecea1f0 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java @@ -70,7 +70,7 @@ import java.util.*; * * */ -public class CountRODsWalker extends RodWalker, Long>> implements TreeReducible, Long>> { +public class CountRODs extends RodWalker, Long>> implements TreeReducible, Long>> { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java similarity index 90% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java index 7c7d6417a..f71362c40 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRefWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java @@ -63,7 +63,7 @@ import java.util.List; * * */ -public class CountRODsByRefWalker extends RefWalker, Long>> { +public class CountRODsByRef extends RefWalker, Long>> { /** * One or more input rod files @@ -77,14 +77,14 @@ public class CountRODsByRefWalker extends RefWalker, Long> reduce(CountRODsWalker.Datum point, Pair, Long> sum) { + public Pair, Long> reduce(CountRODs.Datum point, Pair, Long> sum) { return crw.reduce(point, sum); } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java index c5ab0426d..d0c917650 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEventsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java @@ -42,7 +42,7 @@ import java.util.Map; @Requires({DataSource.READS, DataSource.REFERENCE}) -public class CountReadEventsWalker extends ReadWalker> , Map>> { +public class CountReadEvents extends ReadWalker> , Map>> { @Output (doc = "GATKReport table output") PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java index b5a2d183f..c9108054e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java @@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; * */ @Requires({DataSource.READS, DataSource.REFERENCE}) -public class CountReadsWalker extends ReadWalker { +public class CountReads extends ReadWalker { public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { return 1; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java index 9208cbae8..1fff50800 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEventWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java @@ -37,7 +37,7 @@ import java.util.List; * */ @Requires({DataSource.READS, DataSource.REFERENCE}) -public class CountTerminusEventWalker extends ReadWalker, Pair> { +public class CountTerminusEvent extends ReadWalker, Pair> { public Pair map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker tracker) { List cigarElements = read.getCigar().getCigarElements(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java index 1cb1579d0..86d8458de 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQuality.java @@ -56,7 +56,7 @@ import java.util.*; * --read-filter command line argument). Simplest example of a read-backed analysis. */ @Requires({DataSource.READS}) -public class CycleQualityWalker extends ReadWalker { +public class CycleQuality extends ReadWalker { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java index 6f0490fd3..500f27980 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java @@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException; /** * a walker that simply throws errors. Allows us to test that the engine is behaving as expected with error handling */ -public class ErrorThrowingWalker extends RodWalker implements TreeReducible { +public class ErrorThrowing extends RodWalker implements TreeReducible { @Input(fullName="exception", shortName = "E", doc="Java class of exception to throw", required=true) public String exceptionToThrow; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java similarity index 90% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java index ab5324e39..814f1c8c2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java @@ -26,24 +26,15 @@ package org.broadinstitute.sting.gatk.walkers.qc; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.ReferenceSequence; -import net.sf.samtools.SAMSequenceRecord; -import org.broad.tribble.Feature; -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.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.BaseUtils; -import org.broadinstitute.sting.utils.collections.ExpandingArrayList; -import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.StingException; import java.io.PrintStream; -import java.util.Collections; -import java.util.List; /** * Prints out counts of the number of reference ordered data objects encountered. @@ -67,7 +58,7 @@ import java.util.List; * * */ -public class QCRefWalker extends RefWalker { +public class QCRef extends RefWalker { @Output public PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java index 27f9d7b6d..92030a7d9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java @@ -52,7 +52,7 @@ import java.util.Arrays; * of the clipping to the output stream. */ @Requires({DataSource.READS}) -public class ReadClippingStatsWalker extends ReadWalker { +public class ReadClippingStats extends ReadWalker { @Output protected PrintStream out; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java index 4425f92c4..5f062c861 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidation.java @@ -44,7 +44,7 @@ import java.util.List; * the same read is not passed to the walker multiple consecutive times. * @author aaron */ -public class ReadValidationWalker extends ReadWalker { +public class ReadValidation extends ReadWalker { // our MD5 sum private MessageDigest m; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java index c9602cd6f..3a9add950 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java @@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; @@ -51,7 +50,7 @@ import java.util.List; * a walker for validating (in the style of validating pile-up) the ROD system. */ @Reference(window=@Window(start=-40,stop=40)) -public class RodSystemValidationWalker extends RodWalker { +public class RodSystemValidation extends RodWalker { // the divider to use in some of the text output private static final String DIVIDER = ","; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java index cd17e4592..f249df475 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java @@ -32,9 +32,12 @@ import org.broadinstitute.sting.commandline.RodBinding; 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.codecs.sampileup.SAMPileupFeature; -import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -48,7 +51,7 @@ import java.util.Arrays; * should be specified using the command-line argument '-B pileup,SAMPileup,'. */ @Requires(value={DataSource.READS,DataSource.REFERENCE}) -public class ValidatingPileupWalker extends LocusWalker implements TreeReducible { +public class ValidatingPileup extends LocusWalker implements TreeReducible { @Input(fullName = "pileup", doc="The SAMPileup containing the expected output", required = true) RodBinding pileup; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java index 2e3fc26f6..3d008de43 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java @@ -38,10 +38,10 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.util.Map; import java.util.Set; @@ -195,7 +195,7 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel; @Reference(window=@Window(start=-200,stop=200)) -public class GenotypeAndValidateWalker extends RodWalker implements TreeReducible { +public class GenotypeAndValidate extends RodWalker implements TreeReducible { /** * The optional output file that will have all the variants used in the Genotype and Validation essay. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java index 78fe37fa3..cdcac2300 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -30,10 +30,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import java.io.File; import java.util.*; @@ -94,7 +96,7 @@ import java.util.*; * * */ -public class ValidationSiteSelectorWalker extends RodWalker { +public class ValidationSiteSelector extends RodWalker { public enum AF_COMPUTATION_MODE { KEEP_AF_SPECTRUM, diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index b9e768274..cdf7b19c6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -1,6 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; -import com.google.java.contract.Requires; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.util.IntervalTree; import net.sf.samtools.SAMSequenceRecord; @@ -88,7 +87,7 @@ import java.util.*; */ @Reference(window=@Window(start=-50, stop=50)) @PartitionBy(PartitionType.NONE) -public class VariantEvalWalker extends RodWalker implements TreeReducible { +public class VariantEval extends RodWalker implements TreeReducible { public static final String IS_SINGLETON_KEY = "ISSINGLETON"; @Output 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 index ff3bf66f7..97a8b4dda 100755 --- 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 @@ -4,7 +4,7 @@ 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.samples.Sample; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +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; @@ -104,7 +104,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator { MendelianViolation mv; Map> families; - public void initialize(VariantEvalWalker walker) { + public void initialize(VariantEval walker) { super.initialize(walker); mv = new MendelianViolation(walker.getMendelianViolationQualThreshold(),false); families = walker.getSampleDB().getFamilies(); 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 index df4c3e860..c08ff379b 100755 --- 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 @@ -3,23 +3,23 @@ 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.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.variantcontext.VariantContext; public abstract class VariantEvaluator implements Comparable { - private VariantEvalWalker walker; + private VariantEval walker; private final String simpleName; protected VariantEvaluator() { this.simpleName = getClass().getSimpleName(); } - public void initialize(VariantEvalWalker walker) { + public void initialize(VariantEval walker) { this.walker = walker; } - public VariantEvalWalker getWalker() { + public VariantEval getWalker() { return walker; } @@ -57,7 +57,7 @@ public abstract class VariantEvaluator implements Comparable { * @return true if eval was originally a singleton site */ protected static boolean variantWasSingleton(final VariantContext eval) { - return eval.getAttributeAsBoolean(VariantEvalWalker.IS_SINGLETON_KEY, false); + return eval.getAttributeAsBoolean(VariantEval.IS_SINGLETON_KEY, false); } public final String getSimpleName() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java index 014381bea..71ea6af98 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java @@ -29,7 +29,7 @@ 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.VariantEvalWalker; +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.GenomeLoc; @@ -150,7 +150,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval { } - public void initialize(VariantEvalWalker walker) { + public void initialize(VariantEval walker) { super.initialize(walker); nSamples = walker.getSampleNamesForEvaluation().size(); 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 index 07ba424a2..90b6230ca 100755 --- 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 @@ -2,7 +2,7 @@ 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.VariantEvalWalker; +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.sting.utils.variantcontext.VariantContext; @@ -13,7 +13,7 @@ import java.util.List; import java.util.Set; public abstract class VariantStratifier implements Comparable, Stratifier { - private VariantEvalWalker variantEvalWalker; + private VariantEval variantEvalWalker; final private String name; final protected ArrayList states = new ArrayList(); @@ -40,7 +40,7 @@ public abstract class VariantStratifier implements Comparable /** * @return a reference to the parent VariantEvalWalker running this stratification */ - public final VariantEvalWalker getVariantEvalWalker() { + public final VariantEval getVariantEvalWalker() { return variantEvalWalker; } @@ -48,7 +48,7 @@ public abstract class VariantStratifier implements Comparable * Should only be called by VariantEvalWalker itself * @param variantEvalWalker */ - public final void setVariantEvalWalker(VariantEvalWalker variantEvalWalker) { + public final void setVariantEvalWalker(VariantEval variantEvalWalker) { this.variantEvalWalker = variantEvalWalker; } 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 index 390682837..c98c05a9a 100755 --- 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 @@ -3,27 +3,27 @@ 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.VariantEvalWalker; +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.VariantStratifier; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import java.util.*; +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 VariantEvalWalker walker; + final VariantEval walker; private final ArrayList evaluationInstances; private final Set> evaluationClasses; - public EvaluationContext(final VariantEvalWalker walker, final Set> evaluationClasses) { + public EvaluationContext(final VariantEval walker, final Set> evaluationClasses) { this(walker, evaluationClasses, true); } - private EvaluationContext(final VariantEvalWalker walker, final Set> evaluationClasses, final boolean doInitialize) { + private EvaluationContext(final VariantEval walker, final Set> evaluationClasses, final boolean doInitialize) { this.walker = walker; this.evaluationClasses = evaluationClasses; this.evaluationInstances = new ArrayList(evaluationClasses.size()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index 3b28747fb..3dcc1f85f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -28,7 +28,7 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker; +import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.StandardEval; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.RequiredStratification; @@ -45,10 +45,10 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.util.*; public class VariantEvalUtils { - private final VariantEvalWalker variantEvalWalker; + private final VariantEval variantEvalWalker; Logger logger; - public VariantEvalUtils(VariantEvalWalker variantEvalWalker) { + public VariantEvalUtils(VariantEval variantEvalWalker) { this.variantEvalWalker = variantEvalWalker; this.logger = variantEvalWalker.getLogger(); } @@ -216,7 +216,7 @@ public class VariantEvalUtils { VariantContextBuilder builder = new VariantContextBuilder(vcsub); if ( isSingleton ) - builder.attribute(VariantEvalWalker.IS_SINGLETON_KEY, true); + builder.attribute(VariantEval.IS_SINGLETON_KEY, true); if ( ! hasChrCountAnnotations ) VariantContextUtils.calculateChromosomeCounts(builder, true); @@ -270,7 +270,7 @@ public class VariantEvalUtils { } if ((byFilter || !vcsub.isFiltered())) { - addMapping(mapping, VariantEvalWalker.getAllSampleName(), vcsub); + addMapping(mapping, VariantEval.getAllSampleName(), vcsub); } // Now, if stratifying, split the subsetted vc per sample and add each as a new context diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java index cd645943b..b4e07716c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * 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 @@ -25,11 +25,17 @@ package org.broadinstitute.sting.utils.help; public class GATKDocUtils { - /** The URL root for RELEASED GATKDOC units */ + /** + * The URL root for RELEASED GATKDOC units + */ public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/"; - /** The URL root for STABLE GATKDOC units */ + /** + * The URL root for STABLE GATKDOC units + */ public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/"; - /** The URL root for UNSTABLE GATKDOC units */ + /** + * The URL root for UNSTABLE GATKDOC units + */ public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/"; /** @@ -49,6 +55,7 @@ public class GATKDocUtils { /** * Returns a full URL http://etc/ linking to the documentation for class (assuming it * exists). Currently points to the RELEASE doc path only. + * * @param c * @return */ diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java index 41c855329..0ff5ddc6a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocWorkUnit.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * 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 @@ -25,41 +25,63 @@ package org.broadinstitute.sting.utils.help; import com.sun.javadoc.ClassDoc; +import org.broadinstitute.sting.gatk.Category; import java.util.HashMap; +import java.util.List; import java.util.Map; /** * Simple collection of all relevant information about something the GATKDoclet can document - * + *

* Created by IntelliJ IDEA. * User: depristo * Date: 7/24/11 * Time: 7:59 PM */ class GATKDocWorkUnit implements Comparable { - /** The class that's being documented */ + /** + * The class that's being documented + */ final Class clazz; - /** The name of the thing we are documenting */ + /** + * The name of the thing we are documenting + */ final String name; - /** the filename where we will be writing the docs for this class */ + /** + * the filename where we will be writing the docs for this class + */ final String filename; - /** The name of the documentation group (e.g., walkers, read filters) class belongs to */ + /** + * The name of the documentation group (e.g., walkers, read filters) class belongs to + */ final String group; - /** The documentation handler for this class */ + /** + * The categories that this class belongs to + */ + final List categories; + /** + * The documentation handler for this class + */ final DocumentedGATKFeatureHandler handler; - /** The javadoc documentation for clazz */ + /** + * The javadoc documentation for clazz + */ final ClassDoc classDoc; - /** The annotation that lead to this Class being in GATKDoc */ + /** + * The annotation that lead to this Class being in GATKDoc + */ final DocumentedGATKFeatureObject annotation; - /** When was this walker built, and what's the absolute version number */ + /** + * When was this walker built, and what's the absolute version number + */ final String buildTimestamp, absoluteVersion; // set by the handler String summary; Map forTemplate; - public GATKDocWorkUnit(String name, String filename, String group, + public GATKDocWorkUnit(String name, String filename, String group, List categories, DocumentedGATKFeatureObject annotation, DocumentedGATKFeatureHandler handler, ClassDoc classDoc, Class clazz, String buildTimestamp, String absoluteVersion) { @@ -67,6 +89,7 @@ class GATKDocWorkUnit implements Comparable { this.name = name; this.filename = filename; this.group = group; + this.categories = categories; this.handler = handler; this.classDoc = classDoc; this.clazz = clazz; @@ -76,6 +99,7 @@ class GATKDocWorkUnit implements Comparable { /** * Called by the GATKDoclet to set handler provided context for this work unit + * * @param summary * @param forTemplate */ @@ -86,6 +110,7 @@ class GATKDocWorkUnit implements Comparable { /** * Return a String -> String map suitable for FreeMarker to create an index to this WorkUnit + * * @return */ public Map indexDataMap() { @@ -99,6 +124,7 @@ class GATKDocWorkUnit implements Comparable { /** * Sort in order of the name of this WorkUnit + * * @param other * @return */ diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java index 7f26f22f5..f40675a43 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * 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 @@ -24,6 +24,7 @@ package org.broadinstitute.sting.utils.help; +import com.google.gson.Gson; import com.sun.javadoc.ClassDoc; import com.sun.javadoc.RootDoc; import freemarker.template.Configuration; @@ -34,41 +35,51 @@ import org.apache.commons.io.FileUtils; import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.broad.tribble.FeatureCodec; +import org.broadinstitute.sting.gatk.Categorize; +import org.broadinstitute.sting.gatk.Category; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.walkers.qc.DocumentationTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.*; +import java.lang.annotation.Annotation; +import java.net.HttpURLConnection; +import java.net.MalformedURLException; +import java.net.URL; import java.util.*; /** * Javadoc Doclet that combines javadoc, GATK ParsingEngine annotations, and FreeMarker * templates to produce html formatted GATKDocs for walkers * and other classes. - * + *

* This document has the following workflow: - * + *

* 1 -- walk the javadoc heirarchy, looking for class that have the - * DocumentedGATKFeature annotation or are in the type heirarchy in the - * static list of things to document, and are to be documented + * DocumentedGATKFeature annotation or are in the type heirarchy in the + * static list of things to document, and are to be documented * 2 -- construct for each a GATKDocWorkUnit, resulting in the complete - * set of things to document + * set of things to document * 3 -- for each unit, actually generate an html page documenting it - * as well as links to related features via their units. Writing - * of a specific class HTML is accomplished by a generate DocumentationHandler + * as well as links to related features via their units. Writing + * of a specific class HTML is accomplished by a generate DocumentationHandler * 4 -- write out an index of all units, organized by group - * + *

* The documented classes are restricted to only those with @DocumentedGATKFeature * annotation or are in the STATIC_DOCS class. */ public class GATKDoclet { final protected static Logger logger = Logger.getLogger(GATKDoclet.class); - /** Where we find the help FreeMarker templates */ + /** + * Where we find the help FreeMarker templates + */ final protected static File SETTINGS_DIR = new File("settings/helpTemplates"); - /** Where we write the GATKDoc html directory */ + /** + * Where we write the GATKDoc html directory + */ final protected static File DESTINATION_DIR = new File("gatkdocs"); // ---------------------------------------------------------------------- @@ -88,10 +99,14 @@ public class GATKDoclet { private static final List> testOnlyKeepers = Arrays.asList( DocumentationTest.class, CommandLineGATK.class, UserException.class); - /** The javadoc root doc */ + /** + * The javadoc root doc + */ RootDoc rootDoc; - /** The set of all things we are going to document */ + /** + * The set of all things we are going to document + */ Set myWorkUnits; /** @@ -103,6 +118,7 @@ public class GATKDoclet { * codecs). */ final static Collection STATIC_DOCS = new ArrayList(); + static { STATIC_DOCS.add(new DocumentedGATKFeatureObject(FeatureCodec.class, "Reference ordered data (ROD) codecs", @@ -112,6 +128,7 @@ public class GATKDoclet { /** * Extracts the contents of certain types of javadoc and adds them to an XML file. + * * @param rootDoc The documentation root. * @return Whether the JavaDoc run succeeded. * @throws java.io.IOException if output can't be written. @@ -120,8 +137,8 @@ public class GATKDoclet { logger.setLevel(Level.INFO); // load arguments - for(String[] options: rootDoc.options()) { - if(options[0].equals("-build-timestamp")) + for (String[] options : rootDoc.options()) { + if (options[0].equals("-build-timestamp")) buildTimestamp = options[1]; if (options[0].equals("-absolute-version")) absoluteVersion = options[1]; @@ -139,15 +156,16 @@ public class GATKDoclet { /** * Validate the given options against options supported by this doclet. + * * @param option Option to validate. * @return Number of potential parameters; 0 if not supported. */ public static int optionLength(String option) { - if(option.equals("-build-timestamp") || + if (option.equals("-build-timestamp") || option.equals("-absolute-version") || option.equals("-include-hidden")) { return 2; - } else if ( option.equals("-test") ) + } else if (option.equals("-test")) return 1; else return 0; @@ -155,6 +173,7 @@ public class GATKDoclet { /** * Are we supposed to include @Hidden annotations in our documented output? + * * @return */ public boolean showHiddenFeatures() { @@ -162,7 +181,6 @@ public class GATKDoclet { } /** - * * @param rootDoc */ private void processDocs(RootDoc rootDoc) { @@ -172,7 +190,11 @@ public class GATKDoclet { try { // basic setup DESTINATION_DIR.mkdirs(); - FileUtils.copyFile(new File(SETTINGS_DIR + "/style.css"), new File(DESTINATION_DIR + "/style.css")); + FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.css"), new File(DESTINATION_DIR + "/bootstrap.min.css")); + FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.js"), new File(DESTINATION_DIR + "/bootstrap.min.js")); + FileUtils.copyFile(new File(SETTINGS_DIR + "/jquery.min.js"), new File(DESTINATION_DIR + "/jquery.min.js")); + // print the Version number + FileUtils.writeByteArrayToFile(new File(DESTINATION_DIR + "/current.version.txt"), getSimpleVersion(absoluteVersion).getBytes()); /* ------------------------------------------------------------------- */ /* You should do this ONLY ONCE in the whole application life-cycle: */ @@ -184,31 +206,109 @@ public class GATKDoclet { cfg.setObjectWrapper(new DefaultObjectWrapper()); myWorkUnits = computeWorkUnits(); - for ( GATKDocWorkUnit workUnit : myWorkUnits ) { - processDocWorkUnit(cfg, workUnit); + + Map>> catNav = getCategories(new ArrayList(myWorkUnits)); + + processCategories(catNav, myWorkUnits); + + for (GATKDocWorkUnit workUnit : myWorkUnits) { + processDocWorkUnit(cfg, workUnit, catNav); } processIndex(cfg, new ArrayList(myWorkUnits)); - } catch ( FileNotFoundException e ) { + } catch (FileNotFoundException e) { throw new RuntimeException(e); - } catch ( IOException e ) { + } catch (IOException e) { throw new RuntimeException(e); } } + private void processCategories(Map>> getCategories, Set classes) throws IOException { + List categories = new LinkedList(); + for (Category cat : getCategories.keySet()) { + Map properties = new HashMap(); + properties.put("Name", cat.getDescription()); + properties.put("UrlSlug", cat.name().toLowerCase().replace('_', '-')); + categories.add(properties); + } + writeJson(DESTINATION_DIR + "/categories.json", categories); + + List posts = new LinkedList(); + for (GATKDocWorkUnit unit : classes) { + Map properties = new HashMap(); + properties.put("Post Title", unit.name + " Documentation"); + properties.put("Categories", unit.categories); + List tags = new ArrayList(); + tags.add(unit.name); + tags.add(unit.group); + properties.put("Tags", tags); + String body = String.format("%s

%s

", + GATKDocUtils.URL_ROOT_FOR_RELEASE_GATKDOCS + unit.filename, unit.name + " Documentation", unit.summary); + properties.put("Body", body); + posts.add(properties); + } + + writeJson(DESTINATION_DIR + "/posts.json", posts); + } + + private void writeJson(String filename, Object source) throws IOException { + Gson gson = new Gson(); + BufferedWriter out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(new File(filename))), 1024 * 1024); + + out.write(gson.toJson(source)); + + out.close(); + + } + + public static void postRestJson(String URL, String json) { + try { + URL url = new URL(URL); + HttpURLConnection conn = (HttpURLConnection) url.openConnection(); + conn.setDoOutput(true); + conn.setRequestMethod("POST"); + conn.setRequestProperty("Content-Type", "application/json"); + + OutputStream os = conn.getOutputStream(); + os.write(json.getBytes()); + os.flush(); + + if (conn.getResponseCode() != HttpURLConnection.HTTP_CREATED) { + throw new RuntimeException("Failed : HTTP error code : " + + conn.getResponseCode()); + } + + BufferedReader br = new BufferedReader(new InputStreamReader( + (conn.getInputStream()))); + + String output; + System.out.println("Output from Server .... \n"); + while ((output = br.readLine()) != null) { + System.out.println(output); + } + + conn.disconnect(); + } catch (MalformedURLException e) { + e.printStackTrace(); + } catch (IOException e) { + e.printStackTrace(); + } + } + /** * Returns the set of all GATKDocWorkUnits that we are going to generate docs for. + * * @return */ private Set computeWorkUnits() { TreeSet m = new TreeSet(); - for ( ClassDoc doc : rootDoc.classes() ) { + for (ClassDoc doc : rootDoc.classes()) { //logger.debug("Considering " + doc); Class clazz = getClassForClassDoc(doc); // don't add anything that's not DocumentationTest if we are in test mode - if ( clazz != null && testOnly && ! testOnlyKeepers.contains(clazz) ) + if (clazz != null && testOnly && !testOnlyKeepers.contains(clazz)) continue; //if ( clazz != null && clazz.getName().equals("org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance")) @@ -216,11 +316,12 @@ public class GATKDoclet { DocumentedGATKFeatureObject feature = getFeatureForClassDoc(doc); DocumentedGATKFeatureHandler handler = createHandler(doc, feature); - if ( handler != null && handler.includeInDocs(doc) ) { + if (handler != null && handler.includeInDocs(doc)) { logger.info("Generating documentation for class " + doc); String filename = handler.getDestinationFilename(doc, clazz); + Category[] categories = getClassAnnotationValue(clazz, Categorize.class, "value"); GATKDocWorkUnit unit = new GATKDocWorkUnit(doc.name(), - filename, feature.groupName(), + filename, feature.groupName(), (categories == null) ? new ArrayList() : Arrays.asList(categories), feature, handler, doc, clazz, buildTimestamp, absoluteVersion); m.add(unit); @@ -233,13 +334,14 @@ public class GATKDoclet { /** * Create a handler capable of documenting the class doc according to feature. Returns * null if no appropriate handler is found or doc shouldn't be documented at all. + * * @param doc * @param feature * @return */ private DocumentedGATKFeatureHandler createHandler(ClassDoc doc, DocumentedGATKFeatureObject feature) { - if ( feature != null ) { - if ( feature.enable() ) { + if (feature != null) { + if (feature.enable()) { DocumentedGATKFeatureHandler handler = new GenericDocumentationHandler(); handler.setDoclet(this); return handler; @@ -261,15 +363,15 @@ public class GATKDoclet { private DocumentedGATKFeatureObject getFeatureForClassDoc(ClassDoc doc) { Class docClass = getClassForClassDoc(doc); - if ( docClass == null ) + if (docClass == null) return null; // not annotated so it shouldn't be documented - if ( docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) { + if (docClass.isAnnotationPresent(DocumentedGATKFeature.class)) { DocumentedGATKFeature f = docClass.getAnnotation(DocumentedGATKFeature.class); return new DocumentedGATKFeatureObject(docClass, f.enable(), f.groupName(), f.summary(), f.extraDocs()); } else { - for ( DocumentedGATKFeatureObject staticDocs : STATIC_DOCS ) { - if ( staticDocs.getClassToDoc().isAssignableFrom(docClass) ) { + for (DocumentedGATKFeatureObject staticDocs : STATIC_DOCS) { + if (staticDocs.getClassToDoc().isAssignableFrom(docClass)) { return new DocumentedGATKFeatureObject(docClass, staticDocs.enable(), staticDocs.groupName(), staticDocs.summary(), staticDocs.extraDocs()); } } @@ -279,26 +381,28 @@ public class GATKDoclet { /** * Return the Java class described by the ClassDoc doc + * * @param doc * @return */ private Class getClassForClassDoc(ClassDoc doc) { try { // todo -- what do I need the ? extends Object to pass the compiler? - return (Class)HelpUtils.getClassForDoc(doc); - } catch ( ClassNotFoundException e) { + return (Class) HelpUtils.getClassForDoc(doc); + } catch (ClassNotFoundException e) { //logger.warn("Couldn't find class for ClassDoc " + doc); // we got a classdoc for a class we can't find. Maybe in a library or something return null; - } catch ( NoClassDefFoundError e ) { + } catch (NoClassDefFoundError e) { return null; - } catch ( UnsatisfiedLinkError e) { + } catch (UnsatisfiedLinkError e) { return null; // naughty BWA bindings } } /** * Create the html index listing all of the GATKDocs features + * * @param cfg * @param indexData * @throws IOException @@ -312,7 +416,7 @@ public class GATKDoclet { try { temp.process(groupIndexData(indexData), out); out.flush(); - } catch ( TemplateException e ) { + } catch (TemplateException e) { throw new ReviewedStingException("Failed to create GATK documentation", e); } } @@ -320,6 +424,7 @@ public class GATKDoclet { /** * Helpful function to create the html index. Given all of the already run GATKDocWorkUnits, * create the high-level grouping data listing individual features by group. + * * @param indexData * @return */ @@ -334,9 +439,9 @@ public class GATKDoclet { List> groups = new ArrayList>(); Set seenDocumentationFeatures = new HashSet(); List> data = new ArrayList>(); - for ( GATKDocWorkUnit workUnit : indexData ) { + for (GATKDocWorkUnit workUnit : indexData) { data.add(workUnit.indexDataMap()); - if ( ! seenDocumentationFeatures.contains(workUnit.annotation.groupName()) ) { + if (!seenDocumentationFeatures.contains(workUnit.annotation.groupName())) { groups.add(toMap(workUnit.annotation)); seenDocumentationFeatures.add(workUnit.annotation.groupName()); } @@ -347,16 +452,20 @@ public class GATKDoclet { root.put("timestamp", buildTimestamp); root.put("version", absoluteVersion); + root.put("categories", getCategories(indexData)); + return root; } /** * Trivial helper routine that returns the map of name and summary given the annotation + * * @param annotation * @return */ private static final Map toMap(DocumentedGATKFeatureObject annotation) { Map root = new HashMap(); + root.put("id", annotation.groupName().replaceAll("\\W", "")); root.put("name", annotation.groupName()); root.put("summary", annotation.summary()); return root; @@ -364,18 +473,20 @@ public class GATKDoclet { /** * Helper function that finding the GATKDocWorkUnit associated with class from among all of the work units + * * @param c the class we are looking for * @return the GATKDocWorkUnit whose .clazz.equals(c), or null if none could be found */ public final GATKDocWorkUnit findWorkUnitForClass(Class c) { - for ( final GATKDocWorkUnit unit : this.myWorkUnits ) - if ( unit.clazz.equals(c) ) + for (final GATKDocWorkUnit unit : this.myWorkUnits) + if (unit.clazz.equals(c)) return unit; return null; } /** * Return the ClassDoc associated with clazz + * * @param clazz * @return */ @@ -390,12 +501,12 @@ public class GATKDoclet { * @param unit * @throws IOException */ - private void processDocWorkUnit(Configuration cfg, GATKDocWorkUnit unit) + private void processDocWorkUnit(Configuration cfg, GATKDocWorkUnit unit, Map>> categories) throws IOException { //System.out.printf("Processing documentation for class %s%n", unit.classDoc); unit.handler.processOne(unit); - + unit.forTemplate.put("catNav", categories); // Get or create a template Template temp = cfg.getTemplate(unit.handler.getTemplateName(unit.classDoc)); @@ -405,8 +516,59 @@ public class GATKDoclet { Writer out = new OutputStreamWriter(new FileOutputStream(outputPath)); temp.process(unit.forTemplate, out); out.flush(); - } catch ( TemplateException e ) { + } catch (TemplateException e) { throw new ReviewedStingException("Failed to create GATK documentation", e); } } -} + + // hack - todo - is there a better way to process annotations? + private Category[] getClassAnnotationValue(Class classType, Class annotationType, String attributeName) { + Category[] value = null; + + Annotation annotation = classType.getAnnotation(annotationType); + if (annotation != null) { + try { + value = (Category[]) annotation.annotationType().getMethod(attributeName).invoke(annotation); + } catch (Exception ex) { + } + } + + return value; + } + + private Map>> getCategories(List classes) { + Map>> output = new TreeMap>>(); + + for (Category cat : Category.values()) { + output.put(cat, new ArrayList>()); + } + + for (GATKDocWorkUnit unit : classes) { + Category[] categories = getClassAnnotationValue(unit.clazz, Categorize.class, "value"); + + if (categories != null) { + for (Category cat : categories) { + unit.handler.processOne(unit); + + Map datum = unit.indexDataMap(); + + output.get(cat).add(datum); + } + } + } + + return output; + } + + private static String getSimpleVersion(String absoluteVersion) { + String[] parts = absoluteVersion.split("-"); + + // by skipping i=0, there is no trailing separator + for (int i = 1; i < 2; i++) { + parts[0] = parts[0].concat("-"); + parts[0] = parts[0].concat(parts[i]); + } + + return parts[0]; + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java index 20f9eccd3..71c82053f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java @@ -1,5 +1,5 @@ /* - * Copyright (c) 2011, The Broad Institute + * 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 @@ -28,14 +28,11 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import com.sun.javadoc.ClassDoc; import com.sun.javadoc.FieldDoc; -import com.sun.javadoc.RootDoc; import com.sun.javadoc.Tag; import org.apache.log4j.Logger; import org.broad.tribble.Feature; -import org.broad.tribble.bed.FullBEDFeature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.classloader.JVMUtils; @@ -43,7 +40,7 @@ import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; -import java.io.*; +import java.io.IOException; import java.lang.reflect.*; import java.util.*; @@ -59,16 +56,18 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { */ private static final int MAX_DISPLAY_NAME = 30; - /** The Class we are documenting */ + /** + * The Class we are documenting + */ private GATKDocWorkUnit toProcess; @Override public boolean includeInDocs(ClassDoc doc) { try { Class type = HelpUtils.getClassForDoc(doc); - boolean hidden = ! getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class); - return ! hidden && JVMUtils.isConcrete(type); - } catch ( ClassNotFoundException e ) { + boolean hidden = !getDoclet().showHiddenFeatures() && type.isAnnotationPresent(Hidden.class); + return !hidden && JVMUtils.isConcrete(type); + } catch (ClassNotFoundException e) { return false; } } @@ -90,7 +89,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { addArgumentBindings(root); addRelatedBindings(root); - toProcess.setHandlerContent((String)root.get("summary"), root); + toProcess.setHandlerContent((String) root.get("summary"), root); } /** @@ -104,34 +103,37 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { // Extract overrides from the doc tags. StringBuilder summaryBuilder = new StringBuilder(); - for(Tag tag: toProcess.classDoc.firstSentenceTags()) + for (Tag tag : toProcess.classDoc.firstSentenceTags()) summaryBuilder.append(tag.text()); root.put("summary", summaryBuilder.toString()); root.put("description", toProcess.classDoc.commentText().substring(summaryBuilder.toString().length())); root.put("timestamp", toProcess.buildTimestamp); root.put("version", toProcess.absoluteVersion); + root.put("categories", toProcess.categories); - for(Tag tag: toProcess.classDoc.tags()) { + for (Tag tag : toProcess.classDoc.tags()) { root.put(tag.name(), tag.text()); } } /** * Add bindings describing related GATK capabilites to toProcess + * * @param root */ protected void addRelatedBindings(Map root) { List> extraDocsData = new ArrayList>(); // add in all of the explicitly related items - for ( final Class extraDocClass : toProcess.annotation.extraDocs() ) { + for (final Class extraDocClass : toProcess.annotation.extraDocs()) { final GATKDocWorkUnit otherUnit = getDoclet().findWorkUnitForClass(extraDocClass); - if ( otherUnit == null ) + if (otherUnit == null) throw new ReviewedStingException("Requested extraDocs for class without any documentation: " + extraDocClass); extraDocsData.add( - new HashMap(){{ + new HashMap() {{ put("filename", otherUnit.filename); - put("name", otherUnit.name);}}); + put("name", otherUnit.name); + }}); } root.put("extradocs", extraDocsData); @@ -149,16 +151,16 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { root.put("arguments", args); try { // loop over all of the arguments according to the parsing engine - for ( final ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(toProcess.classDoc)) ) { + for (final ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(toProcess.classDoc))) { // todo -- why can you have multiple ones? ArgumentDefinition argDef = argumentSource.createArgumentDefinitions().get(0); FieldDoc fieldDoc = getFieldDoc(toProcess.classDoc, argumentSource.field.getName()); Map argBindings = docForArgument(fieldDoc, argumentSource, argDef); - if ( ! argumentSource.isHidden() || getDoclet().showHiddenFeatures() ) { + if (!argumentSource.isHidden() || getDoclet().showHiddenFeatures()) { final String kind = docKindOfArg(argumentSource); final Object value = argumentValue(toProcess.clazz, argumentSource); - if ( value != null ) + if (value != null) argBindings.put("defaultValue", prettyPrintValueString(value)); args.get(kind).add(argBindings); @@ -167,31 +169,33 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { } // sort the arguments - for (Map.Entry>> entry : args.entrySet()) { + for (Map.Entry>> entry : args.entrySet()) { entry.setValue(sortArguments(entry.getValue())); } - } catch ( ClassNotFoundException e ) { + } catch (ClassNotFoundException e) { throw new RuntimeException(e); } } /** * Return the argument kind (required, advanced, hidden, etc) of this argumentSource + * * @param argumentSource * @return */ @Requires("argumentSource != null") @Ensures("result != null") private String docKindOfArg(ArgumentSource argumentSource) { - if ( argumentSource.isRequired() ) return "required"; - else if ( argumentSource.isAdvanced() ) return "advanced"; - else if ( argumentSource.isHidden() ) return "hidden"; - else if ( argumentSource.isDeprecated() ) return "depreciated"; + if (argumentSource.isRequired()) return "required"; + else if (argumentSource.isAdvanced()) return "advanced"; + else if (argumentSource.isHidden()) return "hidden"; + else if (argumentSource.isDeprecated()) return "depreciated"; else return "optional"; } /** * Attempts to determine the value of argumentSource in an instantiated version of c + * * @param c * @param argumentSource * @return value of argumentSource, or null if this isn't possible @@ -201,12 +205,12 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { // get the value of the field // attempt to instantiate the class final Object instance = makeInstanceIfPossible(toProcess.clazz); - if ( instance != null ) { + if (instance != null) { final Object value = getFieldValue(instance, argumentSource.field.getName()); - if ( value != null ) + if (value != null) return value; - if ( argumentSource.createsTypeDefault() ) { + if (argumentSource.createsTypeDefault()) { try { // handle the case where there's an implicit default return argumentSource.typeDefaultDocString(); } catch (ReviewedStingException e) { @@ -220,6 +224,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Create the argument map for holding class arguments + * * @return */ private Map>> createArgumentMap() { @@ -236,6 +241,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Sorts the individual argument list in unsorted according to CompareArgumentsByName + * * @param unsorted * @return */ @@ -254,9 +260,9 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { private String elt(Map m) { String v = m.get("name").toString().toLowerCase(); - if ( v.startsWith("--") ) + if (v.startsWith("--")) return v.substring(2); - else if ( v.startsWith("-") ) + else if (v.startsWith("-")) return v.substring(1); else throw new RuntimeException("Expect to see arguments beginning with at least one -, but found " + v); @@ -267,7 +273,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * Utility function that finds the value of fieldName in any fields of ArgumentCollection fields in * instance of class c. * - * @param instance the object to query for the field value + * @param instance the object to query for the field value * @param fieldName the name of the field we are looking for in instance * @return The value assigned to field in the ArgumentCollection, otherwise null */ @@ -280,14 +286,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { // @ArgumentCollection // protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection(); // - for ( Field field : JVMUtils.getAllFields(instance.getClass()) ) { - if ( field.isAnnotationPresent(ArgumentCollection.class) ) { + for (Field field : JVMUtils.getAllFields(instance.getClass())) { + if (field.isAnnotationPresent(ArgumentCollection.class)) { //System.out.printf("Searching for %s in argument collection field %s%n", fieldName, field); Object fieldValue = JVMUtils.getFieldValue(field, instance); Object value = getFieldValue(fieldValue, fieldName); - if ( value != null ) + if (value != null) return value; - } else if ( field.getName().equals(fieldName) ) { + } else if (field.getName().equals(fieldName)) { return JVMUtils.getFieldValue(field, instance); } } @@ -297,38 +303,39 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Pretty prints value - * + *

* Assumes value != null + * * @param value * @return */ private Object prettyPrintValueString(Object value) { - if ( value.getClass().isArray() ) { + if (value.getClass().isArray()) { Class type = value.getClass().getComponentType(); - if ( boolean.class.isAssignableFrom(type) ) - return Arrays.toString((boolean[])value); - if ( byte.class.isAssignableFrom(type) ) - return Arrays.toString((byte[])value); - if ( char.class.isAssignableFrom(type) ) - return Arrays.toString((char[])value); - if ( double.class.isAssignableFrom(type) ) - return Arrays.toString((double[])value); - if ( float.class.isAssignableFrom(type) ) - return Arrays.toString((float[])value); - if ( int.class.isAssignableFrom(type) ) - return Arrays.toString((int[])value); - if ( long.class.isAssignableFrom(type) ) - return Arrays.toString((long[])value); - if ( short.class.isAssignableFrom(type) ) - return Arrays.toString((short[])value); - if ( Object.class.isAssignableFrom(type) ) - return Arrays.toString((Object[])value); + if (boolean.class.isAssignableFrom(type)) + return Arrays.toString((boolean[]) value); + if (byte.class.isAssignableFrom(type)) + return Arrays.toString((byte[]) value); + if (char.class.isAssignableFrom(type)) + return Arrays.toString((char[]) value); + if (double.class.isAssignableFrom(type)) + return Arrays.toString((double[]) value); + if (float.class.isAssignableFrom(type)) + return Arrays.toString((float[]) value); + if (int.class.isAssignableFrom(type)) + return Arrays.toString((int[]) value); + if (long.class.isAssignableFrom(type)) + return Arrays.toString((long[]) value); + if (short.class.isAssignableFrom(type)) + return Arrays.toString((short[]) value); + if (Object.class.isAssignableFrom(type)) + return Arrays.toString((Object[]) value); else throw new RuntimeException("Unexpected array type in prettyPrintValue. Value was " + value + " type is " + type); - } else if ( RodBinding.class.isAssignableFrom(value.getClass() ) ) { + } else if (RodBinding.class.isAssignableFrom(value.getClass())) { // annoying special case to handle the UnBound() constructor return "none"; - } else if ( value instanceof String ) { + } else if (value instanceof String) { return value.equals("") ? "\"\"" : value; } else { return value.toString(); @@ -337,6 +344,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Attempt to instantiate class c, if possible. Returns null if this proves impossible. + * * @param c * @return */ @@ -344,21 +352,22 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { Object instance = null; try { // don't try to make something where we will obviously fail - if (! c.isEnum() && ! c.isAnnotation() && ! c.isAnonymousClass() && - ! c.isArray() && ! c.isPrimitive() & JVMUtils.isConcrete(c) ) { + if (!c.isEnum() && !c.isAnnotation() && !c.isAnonymousClass() && + !c.isArray() && !c.isPrimitive() & JVMUtils.isConcrete(c)) { instance = c.newInstance(); //System.out.printf("Created object of class %s => %s%n", c, instance); return instance; } else return null; + } catch (IllegalAccessException e) { + } catch (InstantiationException e) { + } catch (ExceptionInInitializerError e) { + } catch (SecurityException e) { } - catch (IllegalAccessException e ) { } - catch (InstantiationException e ) { } - catch (ExceptionInInitializerError e ) { } - catch (SecurityException e ) { } // this last one is super dangerous, but some of these methods catch ClassNotFoundExceptions // and rethrow then as RuntimeExceptions - catch (RuntimeException e) {} + catch (RuntimeException e) { + } return instance; } @@ -366,6 +375,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Create an instance of the GATK parsing engine, for argument processing with GATKDoclet + * * @return */ private ParsingEngine createStandardGATKParsingEngine() { @@ -392,6 +402,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Recursive helper routine to getFieldDoc() + * * @param classDoc * @param name * @param primary @@ -399,21 +410,21 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { */ private FieldDoc getFieldDoc(ClassDoc classDoc, String name, boolean primary) { //System.out.printf("Looking for %s in %s%n", name, classDoc.name()); - for ( FieldDoc fieldDoc : classDoc.fields(false) ) { + for (FieldDoc fieldDoc : classDoc.fields(false)) { //System.out.printf("fieldDoc " + fieldDoc + " name " + fieldDoc.name()); - if ( fieldDoc.name().equals(name) ) + if (fieldDoc.name().equals(name)) return fieldDoc; Field field = HelpUtils.getFieldForFieldDoc(fieldDoc); - if ( field == null ) + if (field == null) throw new RuntimeException("Could not find the field corresponding to " + fieldDoc + ", presumably because the field is inaccessible"); - if ( field.isAnnotationPresent(ArgumentCollection.class) ) { + if (field.isAnnotationPresent(ArgumentCollection.class)) { ClassDoc typeDoc = getRootDoc().classNamed(fieldDoc.type().qualifiedTypeName()); - if ( typeDoc == null ) + if (typeDoc == null) throw new ReviewedStingException("Tried to get javadocs for ArgumentCollection field " + fieldDoc + " but could't find the class in the RootDoc"); else { FieldDoc result = getFieldDoc(typeDoc, name, false); - if ( result != null ) + if (result != null) return result; // else keep searching } @@ -421,11 +432,11 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { } // if we didn't find it here, wander up to the superclass to find the field - if ( classDoc.superclass() != null ) { + if (classDoc.superclass() != null) { return getFieldDoc(classDoc.superclass(), name, false); } - if ( primary ) + if (primary) throw new RuntimeException("No field found for expected field " + name); else return null; @@ -439,20 +450,20 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * @param s1 the short argument name without -, or null if not provided * @param s2 the long argument name without --, or null if not provided * @return A pair of fully qualified names (with - or --) for the argument. The first - * element is the primary display name while the second (potentially null) is a - * synonymous name. + * element is the primary display name while the second (potentially null) is a + * synonymous name. */ Pair displayNames(String s1, String s2) { s1 = s1 == null ? null : "-" + s1; s2 = s2 == null ? null : "--" + s2; - if ( s1 == null ) return new Pair(s2, null); - if ( s2 == null ) return new Pair(s1, null); + if (s1 == null) return new Pair(s2, null); + if (s2 == null) return new Pair(s1, null); String l = s1.length() > s2.length() ? s1 : s2; String s = s1.length() > s2.length() ? s2 : s1; - if ( l.length() > MAX_DISPLAY_NAME ) + if (l.length() > MAX_DISPLAY_NAME) return new Pair(s, l); else return new Pair(l, s); @@ -460,7 +471,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Returns a human readable string that describes the Type type of a GATK argument. - * + *

* This will include parameterized types, so that Set{T} shows up as Set(T) and not * just Set in the docs. * @@ -469,13 +480,13 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { */ protected String argumentTypeString(Type type) { if (type instanceof ParameterizedType) { - ParameterizedType parameterizedType = (ParameterizedType)type; + ParameterizedType parameterizedType = (ParameterizedType) type; List subs = new ArrayList(); - for (Type actualType: parameterizedType.getActualTypeArguments()) + for (Type actualType : parameterizedType.getActualTypeArguments()) subs.add(argumentTypeString(actualType)); - return argumentTypeString(((ParameterizedType)type).getRawType()) + "[" + Utils.join(",", subs) + "]"; + return argumentTypeString(((ParameterizedType) type).getRawType()) + "[" + Utils.join(",", subs) + "]"; } else if (type instanceof GenericArrayType) { - return argumentTypeString(((GenericArrayType)type).getGenericComponentType()) + "[]"; + return argumentTypeString(((GenericArrayType) type).getGenericComponentType()) + "[]"; } else if (type instanceof WildcardType) { throw new RuntimeException("We don't support wildcards in arguments: " + type); } else if (type instanceof Class) { @@ -489,18 +500,19 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { * Helper routine that returns the Feature.class required by a RodBinding, * either T for RodBinding{T} or List{RodBinding{T}}. Returns null if * the Type doesn't fit either model. + * * @param type * @return */ protected Class getFeatureTypeIfPossible(Type type) { - if ( type instanceof ParameterizedType) { - ParameterizedType paramType = (ParameterizedType)type; - if ( RodBinding.class.isAssignableFrom((Class)paramType.getRawType()) ) { - return (Class)JVMUtils.getParameterizedTypeClass(type); + if (type instanceof ParameterizedType) { + ParameterizedType paramType = (ParameterizedType) type; + if (RodBinding.class.isAssignableFrom((Class) paramType.getRawType())) { + return (Class) JVMUtils.getParameterizedTypeClass(type); } else { - for ( Type paramtype : paramType.getActualTypeArguments() ) { + for (Type paramtype : paramType.getActualTypeArguments()) { Class x = getFeatureTypeIfPossible(paramtype); - if ( x != null ) + if (x != null) return x; } } @@ -512,6 +524,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * High-level entry point for creating a FreeMarker map describing the GATK argument * source with definition def, with associated javadoc fieldDoc. + * * @param fieldDoc * @param source * @param def @@ -521,9 +534,9 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { Map root = new HashMap(); Pair names = displayNames(def.shortName, def.fullName); - root.put("name", names.getFirst() ); + root.put("name", names.getFirst()); - if ( names.getSecond() != null ) + if (names.getSecond() != null) root.put("synonyms", names.getSecond()); root.put("required", def.required ? "yes" : "no"); @@ -532,11 +545,11 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { root.put("type", argumentTypeString(source.field.getGenericType())); Class featureClass = getFeatureTypeIfPossible(source.field.getGenericType()); - if ( featureClass != null ) { + if (featureClass != null) { // deal with the allowable types FeatureManager manager = new FeatureManager(); List rodTypes = new ArrayList(); - for (FeatureManager.FeatureDescriptor descriptor : manager.getByFeature(featureClass) ) { + for (FeatureManager.FeatureDescriptor descriptor : manager.getByFeature(featureClass)) { rodTypes.add(String.format("%s", GATKDocUtils.htmlFilenameForClass(descriptor.getCodecClass()), descriptor.getName())); @@ -550,14 +563,14 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { root.put("fulltext", fieldDoc.commentText()); // What are our enum options? - if ( def.validOptions != null ) + if (def.validOptions != null) root.put("options", docForEnumArgument(source.field.getType())); // general attributes List attributes = new ArrayList(); - if ( def.required ) attributes.add("required"); - if ( source.isDeprecated() ) attributes.add("depreciated"); - if ( attributes.size() > 0 ) + if (def.required) attributes.add("required"); + if (source.isDeprecated()) attributes.add("depreciated"); + if (attributes.size() > 0) root.put("attributes", Utils.join(", ", attributes)); return root; @@ -566,21 +579,23 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { /** * Helper routine that provides a FreeMarker map for an enumClass, grabbing the * values of the enum and their associated javadoc documentation. + * * @param enumClass * @return */ @Requires("enumClass.isEnum()") private List> docForEnumArgument(Class enumClass) { ClassDoc doc = this.getDoclet().getClassDocForClass(enumClass); - if ( doc == null ) // || ! doc.isEnum() ) + if (doc == null) // || ! doc.isEnum() ) throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got instead: " + doc); List> bindings = new ArrayList>(); - for (final FieldDoc field : doc.fields(false) ) { + for (final FieldDoc field : doc.fields(false)) { bindings.add( - new HashMap(){{ + new HashMap() {{ put("name", field.name()); - put("summary", field.commentText());}}); + put("summary", field.commentText()); + }}); } return bindings; diff --git a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java index 2f8b1e9b5..d8905ad35 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java @@ -28,7 +28,7 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.ArgumentException; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; -import org.broadinstitute.sting.gatk.walkers.PrintReadsWalker; +import org.broadinstitute.sting.gatk.walkers.PrintReads; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.testng.annotations.Test; @@ -71,7 +71,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest { public void testEmptyIntervalSetHandling() throws Exception { GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine(); - testEngine.setWalker(new PrintReadsWalker()); + testEngine.setWalker(new PrintReads()); testEngine.setIntervals(new GenomeLocSortedSet(null)); testEngine.validateSuppliedIntervals(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java index 6149a1e51..38be6d2a8 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java @@ -24,13 +24,12 @@ package org.broadinstitute.sting.gatk; -import org.testng.Assert; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker; +import org.broadinstitute.sting.gatk.walkers.qc.CountLoci; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.broadinstitute.sting.utils.exceptions.UserException; - +import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -48,7 +47,7 @@ public class WalkerManagerUnitTest { @Test public void testPresentWalker() { Walker countLociWalker = walkerManager.createByName("CountLoci"); - Assert.assertEquals(CountLociWalker.class,countLociWalker.getClass()); + Assert.assertEquals(CountLoci.class,countLociWalker.getClass()); } @Test(expectedExceptions=UserException.class) diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java index 564d1e2a3..66585c872 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java +++ b/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java @@ -35,8 +35,8 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker; -import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker; +import org.broadinstitute.sting.gatk.walkers.qc.CountLoci; +import org.broadinstitute.sting.gatk.walkers.qc.CountReads; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -99,7 +99,7 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark { private enum WalkerType { COUNT_READS { @Override - Walker create() { return new CountReadsWalker(); } + Walker create() { return new CountReads(); } }, COUNT_BASES_IN_READ { @Override @@ -108,8 +108,8 @@ public class GATKWalkerBenchmark extends ReadProcessingBenchmark { COUNT_LOCI { @Override Walker create() { - CountLociWalker walker = new CountLociWalker(); - JVMUtils.setFieldValue(JVMUtils.findField(CountLociWalker.class,"out"),walker,System.out); + CountLoci walker = new CountLoci(); + JVMUtils.setFieldValue(JVMUtils.findField(CountLoci.class,"out"),walker,System.out); return walker; } }; 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 9226f97e2..7845515d8 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java @@ -1,25 +1,22 @@ package org.broadinstitute.sting.gatk.traversals; -import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile; +import net.sf.picard.reference.ReferenceSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; +import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; import org.broadinstitute.sting.gatk.datasources.reads.ReadShardBalancer; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; -import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; +import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; -import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker; import org.broadinstitute.sting.gatk.walkers.Walker; +import org.broadinstitute.sting.gatk.walkers.qc.CountReads; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; - -import static org.testng.Assert.fail; - import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; @@ -31,6 +28,8 @@ import java.io.PrintStream; import java.util.ArrayList; import java.util.List; +import static org.testng.Assert.fail; + /** * * User: aaron @@ -106,7 +105,7 @@ public class TraverseReadsUnitTest extends BaseTest { bamList = new ArrayList(); bamList.add(bam); - countReadWalker = new CountReadsWalker(); + countReadWalker = new CountReads(); traversalEngine = new TraverseReads(); traversalEngine.initialize(engine); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java index 0fcaad3bf..1aaa00aee 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java @@ -59,7 +59,7 @@ public class PrintReadsUnitTest extends BaseTest { private ReferenceContext bases = null; //private ReferenceContext ref = new ReferenceContext() - PrintReadsWalker walker; + PrintReads walker; ArtificialSAMFileWriter writer; @BeforeMethod @@ -67,7 +67,7 @@ public class PrintReadsUnitTest extends BaseTest { trav = new ArtificialReadsTraversal(); readTotal = ( ( trav.endingChr - trav.startingChr ) + 1 ) * trav.readsPerChr + trav.unMappedReads; - walker = new PrintReadsWalker(); + walker = new PrintReads(); writer = new ArtificialSAMFileWriter(); walker.out = writer; walker.initialize(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java index ca06ca699..f6c12f443 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java @@ -49,13 +49,13 @@ import java.util.*; public class VariantEvalWalkerUnitTest extends BaseTest { - VariantEvalWalker VEwalker; + VariantEval VEwalker; VariantContext eval; @BeforeMethod public void init() { - VEwalker = new VariantEvalWalker(); + VEwalker = new VariantEval(); eval = new VariantContextBuilder("x", "chr1", 1, 1, Collections.singleton(Allele.create("A", true))).make(); } diff --git a/public/packages/GATK-Picard.xml b/public/packages/GATK-Picard.xml index 29057d398..251f584f7 100644 --- a/public/packages/GATK-Picard.xml +++ b/public/packages/GATK-Picard.xml @@ -17,12 +17,12 @@ - - - - - - + + + + + + diff --git a/settings/helpTemplates/bootstrap.min.css b/settings/helpTemplates/bootstrap.min.css new file mode 100755 index 000000000..a4b669001 --- /dev/null +++ b/settings/helpTemplates/bootstrap.min.css @@ -0,0 +1,727 @@ +/*! + * Bootstrap v2.0.4 + * + * Copyright 2012 Twitter, Inc + * Licensed under the Apache License v2.0 + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Designed and built with all the love in the world @twitter by @mdo and @fat. + */ +.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";} +.clearfix:after{clear:both;} +.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;} 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.caret{border-top-color:#ffffff;border-bottom-color:#ffffff;opacity:0.75;filter:alpha(opacity=75);} +.nav{margin-left:0;margin-bottom:18px;list-style:none;} +.nav>li>a{display:block;} +.nav>li>a:hover{text-decoration:none;background-color:#eeeeee;} +.nav>.pull-right{float:right;} +.nav .nav-header{display:block;padding:3px 15px;font-size:11px;font-weight:bold;line-height:18px;color:#999999;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);text-transform:uppercase;} +.nav li+.nav-header{margin-top:9px;} +.nav-list{padding-left:15px;padding-right:15px;margin-bottom:0;} +.nav-list>li>a,.nav-list .nav-header{margin-left:-15px;margin-right:-15px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);} +.nav-list>li>a{padding:3px 15px;} +.nav-list>.active>a,.nav-list>.active>a:hover{color:#ffffff;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.2);background-color:#0088cc;} +.nav-list [class^="icon-"]{margin-right:2px;} +.nav-list .divider{*width:100%;height:1px;margin:8px 1px;*margin:-5px 0 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#c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);} +.progress-danger.progress-striped .bar{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 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solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;} +.popover .arrow{position:absolute;width:0;height:0;} +.popover-inner{padding:3px;width:280px;overflow:hidden;background:#000000;background:rgba(0, 0, 0, 0.8);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);} +.popover-title{padding:9px 15px;line-height:1;background-color:#f5f5f5;border-bottom:1px solid #eee;-webkit-border-radius:3px 3px 0 0;-moz-border-radius:3px 3px 0 0;border-radius:3px 3px 0 0;} +.popover-content{padding:14px;background-color:#ffffff;-webkit-border-radius:0 0 3px 3px;-moz-border-radius:0 0 3px 3px;border-radius:0 0 3px 3px;-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;}.popover-content p,.popover-content ul,.popover-content ol{margin-bottom:0;} +.modal-open 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+.pull-left{float:left;} +.hide{display:none;} +.show{display:block;} +.invisible{visibility:hidden;} +.fade{opacity:0;-webkit-transition:opacity 0.15s linear;-moz-transition:opacity 0.15s linear;-ms-transition:opacity 0.15s linear;-o-transition:opacity 0.15s linear;transition:opacity 0.15s linear;}.fade.in{opacity:1;} +.collapse{position:relative;height:0;overflow:hidden;-webkit-transition:height 0.35s ease;-moz-transition:height 0.35s ease;-ms-transition:height 0.35s ease;-o-transition:height 0.35s ease;transition:height 0.35s ease;}.collapse.in{height:auto;} +.hidden{display:none;visibility:hidden;} +.visible-phone{display:none !important;} +.visible-tablet{display:none !important;} +.hidden-desktop{display:none !important;} +@media (max-width:767px){.visible-phone{display:inherit !important;} .hidden-phone{display:none !important;} .hidden-desktop{display:inherit !important;} .visible-desktop{display:none !important;}}@media (min-width:768px) and 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    • '},a.fn.typeahead.Constructor=b,a(function(){a("body").on("focus.typeahead.data-api",'[data-provide="typeahead"]',function(b){var c=a(this);if(c.data("typeahead"))return;b.preventDefault(),c.typeahead(c.data())})})}(window.jQuery) \ No newline at end of file diff --git a/settings/helpTemplates/common.html b/settings/helpTemplates/common.html index 1554a1d40..a753b9ded 100644 --- a/settings/helpTemplates/common.html +++ b/settings/helpTemplates/common.html @@ -1,15 +1,147 @@ -<#macro makeHeader title> - - ${title} - - - + -<#macro headerInfo> - +<#-- + This file contains all the theming neccesary to present GATKDocs on the GATK website + Included are the paths to our bootstrap assets as well as helper functions to generate relevant links -<#macro footerInfo> -

    See also Main index | GATK wiki | GATK support forum

    -

    GATK version ${version} built at ${timestamp}.

    - + --> + <#global siteRoot = "http://gsa-stage:8080/" /> + <#global forum = "http://gatk.vanillaforums.com/" /> + + <#macro makeHeader title isIndex> + + + + + + ${title} documentation + + + + + + + + + + + +
    +
    +
    + GATK Documentation +
    +
    +
    +
    + + +
    + <#if isIndex> +
    + +
    +
    + + + + + <#macro footerInfo> +
    +

    See also Documentation index | GATK Site | GATK support forum

    + +

    GATK version ${version} built at ${timestamp}.

    + + + <#macro pageFooter> +
    +
    + + + + + <#macro getCategories map filter> + + + + \ No newline at end of file diff --git a/settings/helpTemplates/generic.index.template.html b/settings/helpTemplates/generic.index.template.html index 6c9e9f4e8..d092ec5a0 100644 --- a/settings/helpTemplates/generic.index.template.html +++ b/settings/helpTemplates/generic.index.template.html @@ -1,36 +1,50 @@ <#include "common.html"/> <#macro emitGroup group> - -

    ${group.name}

    -

    - ${group.summary} -

    -

    - - - - <#list data as datum> - <#if datum.group == group.name> - - - - - - -
    NameSummary
    ${datum.name}${datum.summary}
    - - -<@makeHeader title="GATK documentation index"/> - -

    GATK documentation index

    - <@headerInfo /> - <#list groups?sort_by("name") as group> +
    +
    +
    +

    + ${group.name}

     +
    +
    +
    +

    ${group.summary} + +

    + <#if group.id == "GATKwalkers"> +

    Categories

    + <@getCategories map=categories filter="GATK walkers" /> + <#else> + + + + + + <#list data as datum> + <#if datum.group == group.name> + + + + + + +
    NameSummary
    ${datum.name}${datum.summary}
    + +
    +
    +
    +
    + + +<@makeHeader title="GATK documentation index" isIndex=true /> +

    GATK documentation index +${version}

    +
    +<#list groups?sort_by("name") as group> <@emitGroup group=group/> - - - <@footerInfo /> - - + +<@footerInfo /> +<@pageFooter /> diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html index 7fc8cd7bd..7d02fa865 100644 --- a/settings/helpTemplates/generic.template.html +++ b/settings/helpTemplates/generic.template.html @@ -1,8 +1,10 @@ <#include "common.html"/> <#macro argumentlist name myargs> - <#if myargs?size != 0> - ${name} + <#if myargs?size != 0> + + ${name} + <#list myargs as arg> ${arg.name} @@ -11,116 +13,145 @@ ${arg.summary} <#-- - ${arg.required} + < + td>${arg.required} --> - - + + <#macro argumentDetails arg> -

    ${arg.name}<#if arg.synonyms??> / ${arg.synonyms} - (<#if arg.attributes??>${arg.attributes} ${arg.type}<#if arg.defaultValue??> with default value ${arg.defaultValue})

    +

    ${arg.name} + <#if arg.synonyms??> / ${arg.synonyms} + + ( + <#if arg.attributes??>${arg.attributes} + ${arg.type} + <#if arg.defaultValue??> with default value ${arg.defaultValue} + ) +

    - ${arg.summary}. ${arg.fulltext} - <#if arg.rodTypes??>${arg.name} binds reference ordered data. This argument supports ROD files of the - following types: ${arg.rodTypes} - <#if arg.options??> -
    - The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values: -

    - <#list arg.options as option> -
    ${option.name}
    -
    ${option.summary}
    - -
    - + ${arg.summary}. ${arg.fulltext} + <#if arg.rodTypes??>${arg.name} binds reference ordered data. This argument supports ROD files of the + following types: ${arg.rodTypes} + + <#if arg.options??> +
    + The ${arg.name} argument is an enumerated type (${arg.type}), which can have one of the following values: +
    + <#list arg.options as option> +
    ${option.name}
    +
    ${option.summary}
    + +
    +

    - - + + <#macro relatedByType name type> <#list relatedDocs as relatedDoc> <#if relatedDoc.relation == type>

    ${name}

      - <#list relatedDocs as relatedDoc> - <#if relatedDoc.relation == type> -
    • ${relatedDoc.name} is a ${relatedDoc.relation}
      • - - + <#list relatedDocs as relatedDoc> + <#if relatedDoc.relation == type> +
    • ${relatedDoc.name} is a ${relatedDoc.relation}
      • + +
    - <#break> + <#break> - -<@makeHeader title="${name} documentation"/> - -

    ${name}

    - <@headerInfo /> -

    ${summary}

    - <#if author??> -

    Author

    - ${author} - -

    Introduction

    - ${description} - - <#-- Create the argument summary --> - <#if arguments.all?size != 0> -
    -

    ${name} specific arguments

    - - - - - - - - - - - <@argumentlist name="Required" myargs=arguments.required/> - <@argumentlist name="Optional" myargs=arguments.optional/> - <@argumentlist name="Advanced" myargs=arguments.advanced/> - <@argumentlist name="Hidden" myargs=arguments.hidden/> - <@argumentlist name="Depreciated" myargs=arguments.depreciated/> - -
    NameTypeDefault valueSummary
    - +<#list categories as cat> + + +<@makeHeader title="${name} documentation" isIndex=false /> +
    + + - <#-- Create references to additional capabilities if appropriate --> - <#if extradocs?size != 0> -
    -

    Additional capabilities

    - The arguments described in the entries below can be supplied to this tool to modify - its behavior. For example, the -L argument directs the GATK engine restricts processing - to specific genomic intervals. This capability is available to all GATK walkers. - - - - <#-- This class is related to other documented classes via sub/super relationships --> - <#if relatedDocs?? && relatedDocs?size != 0> -
    -

    Related capabilities

    - <@relatedByType name="Superclasses" type="superclass"/> - <@relatedByType name="Subclasses" type="subclass"/> - - - <#-- List all of the --> - <#if arguments.all?size != 0> -
    - <#-- Create the argument details --> -

    Argument details

    - <#list arguments.all as arg> - <@argumentDetails arg=arg/> - - - - <@footerInfo /> - - +
    + +
    + +

    ${name}

    + +

    ${summary}

    + <#if author??> +

    Author
    + ${author} +

    + + <#if (categories?size > 0) > +

    Categories

    +
      + <#list categories as cat> +
    • ${cat.getDescription()}
      • + +
    + +

    Introduction

    + ${description} + + <#-- Create the argument summary --> + <#if arguments.all?size != 0> +
    +

    ${name} specific arguments

    + + + + + + + + + + + <@argumentlist name="Required" myargs=arguments.required/> + <@argumentlist name="Optional" myargs=arguments.optional/> + <@argumentlist name="Advanced" myargs=arguments.advanced/> + <@argumentlist name="Hidden" myargs=arguments.hidden/> + <@argumentlist name="Depreciated" myargs=arguments.depreciated/> + +
    NameTypeDefault valueSummary
    + + + <#-- Create references to additional capabilities if appropriate --> + <#if extradocs?size != 0> +
    +

    Additional capabilities

    + The arguments described in the entries below can be supplied to this tool to modify + its behavior. For example, the -L argument directs the GATK engine restricts processing + to specific genomic intervals. This capability is available to all GATK walkers. + + + + <#-- This class is related to other documented classes via sub/super relationships --> + <#if relatedDocs?? && relatedDocs?size != 0> +
    +

    Related capabilities

    + <@relatedByType name="Superclasses" type="superclass"/> + <@relatedByType name="Subclasses" type="subclass"/> + + + <#-- List all of the --> + <#if arguments.all?size != 0> +
    + <#-- Create the argument details --> +

    Argument details

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a=this[0];return a?a.style?parseFloat(f.css(a,c,"padding")):this[c]():null},f.fn["outer"+a]=function(a){var b=this[0];return b?b.style?parseFloat(f.css(b,c,a?"margin":"border")):this[c]():null},f.fn[c]=function(a){return f.access(this,function(a,c,h){var i,j,k,l;if(f.isWindow(a)){i=a.document,j=i.documentElement[d];return f.support.boxModel&&j||i.body&&i.body[d]||j}if(a.nodeType===9){i=a.documentElement;if(i[d]>=i[e])return i[d];return Math.max(a.body[e],i[e],a.body[g],i[g])}if(h===b){k=f.css(a,c),l=parseFloat(k);return f.isNumeric(l)?l:k}f(a).css(c,h)},c,a,arguments.length,null)}}),a.jQuery=a.$=f,typeof define=="function"&&define.amd&&define.amd.jQuery&&define("jquery",[],function(){return f})})(window); \ No newline at end of file From d446d34227e3b3859fe34f4719df00f9ca3539e8 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 20 Jul 2012 17:16:24 -0400 Subject: [PATCH 06/12] GATK Error messages now point to the new website instead of GetSatisfaction. --- .../sting/utils/R/gsalib/man/gsalib-package.Rd | 4 ++-- .../sting/commandline/CommandLineProgram.java | 4 ++-- .../org/broadinstitute/sting/gatk/CommandLineGATK.java | 8 ++++---- .../sting/gatk/walkers/indels/SomaticIndelDetector.java | 1 + .../sting/gatk/walkers/varianteval/VariantEval.java | 1 + .../src/org/broadinstitute/sting/queue/QCommandLine.scala | 3 +-- 6 files changed, 11 insertions(+), 10 deletions(-) diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd index 2b8d6db9f..dc7a08287 100644 --- a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd +++ b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd @@ -19,9 +19,9 @@ Medical and Population Genetics Program Maintainer: Kiran Garimella } \references{ -GSA wiki page: http://www.broadinstitute.org/gsa/wiki +GSA wiki page: http://www.broadinstitute.org/gatk -GATK help forum: http://www.getsatisfaction.com/gsa +GATK help forum: http://www.broadinstitute.org/gatk } \examples{ ## get script arguments in interactive and non-interactive mode diff --git a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java index 976889613..15ec9dfe5 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java +++ b/public/java/src/org/broadinstitute/sting/commandline/CommandLineProgram.java @@ -287,8 +287,8 @@ public abstract class CommandLineProgram { * a function used to indicate an error occurred in the command line tool */ private static void printDocumentationReference() { - errorPrintf("Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki%n"); - errorPrintf("Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa%n"); + errorPrintf("Visit our website and forum for extensive documentation and answers to %n"); + errorPrintf("commonly asked questions http://www.broadinstitute.org/gatk%n"); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java index c0865e656..d8674c606 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -35,9 +35,10 @@ import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.gatk.walkers.Attribution; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.help.*; +import org.broadinstitute.sting.utils.help.ApplicationDetails; +import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; +import org.broadinstitute.sting.utils.help.GATKDocUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import java.util.*; @@ -142,8 +143,7 @@ public class CommandLineGATK extends CommandLineExecutable { List header = new ArrayList(); header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime())); header.add("Copyright (c) 2010 The Broad Institute"); - header.add("Please view our documentation at http://www.broadinstitute.org/gsa/wiki"); - header.add("For support, please view our support site at http://getsatisfaction.com/gsa"); + header.add("For support and documentation go to http://www.broadinstitute.org/gatk"); return header; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index ef0909c2f..21db1412b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -25,6 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.indels; +import net.sf.samtools.*; import org.apache.commons.jexl2.Expression; import org.apache.commons.jexl2.JexlContext; import org.apache.commons.jexl2.JexlEngine; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index cdf7b19c6..1b5474777 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; +import com.google.java.contract.Requires; import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.util.IntervalTree; import net.sf.samtools.SAMSequenceRecord; diff --git a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala index 7a22e700b..041e84a8c 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala @@ -205,8 +205,7 @@ class QCommandLine extends CommandLineProgram with Logging { private def createQueueHeader() : Seq[String] = { Seq(String.format("Queue v%s, Compiled %s", getQueueVersion, getBuildTimestamp), "Copyright (c) 2012 The Broad Institute", - "Please view our documentation at http://www.broadinstitute.org/gsa/wiki", - "For support, please view our support site at http://getsatisfaction.com/gsa") + "Fro support and documentation go to http://www.broadinstitute.org/gatk") } private def getQueueVersion : String = { From 5dc21431420989c0c6ea969467d52e3ac79db08b Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 20 Jul 2012 17:26:28 -0400 Subject: [PATCH 07/12] Removed support for walkers ending with "Walker" from the engine. If your walker has "Walker" in the name, you will have to use "Walker" on the -T to access it. --- .../java/src/org/broadinstitute/sting/gatk/WalkerManager.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java index f053c299c..8843d4bfe 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/WalkerManager.java @@ -49,7 +49,7 @@ public class WalkerManager extends PluginManager { private ResourceBundle helpText; public WalkerManager() { - super(Walker.class,"walker","Walker"); + super(Walker.class,"walker",""); helpText = TextFormattingUtils.loadResourceBundle("StingText"); } From 921eaad33f9979ca52cc59c0a6ac0db435a35b10 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 18 Jul 2012 14:20:48 -0400 Subject: [PATCH 08/12] Generalized the default platform parameter in BQSRv2 Parameter wasn't working outside of the BQSR walker. It now takes the information on the recalibration report in other tools (PrintReads for example) and treats all reads as coming from the defined default platform. --- .../sting/gatk/walkers/bqsr/CycleCovariate.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java index e3b7f2637..f0ff8f2bd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java @@ -49,6 +49,7 @@ public class CycleCovariate implements StandardCovariate { private static final int MAXIMUM_CYCLE_VALUE = 1000; private static final int CUSHION_FOR_INDELS = 4; + private static String default_platform = null; private static final EnumSet DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS); private static final EnumSet FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454, NGSPlatform.ION_TORRENT); @@ -58,13 +59,16 @@ public class CycleCovariate implements StandardCovariate { public void initialize(final RecalibrationArgumentCollection RAC) { if (RAC.DEFAULT_PLATFORM != null && !NGSPlatform.isKnown(RAC.DEFAULT_PLATFORM)) throw new UserException.CommandLineException("The requested default platform (" + RAC.DEFAULT_PLATFORM + ") is not a recognized platform."); + + if (RAC.DEFAULT_PLATFORM != null) + default_platform = RAC.DEFAULT_PLATFORM; } // Used to pick out the covariate's value from attributes of the read @Override public void recordValues(final GATKSAMRecord read, final ReadCovariates values) { final int readLength = read.getReadLength(); - final NGSPlatform ngsPlatform = read.getNGSPlatform(); + final NGSPlatform ngsPlatform = default_platform == null ? read.getNGSPlatform() : NGSPlatform.fromReadGroupPL(default_platform); // Discrete cycle platforms if (DISCRETE_CYCLE_PLATFORMS.contains(ngsPlatform)) { From 65f4b67b868295a321d74e2b060b4ee0e5eb8c43 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 20 Jul 2012 17:50:29 -0400 Subject: [PATCH 09/12] Fixing walker unit test with the new naming convention --- .../org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java index 38be6d2a8..1eb340356 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/WalkerManagerUnitTest.java @@ -57,7 +57,7 @@ public class WalkerManagerUnitTest { @Test(expectedExceptions=DynamicClassResolutionException.class) public void testUninstantiableWalker() { - walkerManager.createByName("Uninstantiable"); + walkerManager.createByName("UninstantiableWalker"); } } From d7bffb002420fbc8f1a6fccdac9b0cfe22b7bf29 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 20 Jul 2012 17:59:26 -0400 Subject: [PATCH 10/12] Final final final version of the license. 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zHn}Oj6FYckZPl^#(#X|i(aU$ATefp#{mlb~Q$Ikv5(7Efltg$S-skr~bwGVUWoZIXF>GkGbzvML!=T5C%Qg!uO`?;qKiv9hq zUs>C$Yd0@wDCzyPIVd8lsP}$FZ|%&=)IIZ#l3VVV9@6G?{{zU!gFigThvC3;4T5~+ z5Jbp>HEC&wiM1AR42#G$4ijzX5DMTgd5p2(W!h@V;}BA%8Vd3O=_QY~87&Tgz$5}w z7ah%%AnD-*K_THdszMYfP+%CUAiY4o*u+$QLc;TNtcz&JEV@|W_!3jXqZwPSe$JzT zKFwl_!J5nE0d@wj zs8&P~aWG~MF)(bd$H2{j z%CwOR6jPuoOpPgV0#l`-s1!aPOE+;R^GNQxOGjj(h$nUf%Me0mA}$Z= zPS^-|I;ALQA#LIiCBJZJC$da#k%?x3x^xLKENz5Bl|c3j2147)*tJHEhQIc8iEvVR zwd3hmieZZm1X54vrO_lNM7mXp(nSe+;#I=ZX2?P%DSiVfi3V4 zVjs{@0;j|pMyUu`mA4&=LXC(t0tb{;tSQw#b`(THWQSu)rMNFar~rxe9*qRN5kP5^R?qsMbuYK zLZNzV6dxV2hQhfm)(D^dVid`zlW07O@a?OHqutvMN7ZWaK5#hr#Xi6>0e<$H1II`} zm%Ya$lxqGE^0EUB?iGXh%pfoue~Qe|BI(FlfOnC V9305PA)!KXK)^#nbhBe6e*@e#?r8u3 From df965d4a5a9b9466240f81dda517a6d5c04cf8f4 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Sat, 21 Jul 2012 10:52:59 -0400 Subject: [PATCH 11/12] Fixing BQSR integration test --- .../sting/gatk/walkers/bqsr/BQSRIntegrationTest.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) 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 dd96dfeb9..635a74399 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 @@ -59,7 +59,7 @@ public class BQSRIntegrationTest extends WalkerTest { @Test(dataProvider = "BQSRTest") public void testBQSR(BQSRTest params) { WalkerTestSpec spec = new WalkerTestSpec( - "-T BaseQualityScoreRecalibrator" + + " -T BQSR" + " -R " + params.reference + " -I " + params.bam + " -L " + params.interval + @@ -74,8 +74,8 @@ public class BQSRIntegrationTest extends WalkerTest { @Test public void testBQSRFailWithoutDBSNP() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + b36KGReference + - " -T BaseQualityScoreRecalibrator" + + " -T BQSR" + + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" + " -L 1:10,000,000-10,200,000" + " --no_plots" + From 39f45127f305456106cdc61eabc623de731f4e91 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Sat, 21 Jul 2012 14:41:38 -0400 Subject: [PATCH 12/12] Fix md5's broken by recent changes to FisherStrand calculation --- .../walkers/genotyper/UnifiedGenotyperIntegrationTest.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 9e960b6ed..f35eb4404 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -36,7 +36,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testWithAllelesPassedIn1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("6f0c49b76225e2099c74015b6f79c96d")); + Arrays.asList("d1e68d4db6585ec00213b1d2d05e01a9")); executeTest("test MultiSample Pilot2 with alleles passed in", spec1); } @@ -44,7 +44,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testWithAllelesPassedIn2() { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("055012eca193a1f12421ea79bef1f4e0")); + Arrays.asList("b53860d209f8440f12b78d01606553e1")); executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); } @@ -341,7 +341,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1, - Arrays.asList("c48c8a1a8ec88c6f3c99187e08496ae0")); + Arrays.asList("d0a66c234056bb83dd84113bc2421f1e")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); }