diff --git a/protected/java/src/org/broadinstitute/sting/gatk/DummyProtectedClass.java b/protected/java/src/org/broadinstitute/sting/gatk/DummyProtectedClass.java deleted file mode 100644 index c1324aea4..000000000 --- a/protected/java/src/org/broadinstitute/sting/gatk/DummyProtectedClass.java +++ /dev/null @@ -1,34 +0,0 @@ -package org.broadinstitute.sting.gatk; - -/* - * Copyright (c) 2009 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. - */ - -import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource; - -public class DummyProtectedClass implements ProtectedPackageSource { - - // THIS CLASS IS USED JUST SO THAT WE CAN TEST WHETHER WE ARE USING THE LITE OR FULL VERSION OF THE GATK - // **** DO NOT REMOVE! **** -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java rename to protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AverageAltAlleleLength.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java similarity index 85% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 5b1a1e236..517cb0df0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -35,10 +35,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import org.broadinstitute.variant.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContextUtils; @@ -52,12 +50,6 @@ import java.util.*; */ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY }; - public static final VCFInfoHeaderLine[] descriptions = { - VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY), - VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY), - VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) }; - private Set founderIds = new HashSet(); public Map annotate(final RefMetaDataTracker tracker, @@ -78,8 +70,8 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn } public List getKeyNames() { - return Arrays.asList(keyNames); + return Arrays.asList(ChromosomeCountConstants.keyNames); } - public List getDescriptions() { return Arrays.asList(descriptions); } + public List getDescriptions() { return Arrays.asList(ChromosomeCountConstants.descriptions); } } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 2c774d94d..3b0cb07d5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -41,7 +41,6 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.baq.BAQ; -import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -55,7 +54,6 @@ import org.broadinstitute.sting.utils.sam.ReadUtils; import java.io.File; import java.io.IOException; import java.io.PrintStream; -import java.lang.reflect.Constructor; import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -159,10 +157,6 @@ public class BaseRecalibrator extends ReadWalker implements NanoSche public void initialize() { baq = new BAQ(BAQGOP); // setup the BAQ object with the provided gap open penalty - // check for unsupported access - if (getToolkit().isGATKLite() && !getToolkit().getArguments().disableIndelQuals) - throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument"); - if (RAC.FORCE_PLATFORM != null) RAC.DEFAULT_PLATFORM = RAC.FORCE_PLATFORM; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationPerformance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationPerformance.java new file mode 100755 index 000000000..dc7c27db0 --- /dev/null +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationPerformance.java @@ -0,0 +1,110 @@ +/* + * Copyright (c) 2010 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk.walkers.bqsr; + +import org.broadinstitute.sting.commandline.*; +import org.broadinstitute.sting.gatk.contexts.AlignmentContext; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.filters.*; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.report.GATKReport; +import org.broadinstitute.sting.gatk.report.GATKReportTable; +import org.broadinstitute.sting.gatk.walkers.*; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.utils.recalibration.*; + +import java.io.*; + +/** + */ + +@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class}) +@PartitionBy(PartitionType.READ) +public class RecalibrationPerformance extends RodWalker implements NanoSchedulable { + + @Output(doc="Write output to this file", required = true) + public PrintStream out; + + @Input(fullName="recal", shortName="recal", required=false, doc="The input covariates table file") + public File RECAL_FILE = null; + + public void initialize() { + out.println("Cycle\tQrep\tQemp\tIsJoint\tObservations\tErrors"); + + final GATKReport report = new GATKReport(RECAL_FILE); + final GATKReportTable table = report.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE); + for ( int row = 0; row < table.getNumRows(); row++ ) { + + final int nObservations = (int)asDouble(table.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME)); + final int nErrors = (int)Math.round(asDouble(table.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME))); + final double empiricalQuality = asDouble(table.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME)); + + final byte QReported = Byte.parseByte((String) table.get(row, RecalUtils.QUALITY_SCORE_COLUMN_NAME)); + + final double jointEstimateQemp = RecalDatum.bayesianEstimateOfEmpiricalQuality(nObservations, nErrors, QReported); + + //if ( Math.abs((int)(jointEstimateQemp - empiricalQuality)) > 1 ) + // System.out.println(String.format("Qreported = %f, nObservations = %f, nErrors = %f, point Qemp = %f, joint Qemp = %f", estimatedQReported, nObservations, nErrors, empiricalQuality, jointEstimateQemp)); + + if ( table.get(row, RecalUtils.COVARIATE_NAME_COLUMN_NAME).equals("Cycle") && + table.get(row, RecalUtils.EVENT_TYPE_COLUMN_NAME).equals("M") && + table.get(row, RecalUtils.READGROUP_COLUMN_NAME).equals("20FUKAAXX100202.6") && + (QReported == 6 || QReported == 10 || QReported == 20 || QReported == 30 || QReported == 45) ) { + out.println(String.format("%s\t%d\t%d\t%s\t%d\t%d", table.get(row, RecalUtils.COVARIATE_VALUE_COLUMN_NAME), QReported, Math.round(empiricalQuality), "False", (int)nObservations, (int)nErrors)); + out.println(String.format("%s\t%d\t%d\t%s\t%d\t%d", table.get(row, RecalUtils.COVARIATE_VALUE_COLUMN_NAME), QReported, (int)jointEstimateQemp, "True", (int)nObservations, (int)nErrors)); + } + } + + } + + @Override + public boolean isDone() { + return true; + } + + private double asDouble(final Object o) { + if ( o instanceof Double ) + return (Double)o; + else if ( o instanceof Integer ) + return (Integer)o; + else if ( o instanceof Long ) + return (Long)o; + else + throw new ReviewedStingException("Object " + o + " is expected to be either a double, long or integer but its not either: " + o.getClass()); + } + + @Override + public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; } + + @Override + public Integer reduceInit() { return 0; } + + @Override + public Integer reduce(Integer counter, Integer sum) { return 0; } + + @Override + public void onTraversalDone(Integer sum) {} +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SimpleGenomeLoc.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java index 98e581e21..5972322f8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java @@ -124,7 +124,7 @@ public class ErrorRatePerCycle extends LocusWalker { public void initialize() { report = new GATKReport(); - report.addTable(reportName, reportDescription, 6); + report.addTable(reportName, reportDescription, 6, GATKReportTable.TableSortingWay.SORT_BY_ROW); table = report.getTable(reportName); table.addColumn("readgroup"); table.addColumn("cycle"); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatistics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatistics.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatistics.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatistics.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java index 290c33b2b..4f108005d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java @@ -31,6 +31,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fragments.FragmentCollection; +import org.broadinstitute.sting.utils.genotyper.DiploidGenotype; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java index 30650e9c0..e51e41e88 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java @@ -60,7 +60,7 @@ public class ErrorModel { boolean hasCalledAlleles = false; - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap(); + final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap(); if (refSampleVC != null) { for (Allele allele : refSampleVC.getAlleles()) { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java index ce66ce8d0..2788f201c 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java @@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -231,7 +232,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup(); if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){ // no likelihoods have been computed for this sample at this site - perReadAlleleLikelihoodMap.put(sample.getKey(), org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap()); + perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap()); } // create the GenotypeLikelihoods object diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 56965c022..ce59a90fc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -119,7 +119,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){ // no likelihoods have been computed for this sample at this site - perReadAlleleLikelihoodMap.put(sample.getKey(), PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap()); + perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap()); } final ReadBackedPileup pileup = context.getBasePileup(); if (pileup != null) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index c10f7264e..4cc152d53 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; +import org.broadinstitute.sting.utils.genotyper.DiploidGenotype; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; @@ -55,7 +56,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC protected SNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) { super(UAC, logger); useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES; - perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap(); + perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap(); } public VariantContext getLikelihoods(final RefMetaDataTracker tracker, diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index b5386ff6b..3dc0c3b71 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; -import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.downsampling.DownsampleType; @@ -41,7 +40,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; 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.variant.GATKVariantContextUtils; import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -230,25 +228,6 @@ public class UnifiedGenotyper extends LocusWalker, Unif **/ public void initialize() { - // Check for protected modes - if (GATKLiteUtils.isGATKLite()) { - // no polyploid/pooled mode in GATK Like - if (UAC.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY || - UAC.referenceSampleName != null || - UAC.referenceSampleRod.isBound()) { - throw new UserException.NotSupportedInGATKLite("you cannot enable usage of ploidy values other than 2"); - } - - if ( UAC.CONTAMINATION_FRACTION > 0.0 ) { - if ( UAC.CONTAMINATION_FRACTION == StandardCallerArgumentCollection.DEFAULT_CONTAMINATION_FRACTION ) { - UAC.CONTAMINATION_FRACTION = 0.0; - logger.warn("setting contamination down-sampling fraction to 0.0 because it is not enabled in GATK-lite"); - } else { - throw new UserException.NotSupportedInGATKLite("you cannot enable usage of contamination down-sampling"); - } - } - } - if ( UAC.TREAT_ALL_READS_AS_SINGLE_POOL ) { samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME); } else { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java index 5aef002fe..7c25ab551 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java @@ -59,16 +59,16 @@ public class GenotypingEngine { } @Requires({"refLoc.containsP(activeRegionWindow)", "haplotypes.size() > 0"}) - public List assignGenotypeLikelihoodsAndCallIndependentEvents( final UnifiedGenotyperEngine UG_engine, - final List haplotypes, - final List samples, - final Map haplotypeReadMap, - final Map> perSampleFilteredReadList, - final byte[] ref, - final GenomeLoc refLoc, - final GenomeLoc activeRegionWindow, - final GenomeLocParser genomeLocParser, - final List activeAllelesToGenotype ) { + public List assignGenotypeLikelihoods( final UnifiedGenotyperEngine UG_engine, + final List haplotypes, + final List samples, + final Map haplotypeReadMap, + final Map> perSampleFilteredReadList, + final byte[] ref, + final GenomeLoc refLoc, + final GenomeLoc activeRegionWindow, + final GenomeLocParser genomeLocParser, + final List activeAllelesToGenotype ) { final List returnCalls = new ArrayList(); final boolean in_GGA_mode = !activeAllelesToGenotype.isEmpty(); @@ -115,63 +115,56 @@ public class GenotypingEngine { } } } else { // we are in GGA mode! + int compCount = 0; for( final VariantContext compVC : activeAllelesToGenotype ) { if( compVC.getStart() == loc ) { - priorityList.clear(); int alleleCount = 0; for( final Allele compAltAllele : compVC.getAlternateAlleles() ) { - HashSet alleleSet = new HashSet(2); + ArrayList alleleSet = new ArrayList(2); alleleSet.add(compVC.getReference()); alleleSet.add(compAltAllele); - priorityList.add("Allele" + alleleCount); - eventsAtThisLoc.add(new VariantContextBuilder(compVC).alleles(alleleSet).source("Allele"+alleleCount).make()); + final String vcSourceName = "Comp" + compCount + "Allele" + alleleCount; + // check if this event is already in the list of events due to a repeat in the input alleles track + final VariantContext candidateEventToAdd = new VariantContextBuilder(compVC).alleles(alleleSet).source(vcSourceName).make(); + boolean alreadyExists = false; + for( final VariantContext eventToTest : eventsAtThisLoc ) { + if( eventToTest.hasSameAllelesAs(candidateEventToAdd) ) { + alreadyExists = true; + } + } + if( !alreadyExists ) { + priorityList.add(vcSourceName); + eventsAtThisLoc.add(candidateEventToAdd); + } alleleCount++; } } + compCount++; } } if( eventsAtThisLoc.isEmpty() ) { continue; } - // Create the allele mapping object which maps the original haplotype alleles to the alleles present in just this event - Map> alleleMapper = createAlleleMapper( loc, eventsAtThisLoc, haplotypes ); + // Create the event mapping object which maps the original haplotype events to the events present at just this locus + final Map> eventMapper = createEventMapper(loc, eventsAtThisLoc, haplotypes); - final Allele refAllele = eventsAtThisLoc.get(0).getReference(); - final ArrayList alleleOrdering = new ArrayList(alleleMapper.size()); - alleleOrdering.add(refAllele); - for( final VariantContext vc : eventsAtThisLoc ) { - alleleOrdering.add(vc.getAlternateAllele(0)); - } - - // Sanity check the priority list - for( final VariantContext vc : eventsAtThisLoc ) { - if( !priorityList.contains(vc.getSource()) ) { - throw new ReviewedStingException("Event found on haplotype that wasn't added to priority list. Something went wrong in the merging of alleles."); - } - } - for( final String name : priorityList ) { - boolean found = false; - for( final VariantContext vc : eventsAtThisLoc ) { - if(vc.getSource().equals(name)) { found = true; break; } - } - if( !found ) { - throw new ReviewedStingException("Event added to priority list but wasn't found on any haplotype. Something went wrong in the merging of alleles."); - } - } + // Sanity check the priority list for mistakes + validatePriorityList( priorityList, eventsAtThisLoc ); // Merge the event to find a common reference representation final VariantContext mergedVC = VariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false); if( mergedVC == null ) { continue; } - // let's update the Allele keys in the mapper because they can change after merging when there are complex events - final Map> updatedAlleleMapper = new HashMap>(alleleMapper.size()); - for ( int i = 0; i < mergedVC.getNAlleles(); i++ ) { - final Allele oldAllele = alleleOrdering.get(i); - final Allele newAllele = mergedVC.getAlleles().get(i); - updatedAlleleMapper.put(newAllele, alleleMapper.get(oldAllele)); - alleleOrdering.set(i, newAllele); + if( eventsAtThisLoc.size() != mergedVC.getAlternateAlleles().size() ) { + throw new ReviewedStingException("Record size mismatch! Something went wrong in the merging of alleles."); } - alleleMapper = updatedAlleleMapper; + final HashMap mergeMap = new HashMap(); + mergeMap.put(null, mergedVC.getReference()); // the reference event (null) --> the reference allele + for(int iii = 0; iii < mergedVC.getAlternateAlleles().size(); iii++) { + mergeMap.put(eventsAtThisLoc.get(iii), mergedVC.getAlternateAllele(iii)); // BUGBUG: This is assuming that the order of alleles is the same as the priority list given to simpleMerge function + } + + final Map> alleleMapper = createAlleleMapper(mergeMap, eventMapper); if( DEBUG ) { System.out.println("Genotyping event at " + loc + " with alleles = " + mergedVC.getAlleles()); @@ -180,20 +173,7 @@ public class GenotypingEngine { final Map alleleReadMap = convertHaplotypeReadMapToAlleleReadMap( haplotypeReadMap, alleleMapper, UG_engine.getUAC().CONTAMINATION_FRACTION, UG_engine.getUAC().contaminationLog ); - // Grab the genotype likelihoods from the appropriate places in the haplotype likelihood matrix -- calculation performed independently per sample - final GenotypesContext genotypes = GenotypesContext.create(samples.size()); - for( final String sample : samples ) { - final int numHaplotypes = alleleMapper.size(); - final double[] genotypeLikelihoods = new double[numHaplotypes * (numHaplotypes+1) / 2]; - final double[][] haplotypeLikelihoodMatrix = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(sample, alleleReadMap, alleleOrdering); - int glIndex = 0; - for( int iii = 0; iii < numHaplotypes; iii++ ) { - for( int jjj = 0; jjj <= iii; jjj++ ) { - genotypeLikelihoods[glIndex++] = haplotypeLikelihoodMatrix[iii][jjj]; // for example: AA,AB,BB,AC,BC,CC - } - } - genotypes.add( new GenotypeBuilder(sample).alleles(noCall).PL(genotypeLikelihoods).make() ); - } + final GenotypesContext genotypes = calculateGLsForThisEvent( samples, alleleReadMap, mergedVC ); final VariantContext call = UG_engine.calculateGenotypes(new VariantContextBuilder(mergedVC).genotypes(genotypes).make(), UG_engine.getUAC().GLmodel); if( call != null ) { final Map alleleReadMap_annotations = ( USE_FILTERED_READ_MAP_FOR_ANNOTATIONS ? alleleReadMap : @@ -212,6 +192,41 @@ public class GenotypingEngine { return returnCalls; } + private GenotypesContext calculateGLsForThisEvent( final List samples, final Map alleleReadMap, final VariantContext mergedVC ) { + final GenotypesContext genotypes = GenotypesContext.create(samples.size()); + // Grab the genotype likelihoods from the appropriate places in the haplotype likelihood matrix -- calculation performed independently per sample + for( final String sample : samples ) { + final int numHaplotypes = mergedVC.getAlleles().size(); + final double[] genotypeLikelihoods = new double[numHaplotypes * (numHaplotypes+1) / 2]; + final double[][] haplotypeLikelihoodMatrix = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(sample, alleleReadMap, mergedVC.getAlleles()); + int glIndex = 0; + for( int iii = 0; iii < numHaplotypes; iii++ ) { + for( int jjj = 0; jjj <= iii; jjj++ ) { + genotypeLikelihoods[glIndex++] = haplotypeLikelihoodMatrix[iii][jjj]; // for example: AA,AB,BB,AC,BC,CC + } + } + genotypes.add( new GenotypeBuilder(sample).alleles(noCall).PL(genotypeLikelihoods).make() ); + } + return genotypes; + } + + private void validatePriorityList( final ArrayList priorityList, final ArrayList eventsAtThisLoc ) { + for( final VariantContext vc : eventsAtThisLoc ) { + if( !priorityList.contains(vc.getSource()) ) { + throw new ReviewedStingException("Event found on haplotype that wasn't added to priority list. Something went wrong in the merging of alleles."); + } + } + for( final String name : priorityList ) { + boolean found = false; + for( final VariantContext vc : eventsAtThisLoc ) { + if(vc.getSource().equals(name)) { found = true; break; } + } + if( !found ) { + throw new ReviewedStingException("Event added to priority list but wasn't found on any haplotype. Something went wrong in the merging of alleles."); + } + } + } + private static Map filterToOnlyOverlappingReads( final GenomeLocParser parser, final Map perSampleReadMap, final Map> perSampleFilteredReadList, @@ -220,7 +235,7 @@ public class GenotypingEngine { final Map returnMap = new HashMap(); final GenomeLoc callLoc = parser.createGenomeLoc(call); for( final Map.Entry sample : perSampleReadMap.entrySet() ) { - final PerReadAlleleLikelihoodMap likelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap(); + final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap(); for( final Map.Entry> mapEntry : sample.getValue().getLikelihoodReadMap().entrySet() ) { // only count the read if it overlaps the event, otherwise it is not added to the output read list at all @@ -274,7 +289,7 @@ public class GenotypingEngine { final Map alleleReadMap = new HashMap(); for( final Map.Entry haplotypeReadMapEntry : haplotypeReadMap.entrySet() ) { // for each sample - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap(); + final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap(); for( final Map.Entry> alleleMapperEntry : alleleMapper.entrySet() ) { // for each output allele final List mappedHaplotypes = alleleMapperEntry.getValue(); for( final Map.Entry> readEntry : haplotypeReadMapEntry.getValue().getLikelihoodReadMap().entrySet() ) { // for each read @@ -437,27 +452,44 @@ public class GenotypingEngine { return ((pa1b1 - pa1*pb1) * (pa1b1 - pa1*pb1)) / ( pa1 * (1.0 - pa1) * pb1 * (1.0 - pb1) ); } + protected static Map> createAlleleMapper( final Map mergeMap, final Map> eventMap ) { + final Map> alleleMapper = new HashMap>(); + for( final Map.Entry entry : mergeMap.entrySet() ) { + alleleMapper.put(entry.getValue(), eventMap.get(new Event(entry.getKey()))); + } + return alleleMapper; + } + @Requires({"haplotypes.size() >= eventsAtThisLoc.size() + 1"}) @Ensures({"result.size() == eventsAtThisLoc.size() + 1"}) - protected static Map> createAlleleMapper( final int loc, final List eventsAtThisLoc, final List haplotypes ) { + protected static Map> createEventMapper( final int loc, final List eventsAtThisLoc, final List haplotypes ) { - final Map> alleleMapper = new HashMap>(eventsAtThisLoc.size()+1); - final Allele refAllele = eventsAtThisLoc.get(0).getReference(); - alleleMapper.put(refAllele, new ArrayList()); - for( final VariantContext vc : eventsAtThisLoc ) - alleleMapper.put(vc.getAlternateAllele(0), new ArrayList()); + final Map> eventMapper = new HashMap>(eventsAtThisLoc.size()+1); + VariantContext refVC = eventsAtThisLoc.get(0); // the genome loc is the only safe thing to pull out of this VC because ref/alt pairs might change reference basis + eventMapper.put(new Event(null), new ArrayList()); + for( final VariantContext vc : eventsAtThisLoc ) { + eventMapper.put(new Event(vc), new ArrayList()); + } final ArrayList undeterminedHaplotypes = new ArrayList(haplotypes.size()); for( final Haplotype h : haplotypes ) { - if( h.isArtificialHaplotype() && loc == h.getArtificialAllelePosition() && alleleMapper.containsKey(h.getArtificialAllele()) ) { - alleleMapper.get(h.getArtificialAllele()).add(h); + if( h.isArtificialHaplotype() && loc == h.getArtificialAllelePosition() ) { + final ArrayList alleles = new ArrayList(2); + alleles.add(h.getArtificialRefAllele()); + alleles.add(h.getArtificialAltAllele()); + final Event artificialVC = new Event( (new VariantContextBuilder()).source("artificialHaplotype") + .alleles(alleles) + .loc(refVC.getChr(), refVC.getStart(), refVC.getStart() + h.getArtificialRefAllele().length() - 1).make() ); + if( eventMapper.containsKey(artificialVC) ) { + eventMapper.get(artificialVC).add(h); + } } else if( h.getEventMap().get(loc) == null ) { // no event at this location so let's investigate later undeterminedHaplotypes.add(h); } else { boolean haplotypeIsDetermined = false; for( final VariantContext vcAtThisLoc : eventsAtThisLoc ) { if( h.getEventMap().get(loc).hasSameAllelesAs(vcAtThisLoc) ) { - alleleMapper.get(vcAtThisLoc.getAlternateAllele(0)).add(h); + eventMapper.get(new Event(vcAtThisLoc)).add(h); haplotypeIsDetermined = true; break; } @@ -469,25 +501,23 @@ public class GenotypingEngine { } for( final Haplotype h : undeterminedHaplotypes ) { - Allele matchingAllele = null; - for( final Map.Entry> alleleToTest : alleleMapper.entrySet() ) { + Event matchingEvent = new Event(null); + for( final Map.Entry> eventToTest : eventMapper.entrySet() ) { // don't test against the reference allele - if( alleleToTest.getKey().equals(refAllele) ) + if( eventToTest.getKey().equals(new Event(null)) ) continue; - final Haplotype artificialHaplotype = alleleToTest.getValue().get(0); + final Haplotype artificialHaplotype = eventToTest.getValue().get(0); if( isSubSetOf(artificialHaplotype.getEventMap(), h.getEventMap(), true) ) { - matchingAllele = alleleToTest.getKey(); + matchingEvent = eventToTest.getKey(); break; } } - if( matchingAllele == null ) - matchingAllele = refAllele; - alleleMapper.get(matchingAllele).add(h); + eventMapper.get(matchingEvent).add(h); } - return alleleMapper; + return eventMapper; } protected static boolean isSubSetOf(final Map subset, final Map superset, final boolean resolveSupersetToSubset) { @@ -636,4 +666,22 @@ public class GenotypingEngine { } return vcs; } + + private static class Event { + public VariantContext vc; + + public Event( final VariantContext vc ) { + this.vc = vc; + } + + @Override + public boolean equals( final Object obj ) { + return obj instanceof Event && ((((Event) obj).vc == null && vc == null) || (((Event) obj).vc != null && vc != null && ((Event) obj).vc.hasSameAllelesAs(vc))) ; + } + + @Override + public int hashCode() { + return (vc == null ? -1 : vc.getAlleles().hashCode()); + } + } } \ No newline at end of file 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 8c8113f46..cde089b34 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 @@ -416,16 +416,16 @@ public class HaplotypeCaller extends ActiveRegionWalker implem // subset down to only the best haplotypes to be genotyped in all samples ( in GGA mode use all discovered haplotypes ) final ArrayList bestHaplotypes = ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? likelihoodCalculationEngine.selectBestHaplotypes( haplotypes, stratifiedReadMap ) : haplotypes ); - for( final VariantContext call : genotypingEngine.assignGenotypeLikelihoodsAndCallIndependentEvents( UG_engine, - bestHaplotypes, - samplesList, - stratifiedReadMap, - perSampleFilteredReadList, - fullReferenceWithPadding, - getPaddedLoc(activeRegion), - activeRegion.getLocation(), - getToolkit().getGenomeLocParser(), - activeAllelesToGenotype ) ) { + for( final VariantContext call : genotypingEngine.assignGenotypeLikelihoods( UG_engine, + bestHaplotypes, + samplesList, + stratifiedReadMap, + perSampleFilteredReadList, + fullReferenceWithPadding, + getPaddedLoc(activeRegion), + activeRegion.getLocation(), + getToolkit().getGenomeLocParser(), + activeAllelesToGenotype ) ) { vcfWriter.add( call ); } diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java index 1be484075..e416b489b 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java @@ -104,7 +104,7 @@ public class LikelihoodCalculationEngine { private PerReadAlleleLikelihoodMap computeReadLikelihoods( final ArrayList haplotypes, final ArrayList reads) { - final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap(); + final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap(); final int numHaplotypes = haplotypes.size(); for( final GATKSAMRecord read : reads ) { final byte[] overallGCP = new byte[read.getReadLength()]; @@ -124,8 +124,8 @@ public class LikelihoodCalculationEngine { final Haplotype haplotype = haplotypes.get(jjj); // TODO -- need to test against a reference/position with non-standard bases - if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) ) - continue; + //if ( !Allele.acceptableAlleleBases(haplotype.getBases(), false) ) + // continue; final int haplotypeStart = ( previousHaplotypeSeen == null ? 0 : computeFirstDifferingPosition(haplotype.getBases(), previousHaplotypeSeen.getBases()) ); previousHaplotypeSeen = haplotype; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java index 0a98f54e9..87db5c9f7 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java @@ -379,8 +379,9 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine { h.setAlignmentStartHapwrtRef( swConsensus2.getAlignmentStart2wrt1() ); h.setCigar( AlignmentUtils.leftAlignIndel(swConsensus2.getCigar(), ref, h.getBases(), swConsensus2.getAlignmentStart2wrt1(), 0) ); - if ( haplotype.isArtificialHaplotype() ) - h.setArtificialAllele(haplotype.getArtificialAllele(), haplotype.getArtificialAllelePosition()); + if ( haplotype.isArtificialHaplotype() ) { + h.setArtificialEvent(haplotype.getArtificialEvent()); + } h.leftBreakPoint = leftBreakPoint; h.rightBreakPoint = rightBreakPoint; if( swConsensus2.getCigar().toString().contains("S") || swConsensus2.getCigar().getReferenceLength() != activeRegionStop - activeRegionStart ) { // protect against SW failures diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 221093759..5f0407b13 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pairhmm.ExactPairHMM; -import org.broadinstitute.sting.utils.pairhmm.LoglessCachingPairHMM; +//import org.broadinstitute.sting.utils.pairhmm.LoglessCachingPairHMM; import org.broadinstitute.sting.utils.pairhmm.OriginalPairHMM; import org.broadinstitute.sting.utils.pairhmm.PairHMM; import org.broadinstitute.sting.utils.pileup.PileupElement; @@ -102,9 +102,9 @@ public class PairHMMIndelErrorModel { break; case CACHING: case LOGLESS_CACHING: //TODO: still not tested so please do not use yet - pairHMM = new LoglessCachingPairHMM(); - System.err.println("warning: this option (LOGLESS_CACHING in UG) is still under development"); - break; + //pairHMM = new LoglessCachingPairHMM(); //TODO - add it back when the figure out how to use the protected LoglessCachingPairHMM class + throw new UserException.BadArgumentValue("pairHMM"," this option (LOGLESS_CACHING in UG) is still under development"); + //break; default: throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL, EXACT or LOGLESS_CACHING (the third option is still under development)."); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java index 91efd1ffd..6dad128fe 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java @@ -162,7 +162,7 @@ public class VariantEvalReportWriter { // create the table final String tableName = ve.getSimpleName(); final String tableDesc = ve.getClass().getAnnotation(Analysis.class).description(); - report.addTable(tableName, tableDesc, 1 + stratifiers.size() + (scanner.hasMoltenField() ? 2 : datamap.size())); + report.addTable(tableName, tableDesc, 1 + stratifiers.size() + (scanner.hasMoltenField() ? 2 : datamap.size()), GATKReportTable.TableSortingWay.SORT_BY_ROW); // grab the table, and add the columns we need to it final GATKReportTable table = report.getTable(tableName); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/StandardEval.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/SamplePhasingStatistics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/SamplePhasingStatistics.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/SamplePhasingStatistics.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/SamplePhasingStatistics.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/RequiredStratification.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/StandardStratification.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNode.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratNodeIterator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManager.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/Stratifier.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Analysis.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/AnalysisModuleScanner.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/DataPoint.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/Molten.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index cffd405b1..dd92961cf 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; +import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; @@ -423,7 +424,7 @@ public class SelectVariants extends RodWalker implements TreeR headerLines.add(new VCFInfoHeaderLine("AF_Orig", 1, VCFHeaderLineType.Float, "Original AF")); headerLines.add(new VCFInfoHeaderLine("AN_Orig", 1, VCFHeaderLineType.Integer, "Original AN")); } - headerLines.addAll(Arrays.asList(ChromosomeCounts.descriptions)); + headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions)); headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); for (int i = 0; i < SELECT_EXPRESSIONS.size(); i++) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java rename to protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java deleted file mode 100644 index 4a13fb615..000000000 --- a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java +++ /dev/null @@ -1,71 +0,0 @@ -/* - * Copyright (c) 2011 The Broad Institute - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR - * THE USE OR OTHER DEALINGS IN THE SOFTWARE. - */ -package org.broadinstitute.sting.utils.genotyper; - - -import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils; -import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; - -import java.io.PrintStream; -import java.util.*; - -public class AdvancedPerReadAlleleLikelihoodMap extends StandardPerReadAlleleLikelihoodMap implements ProtectedPackageSource { - - public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { - return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log); - } - - public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) { - // special case removal of all or no reads - if ( downsamplingFraction <= 0.0 ) - return; - if ( downsamplingFraction >= 1.0 ) { - likelihoodReadMap.clear(); - return; - } - - // start by stratifying the reads by the alleles they represent at this position - final Map> alleleReadMap = new HashMap>(alleles.size()); - for ( Allele allele : alleles ) - alleleReadMap.put(allele, new ArrayList()); - - for ( Map.Entry> entry : likelihoodReadMap.entrySet() ) { - // do not remove reduced reads! - if ( !entry.getKey().isReducedRead() ) { - final Allele bestAllele = getMostLikelyAllele(entry.getValue()); - if ( bestAllele != Allele.NO_CALL ) - alleleReadMap.get(bestAllele).add(entry.getKey()); - } - } - - // compute the reads to remove and actually remove them - final List readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log); - for ( final GATKSAMRecord read : readsToRemove ) - likelihoodReadMap.remove(read); - } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java similarity index 67% rename from public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java rename to protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java index ff85c33a0..2379ccd1d 100644 --- a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java +++ b/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java @@ -25,26 +25,26 @@ package org.broadinstitute.sting.utils.genotyper; -import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.variant.variantcontext.Allele; import java.io.PrintStream; -import java.lang.reflect.Constructor; import java.util.*; -public abstract class PerReadAlleleLikelihoodMap { +public class PerReadAlleleLikelihoodMap { public static final double INFORMATIVE_LIKELIHOOD_THRESHOLD = 0.2; protected List alleles; protected Map> likelihoodReadMap; - public abstract void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log); - public abstract ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log); + public PerReadAlleleLikelihoodMap() { + likelihoodReadMap = new LinkedHashMap>(); + alleles = new ArrayList(); + } public void add(GATKSAMRecord read, Allele a, Double likelihood) { Map likelihoodMap; @@ -63,6 +63,39 @@ public abstract class PerReadAlleleLikelihoodMap { } + public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { + return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log); + } + + public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) { + // special case removal of all or no reads + if ( downsamplingFraction <= 0.0 ) + return; + if ( downsamplingFraction >= 1.0 ) { + likelihoodReadMap.clear(); + return; + } + + // start by stratifying the reads by the alleles they represent at this position + final Map> alleleReadMap = new HashMap>(alleles.size()); + for ( Allele allele : alleles ) + alleleReadMap.put(allele, new ArrayList()); + + for ( Map.Entry> entry : likelihoodReadMap.entrySet() ) { + // do not remove reduced reads! + if ( !entry.getKey().isReducedRead() ) { + final Allele bestAllele = getMostLikelyAllele(entry.getValue()); + if ( bestAllele != Allele.NO_CALL ) + alleleReadMap.get(bestAllele).add(entry.getKey()); + } + } + + // compute the reads to remove and actually remove them + final List readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log); + for ( final GATKSAMRecord read : readsToRemove ) + likelihoodReadMap.remove(read); + } + public int size() { return likelihoodReadMap.size(); } @@ -122,16 +155,4 @@ public abstract class PerReadAlleleLikelihoodMap { } return (maxLike - prevMaxLike > INFORMATIVE_LIKELIHOOD_THRESHOLD ? mostLikelyAllele : Allele.NO_CALL ); } - - public static PerReadAlleleLikelihoodMap getBestAvailablePerReadAlleleLikelihoodMap() { - final Class PerReadAlleleLikelihoodMapClass = GATKLiteUtils.getProtectedClassIfAvailable(PerReadAlleleLikelihoodMap.class); - try { - final Constructor constructor = PerReadAlleleLikelihoodMapClass.getDeclaredConstructor((Class[])null); - constructor.setAccessible(true); - return (PerReadAlleleLikelihoodMap)constructor.newInstance(); - } - catch (Exception e) { - throw new ReviewedStingException("Unable to create RecalibrationEngine class instance " + PerReadAlleleLikelihoodMapClass.getSimpleName()); - } - } } diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java similarity index 73% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java index fae0e8c09..de1ed5602 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java @@ -14,12 +14,15 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; */ public class BQSRReadTransformer extends ReadTransformer { private boolean enabled; - private BaseRecalibration bqsr; + private BaseRecalibration bqsr = null; @Override public ApplicationTime initializeSub(final GenomeAnalysisEngine engine, final Walker walker) { - this.enabled = engine.hasBaseRecalibration(); - this.bqsr = engine.getBaseRecalibration(); + this.enabled = engine.hasBQSRArgumentSet(); + if ( enabled ) { + final BQSRArgumentSet args = engine.getBQSRArgumentSet(); + this.bqsr = new BaseRecalibration(args.getRecalFile(), args.getQuantizationLevels(), args.shouldDisableIndelQuals(), args.getPreserveQscoresLessThan(), args.shouldEmitOriginalQuals()); + } final BQSRMode mode = WalkerManager.getWalkerAnnotation(walker, BQSRMode.class); return mode.ApplicationTime(); } diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index eebc86b6b..7bd21ddaa 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java +++ b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -341,6 +341,8 @@ public class RecalDatum { return log10QempPriorCache[difference]; } + static private final long MAX_NUMBER_OF_OBSERVATIONS = Integer.MAX_VALUE - 1; + static protected double log10QempLikelihood(final double Qempirical, long nObservations, long nErrors) { if ( nObservations == 0 ) return 0.0; @@ -348,15 +350,15 @@ public class RecalDatum { // the binomial code requires ints as input (because it does caching). This should theoretically be fine because // there is plenty of precision in 2^31 observations, but we need to make sure that we don't have overflow // before casting down to an int. - if ( nObservations > Integer.MAX_VALUE ) { + if ( nObservations > MAX_NUMBER_OF_OBSERVATIONS ) { // we need to decrease nErrors by the same fraction that we are decreasing nObservations - final double fraction = (double)Integer.MAX_VALUE / (double)nObservations; + final double fraction = (double)MAX_NUMBER_OF_OBSERVATIONS / (double)nObservations; nErrors = Math.round((double)nErrors * fraction); - nObservations = Integer.MAX_VALUE; + nObservations = MAX_NUMBER_OF_OBSERVATIONS; } // this is just a straight binomial PDF - double log10Prob = MathUtils.log10BinomialProbability((int)nObservations, (int)nErrors, QualityUtils.qualToErrorProbLog10((byte)(int)Qempirical)); + double log10Prob = MathUtils.log10BinomialProbability((int)nObservations, (int)nErrors, QualityUtils.qualToErrorProbLog10(Qempirical)); if ( Double.isInfinite(log10Prob) || Double.isNaN(log10Prob) ) log10Prob = -Double.MAX_VALUE; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java b/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java similarity index 100% rename from public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java rename to protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java similarity index 86% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java index 44bc7de5f..538c027d9 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java @@ -26,6 +26,25 @@ public class BQSRGathererUnitTest extends BaseTest { private static File recal_original = new File(privateTestDir + "HiSeq.1mb.1RG.noSG.table"); + @Test(enabled = true) + public void testManyObservations() { + File recal = new File(privateTestDir + "bqsr.manyObservations.piece.table"); + + final File output = BaseTest.createTempFile("BQSRgathererTest", ".table"); + + List recalFiles = new LinkedList (); + for ( int i=0; i < 5; i++ ) + recalFiles.add(recal); + + BQSRGatherer gatherer = new BQSRGatherer(); + gatherer.gather(recalFiles, output); + + GATKReport originalReport = new GATKReport(new File(privateTestDir + "bqsr.manyObservations.full.table")); + GATKReport calculatedReport = new GATKReport(output); + + testReports(originalReport, calculatedReport); + } + @Test(enabled = true) public void testGatherBQSR() { BQSRGatherer gatherer = new BQSRGatherer(); @@ -42,6 +61,11 @@ public class BQSRGathererUnitTest extends BaseTest { GATKReport originalReport = new GATKReport(recal_original); GATKReport calculatedReport = new GATKReport(output); + testReports(originalReport, calculatedReport); + } + + private void testReports(final GATKReport originalReport, final GATKReport calculatedReport) { + // test the Arguments table List columnsToTest = Arrays.asList(RecalUtils.ARGUMENT_COLUMN_NAME, RecalUtils.ARGUMENT_VALUE_COLUMN_NAME); GATKReportTable originalTable = originalReport.getTable(RecalUtils.ARGUMENT_REPORT_TABLE_TITLE); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 1683044f0..4c2714dde 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -21,7 +21,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "47fdbe5f01d3ce5e53056eea8c488e45"); + HCTest(CEUTRIO_BAM, "", "35c8425b44429ac7468c2cd26f8f5a42"); } @Test @@ -33,7 +33,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleGGA() { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", - "54b7cc3da3d8349ff4302f99883ab188"); + "d918d25b22a551cae5d70ea30d7feed1"); } private void HCTestComplexVariants(String bam, String args, String md5) { @@ -72,7 +72,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void HCTestProblematicReadsModifiedInActiveRegions() { final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965"; - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ece627de486aee69d02872891c6cb0ff")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("2e8e6313228b0387008437feae7f5469")); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java similarity index 95% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java index 4e72b37a4..c6dff6fe7 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java @@ -1,6 +1,5 @@ -package org.broadinstitute.sting.gatk.walkers.genotyper; +package org.broadinstitute.sting.utils.genotyper; -import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 1187039bb..da6e68697 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -53,13 +53,12 @@ import org.broadinstitute.sting.gatk.samples.SampleDB; import org.broadinstitute.sting.gatk.samples.SampleDBBuilder; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.sting.utils.recalibration.BaseRecalibration; +import org.broadinstitute.sting.utils.recalibration.BQSRArgumentSet; import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor; import java.io.File; @@ -210,18 +209,11 @@ public class GenomeAnalysisEngine { /** * Base Quality Score Recalibration helper object */ - private BaseRecalibration baseRecalibration = null; - public BaseRecalibration getBaseRecalibration() { return baseRecalibration; } - public boolean hasBaseRecalibration() { return baseRecalibration != null; } - public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean emitOriginalQuals) { - baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, disableIndelQuals, preserveQLessThan, emitOriginalQuals); - } - - /** - * Utility method to determine whether this is the lite version of the GATK - */ - public boolean isGATKLite() { - return GATKLiteUtils.isGATKLite(); + private BQSRArgumentSet bqsrArgumentSet = null; + public BQSRArgumentSet getBQSRArgumentSet() { return bqsrArgumentSet; } + public boolean hasBQSRArgumentSet() { return bqsrArgumentSet != null; } + public void setBaseRecalibration(final GATKArgumentCollection args) { + bqsrArgumentSet = new BQSRArgumentSet(args); } /** @@ -250,7 +242,7 @@ public class GenomeAnalysisEngine { // if the use specified an input BQSR recalibration table then enable on the fly recalibration if (args.BQSR_RECAL_FILE != null) - setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.disableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN, args.emitOriginalQuals); + setBaseRecalibration(args); // Determine how the threads should be divided between CPU vs. IO. determineThreadAllocation(); @@ -330,10 +322,7 @@ public class GenomeAnalysisEngine { try { return walkerManager.createByName(walkerName); } catch ( UserException e ) { - if ( isGATKLite() && GATKLiteUtils.isAvailableOnlyInFullGATK(walkerName) ) { - e = new UserException.NotSupportedInGATKLite("the " + walkerName + " walker is available only in the full version of the GATK"); - } - else if ( isDeprecatedWalker(walkerName) ) { + if ( isDeprecatedWalker(walkerName) ) { e = new UserException.DeprecatedWalker(walkerName, getDeprecatedMajorVersionNumber(walkerName)); } throw e; diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index d9c7c9008..3a3a3d705 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -284,15 +284,15 @@ public class GATKArgumentCollection { @Argument(fullName = "preserve_qscores_less_than", shortName = "preserveQ", doc = "Bases with quality scores less than this threshold won't be recalibrated (with -BQSR)", required = false) public int PRESERVE_QSCORES_LESS_THAN = QualityUtils.MIN_USABLE_Q_SCORE; - @Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false) - public byte defaultBaseQualities = -1; - // -------------------------------------------------------------------------------------------------------------- // // Other utility arguments // // -------------------------------------------------------------------------------------------------------------- + @Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false) + public byte defaultBaseQualities = -1; + @Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false) public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT; diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java index 6482354a9..1c227170d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java @@ -33,8 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; -import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype; +import org.broadinstitute.sting.utils.genotyper.DiploidGenotype; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -50,6 +49,9 @@ import java.io.PrintStream; */ @DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) public class GATKPaperGenotyper extends LocusWalker implements TreeReducible { + + public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3; + // the possible diploid genotype strings private static enum GENOTYPE { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT } @@ -73,7 +75,7 @@ public class GATKPaperGenotyper extends LocusWalker implements Tre ReadBackedPileup pileup = context.getBasePileup().getPileupWithoutMappingQualityZeroReads(); double likelihoods[] = getReferencePolarizedPriors(ref.getBase(), - UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY, + HUMAN_SNP_HETEROZYGOSITY, 0.01); // get the bases and qualities from the pileup byte bases[] = pileup.getBases(); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java new file mode 100755 index 000000000..26f3bb8d9 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java @@ -0,0 +1,44 @@ +/* + * Copyright (c) 2010. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk.walkers.annotator; + +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; + + +/** + * Keys and descriptions for the common chromosome count annotations + */ +public class ChromosomeCountConstants { + + public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY }; + + public static final VCFInfoHeaderLine[] descriptions = { + VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY), + VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY), + VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) }; +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java index b4ef66aaf..c8304db21 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/FlagStat.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java @@ -1,9 +1,13 @@ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.qc; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.NanoSchedulable; +import org.broadinstitute.sting.gatk.walkers.ReadWalker; +import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java index a3efea9f1..fb08d1c03 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.qc; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.Argument; @@ -34,6 +34,9 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.LocusWalker; +import org.broadinstitute.sting.gatk.walkers.NanoSchedulable; +import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java index d7ae3050e..3ffdf3e9d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODs.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java @@ -23,7 +23,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.qc; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.Input; @@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.io.PrintStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java index 93eaee209..3dd49dea8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.readutils; import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequenceFile; @@ -37,6 +37,9 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.ReadWalker; +import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.clipping.ClippingOp; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java index 37176cbf9..956c0d7d4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.readutils; import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMReadGroupRecord; @@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.iterators.ReadTransformer; import org.broadinstitute.sting.gatk.iterators.ReadTransformersMode; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java index 7d70c470d..07d1f7c23 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFile.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.readutils; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileWriter; @@ -34,6 +34,10 @@ import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.walkers.DataSource; +import org.broadinstitute.sting.gatk.walkers.ReadWalker; +import org.broadinstitute.sting.gatk.walkers.Requires; +import org.broadinstitute.sting.gatk.walkers.WalkerName; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 78b89d615..27b0e5201 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.Window; -import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; +import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.variant.vcf.*; @@ -217,7 +217,7 @@ public class CombineVariants extends RodWalker implements Tree if ( SET_KEY != null ) headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record in CombineVariants")); if ( !ASSUME_IDENTICAL_SAMPLES ) - headerLines.addAll(Arrays.asList(ChromosomeCounts.descriptions)); + headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions)); VCFHeader vcfHeader = new VCFHeader(headerLines, samples); vcfHeader.setWriteCommandLine(!SUPPRESS_COMMAND_LINE_HEADER); vcfWriter.writeHeader(vcfHeader); diff --git a/public/java/src/org/broadinstitute/sting/tools/CatVariants.java b/public/java/src/org/broadinstitute/sting/tools/CatVariants.java new file mode 100644 index 000000000..e5811c423 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/tools/CatVariants.java @@ -0,0 +1,209 @@ +package org.broadinstitute.sting.tools; + +import net.sf.picard.reference.ReferenceSequenceFile; +import net.sf.picard.reference.ReferenceSequenceFileFactory; +import org.apache.log4j.BasicConfigurator; +import org.apache.log4j.Level; +import org.broad.tribble.AbstractFeatureReader; +import org.broad.tribble.FeatureReader; +import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Input; +import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.commandline.CommandLineProgram; +import org.broadinstitute.variant.bcf2.BCF2Codec; +import org.broadinstitute.variant.vcf.VCFCodec; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.writer.Options; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; + +import java.io.*; +import java.util.*; + + +/** + * + * Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.AppendVariants [sorted (optional)]"); + * The input files can be of type: VCF (ends in .vcf or .VCF)"); + * BCF2 (ends in .bcf or .BCF)"); + * Output file must be vcf or bcf file (.vcf or .bcf)"); + * If the input files are already sorted, the last argument can indicate that"); + */ +public class CatVariants extends CommandLineProgram { + // setup the logging system, used by some codecs + private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getRootLogger(); + + @Input(fullName = "reference", shortName = "R", doc = "genome reference file .fasta", required = true) + private File refFile = null; + + @Input(fullName="variant", shortName="V", doc="Input VCF file/s named .vcf or .bcf", required = true) + private List variant = null; + + @Output(fullName = "outputFile", shortName = "out", doc = "output file name .vcf or .bcf", required = true) + private File outputFile = null; + + @Argument(fullName = "assumeSorted", shortName = "assumeSorted", doc = "assumeSorted should be true if he input files are already sorted (based on the position of the variants", required = false) + private Boolean assumeSorted = false; + + /* + * print usage information + */ + private static void printUsage() { + System.err.println("Usage: java -cp dist/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.AppendVariants [sorted (optional)]"); + System.err.println(" The input files can be of type: VCF (ends in .vcf or .VCF)"); + System.err.println(" BCF2 (ends in .bcf or .BCF)"); + System.err.println(" Output file must be vcf or bcf file (.vcf or .bcf)"); + System.err.println(" if the input files are already sorted, the last argument can indicate that"); + } + + @Override + protected int execute() throws Exception { + //if(help){ + // printUsage(); + // return 1; + //} + + BasicConfigurator.configure(); + logger.setLevel(Level.INFO); + + if ( ! refFile.getName().endsWith(".fasta")) { + throw new UserException("Reference file "+refFile+"name must end with .fasta"); + } + + if ( ! refFile.exists() ) { + throw new UserException(String.format("Reference file %s does not exist", refFile.getAbsolutePath())); + } + + // Comparator>> comparator = new PositionComparator(); + Comparator> positionComparator = new PositionComparator(); + + + //PriorityQueue>> queue = + // new PriorityQueue>>(2000, comparator); + Queue> priorityQueue; + if(assumeSorted) + priorityQueue = new LinkedList>(); + else + priorityQueue = new PriorityQueue>(10000, positionComparator); + + Iterator files = variant.iterator(); + File file; + while (files.hasNext()) { + file = files.next(); + if (!(file.getName().endsWith(".vcf") || file.getName().endsWith(".VCF") || file.getName().endsWith(".bcf") || file.getName().endsWith(".BCF"))){ + System.err.println("File " + file.getAbsolutePath() + " should be .vcf or .bcf"); + printUsage(); + return 1; + } + if (assumeSorted){ + priorityQueue.add(new Pair(0,file)); + } + else{ + if (!file.exists()) { + throw new UserException(String.format("File %s doesn't exist",file.getAbsolutePath())); + } + FeatureReader reader; + boolean useVCF = (file.getName().endsWith(".vcf") || file.getName().endsWith(".VCF")); + if(useVCF) + reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new VCFCodec(), false); + else + reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new BCF2Codec(), false); + Iterator it = reader.iterator(); + if(!it.hasNext()){ + System.err.println(String.format("File %s is empty. This file will be ignored",file.getAbsolutePath())); + continue; + } + VariantContext vc = it.next(); + int firstPosition = vc.getStart(); + reader.close(); + //queue.add(new Pair>(firstPosition,reader)); + priorityQueue.add(new Pair(firstPosition,file)); + } + + } + + if (!(outputFile.getName().endsWith(".vcf") || outputFile.getName().endsWith(".VCF"))){ + throw new UserException(String.format("Output file %s should be .vcf", outputFile)); + } + ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFile); + + + FileOutputStream outputStream = new FileOutputStream(outputFile); + EnumSet options = EnumSet.of(Options.INDEX_ON_THE_FLY); + final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), options); + + boolean firstFile = true; + int count =0; + //while(!queue.isEmpty()){ + while(!priorityQueue.isEmpty() ){ + count++; + //FeatureReader reader = queue.remove().getSecond(); + file = priorityQueue.remove().getSecond(); + if (!file.exists()) { + throw new UserException(String.format("File %s doesn't exist",file.getAbsolutePath())); + } + FeatureReader reader; + boolean useVCF = (file.getName().endsWith(".vcf") || file.getName().endsWith(".VCF")); + if(useVCF) + reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new VCFCodec(), false); + else + reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new BCF2Codec(), false); + + if(count%10 ==0) + System.out.print(count); + else + System.out.print("."); + if (firstFile){ + VCFHeader header = (VCFHeader)reader.getHeader(); + outputWriter.writeHeader(header); + firstFile = false; + } + + Iterator it = reader.iterator(); + + while (it.hasNext()){ + VariantContext vc = it.next(); + outputWriter.add(vc); + } + + reader.close(); + + } + System.out.println(); + + outputStream.close(); + outputWriter.close(); + + return 0; + } + + + public static void main(String[] args){ + try { + CatVariants instance = new CatVariants(); + start(instance, args); + System.exit(CommandLineProgram.result); + } catch ( UserException e ) { + printUsage(); + exitSystemWithUserError(e); + } catch ( Exception e ) { + exitSystemWithError(e); + } + } + + private static class PositionComparator implements Comparator> { + + @Override + public int compare(Pair p1, Pair p2) { + int startPositionP1 = p1.getFirst(); + int startPositionP2 = p2.getFirst(); + if (startPositionP1 == startPositionP2) + return 0; + return startPositionP1 < startPositionP2 ? -1 : 1 ; + } + } + +} diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java index 2476a666e..dfca05fcd 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java @@ -46,8 +46,7 @@ public class Haplotype { private int alignmentStartHapwrtRef; public int leftBreakPoint = 0; public int rightBreakPoint = 0; - private Allele artificialAllele = null; - private int artificialAllelePosition = -1; + private Event artificialEvent = null; /** * Create a simple consensus sequence with provided bases and a uniform quality over all bases of qual @@ -70,10 +69,9 @@ public class Haplotype { this(bases, 0); } - protected Haplotype( final byte[] bases, final Allele artificialAllele, final int artificialAllelePosition ) { + protected Haplotype( final byte[] bases, final Event artificialEvent ) { this(bases, 0); - this.artificialAllele = artificialAllele; - this.artificialAllelePosition = artificialAllelePosition; + this.artificialEvent = artificialEvent; } public Haplotype( final byte[] bases, final GenomeLoc loc ) { @@ -152,20 +150,27 @@ public class Haplotype { } public boolean isArtificialHaplotype() { - return artificialAllele != null; + return artificialEvent != null; } - public Allele getArtificialAllele() { - return artificialAllele; + public Event getArtificialEvent() { + return artificialEvent; + } + + public Allele getArtificialRefAllele() { + return artificialEvent.ref; + } + + public Allele getArtificialAltAllele() { + return artificialEvent.alt; } public int getArtificialAllelePosition() { - return artificialAllelePosition; + return artificialEvent.pos; } - public void setArtificialAllele(final Allele artificialAllele, final int artificialAllelePosition) { - this.artificialAllele = artificialAllele; - this.artificialAllelePosition = artificialAllelePosition; + public void setArtificialEvent( final Event artificialEvent ) { + this.artificialEvent = artificialEvent; } @Requires({"refInsertLocation >= 0"}) @@ -179,7 +184,7 @@ public class Haplotype { newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(bases, 0, haplotypeInsertLocation)); // bases before the variant newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, altAllele.getBases()); // the alt allele of the variant newHaplotypeBases = ArrayUtils.addAll(newHaplotypeBases, ArrayUtils.subarray(bases, haplotypeInsertLocation + refAllele.length(), bases.length)); // bases after the variant - return new Haplotype(newHaplotypeBases, altAllele, genomicInsertLocation); + return new Haplotype(newHaplotypeBases, new Event(refAllele, altAllele, genomicInsertLocation)); } public static class HaplotypeBaseComparator implements Comparator, Serializable { @@ -244,4 +249,16 @@ public class Haplotype { return haplotypeMap; } + + private static class Event { + public Allele ref; + public Allele alt; + public int pos; + + public Event( final Allele ref, final Allele alt, final int pos ) { + this.ref = ref; + this.alt = alt; + this.pos = pos; + } + } } diff --git a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java index 844fa6b90..96fd0250c 100755 --- a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java @@ -90,6 +90,10 @@ public class QualityUtils { return qualToErrorProbLog10Cache[(int)qual & 0xff]; // Map: 127 -> 127; -128 -> 128; -1 -> 255; etc. } + static public double qualToErrorProbLog10(final double qual) { + return qual/-10.0; + } + /** * Convert a probability to a quality score. Note, this is capped at Q40. * diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java b/public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java deleted file mode 100755 index 2ab7d0618..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/classloader/GATKLiteUtils.java +++ /dev/null @@ -1,100 +0,0 @@ -/* - * Copyright (c) 2010 The Broad Institute - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR - * THE USE OR OTHER DEALINGS IN THE SOFTWARE. - */ - -package org.broadinstitute.sting.utils.classloader; - -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; - -import java.util.*; - -/** - * Created by IntelliJ IDEA. - * User: ebanks - * - * A set of static utility methods for working with the full vs. Lite GATK build - */ -public class GATKLiteUtils { - /** - * Constructor access disallowed...static utility methods only! - */ - private GATKLiteUtils() { } - - - private static Set fullVersionGATKWalkers = new HashSet(); - static { - fullVersionGATKWalkers.add("HaplotypeCaller"); - fullVersionGATKWalkers.add("ReduceReads"); - } - /** - * Utility method to check whether a given walker is only available in the full GATK release - * - * @param walkerName the walker class name (not the package) to check - */ - public static boolean isAvailableOnlyInFullGATK(final String walkerName) { - return fullVersionGATKWalkers.contains(walkerName); - } - - /** - * Utility method to determine whether this is the lite version of the GATK - */ - public static boolean isGATKLite() { - if ( isLiteVersion == null ) { - try { - Class.forName(DummyProtectedClassName); - isLiteVersion = false; - } catch ( ClassNotFoundException e) { - isLiteVersion = true; - } - } - return isLiteVersion; - } - private static final String DummyProtectedClassName = "org.broadinstitute.sting.gatk.DummyProtectedClass"; - private static Boolean isLiteVersion = null; - - - /** - * Utility method to pull out a protected subclass if possible, otherwise it falls back to a public subclass. - * Important note: the protected classes MUST implement ProtectedPackageSource! - * - * @param interfaceClass the interface class which the target classes implement - */ - public static Class getProtectedClassIfAvailable(final Class interfaceClass) { - List> classes = new PluginManager(interfaceClass).getPlugins(); - if ( classes.isEmpty() ) - throw new ReviewedStingException("No classes implementing the interface class " + interfaceClass.getSimpleName() + " were found"); - - Class result = null; - for ( Class c : classes ) { - if ( ProtectedPackageSource.class.isAssignableFrom(c) ) { - result = c; - break; - } - } - if ( result == null ) - result = classes.get(0); - - return result; - } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index 01c4b7a16..c799479ed 100755 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -92,12 +92,6 @@ public class UserException extends ReviewedStingException { } } - public static class NotSupportedInGATKLite extends UserException { - public NotSupportedInGATKLite(String message) { - super(String.format("GATK Lite does not support all of the features of the full version: %s", message)); - } - } - // todo -- fix up exception cause passing public static class MissingArgument extends CommandLineException { public MissingArgument(String arg, String message) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java rename to public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java index 86047d30b..6d90038d7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers.genotyper; +package org.broadinstitute.sting.utils.genotyper; import org.broadinstitute.variant.utils.BaseUtils; diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java deleted file mode 100644 index 1a27c6ecb..000000000 --- a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java +++ /dev/null @@ -1,46 +0,0 @@ -/* - * Copyright (c) 2011 The Broad Institute - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR - * THE USE OR OTHER DEALINGS IN THE SOFTWARE. - */ -package org.broadinstitute.sting.utils.genotyper; - - -import org.broadinstitute.sting.utils.classloader.PublicPackageSource; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; - -import java.io.PrintStream; -import java.util.*; - -public class StandardPerReadAlleleLikelihoodMap extends PerReadAlleleLikelihoodMap implements PublicPackageSource { - - public StandardPerReadAlleleLikelihoodMap() { - likelihoodReadMap = new LinkedHashMap>(); - alleles = new ArrayList(); - } - - // not implemented in the standard version - public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {} - public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { return pileup; } -} diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java index da66ff33d..21885cba7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpConstants.java @@ -24,13 +24,6 @@ package org.broadinstitute.sting.utils.help; -import com.sun.javadoc.FieldDoc; -import com.sun.javadoc.PackageDoc; -import com.sun.javadoc.ProgramElementDoc; -import org.broadinstitute.sting.utils.classloader.JVMUtils; - -import java.lang.reflect.Field; - public class HelpConstants { public final static String BASE_GATK_URL = "http://www.broadinstitute.org/gatk"; @@ -41,41 +34,4 @@ public class HelpConstants { public static String forumPost(String post) { return GATK_FORUM_URL + post; } - - protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) { - try { - Class type = getClassForDoc(classDoc); - return lhsClass.isAssignableFrom(type) && (!requireConcrete || JVMUtils.isConcrete(type)); - } catch (Throwable t) { - // Ignore errors. - return false; - } - } - - protected static Class getClassForDoc(ProgramElementDoc doc) throws ClassNotFoundException { - return Class.forName(getClassName(doc)); - } - - protected static Field getFieldForFieldDoc(FieldDoc fieldDoc) { - try { - Class clazz = getClassForDoc(fieldDoc.containingClass()); - return JVMUtils.findField(clazz, fieldDoc.name()); - } catch (ClassNotFoundException e) { - throw new RuntimeException(e); - } - } - - /** - * Reconstitute the class name from the given class JavaDoc object. - * - * @param doc the Javadoc model for the given class. - * @return The (string) class name of the given class. - */ - protected static String getClassName(ProgramElementDoc doc) { - PackageDoc containingPackage = doc.containingPackage(); - return containingPackage.name().length() > 0 ? - String.format("%s.%s", containingPackage.name(), doc.name()) : - String.format("%s", doc.name()); - } - } \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java new file mode 100644 index 000000000..fbd69c762 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRArgumentSet.java @@ -0,0 +1,77 @@ +/* + * Copyright (c) 2010 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.utils.recalibration; + +import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; + +import java.io.File; + +public class BQSRArgumentSet { + // declare public, STL-style for easier and more efficient access: + private File BQSR_RECAL_FILE; + private int quantizationLevels; + private boolean disableIndelQuals; + private boolean emitOriginalQuals; + private int PRESERVE_QSCORES_LESS_THAN; + + public BQSRArgumentSet(final GATKArgumentCollection args) { + this.BQSR_RECAL_FILE = args.BQSR_RECAL_FILE; + this.quantizationLevels = args.quantizationLevels; + this.disableIndelQuals = args.disableIndelQuals; + this.emitOriginalQuals = args.emitOriginalQuals; + this.PRESERVE_QSCORES_LESS_THAN = args.PRESERVE_QSCORES_LESS_THAN; + } + + public File getRecalFile() { return BQSR_RECAL_FILE; } + + public int getQuantizationLevels() { return quantizationLevels; } + + public boolean shouldDisableIndelQuals() { return disableIndelQuals; } + + public boolean shouldEmitOriginalQuals() { return emitOriginalQuals; } + + public int getPreserveQscoresLessThan() { return PRESERVE_QSCORES_LESS_THAN; } + + public void setRecalFile(final File BQSR_RECAL_FILE) { + this.BQSR_RECAL_FILE = BQSR_RECAL_FILE; + } + + public void setQuantizationLevels(final int quantizationLevels) { + this.quantizationLevels = quantizationLevels; + } + + public void setDisableIndelQuals(final boolean disableIndelQuals) { + this.disableIndelQuals = disableIndelQuals; + } + + public void setEmitOriginalQuals(final boolean emitOriginalQuals) { + this.emitOriginalQuals = emitOriginalQuals; + } + + public void setPreserveQscoresLessThan(final int PRESERVE_QSCORES_LESS_THAN) { + this.PRESERVE_QSCORES_LESS_THAN = PRESERVE_QSCORES_LESS_THAN; + } +} diff --git a/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java index 5d9a6d476..4d1e70340 100755 --- a/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java @@ -499,7 +499,6 @@ public class VariantContextUtils { final VariantContext first = VCs.get(0); final String name = first.getSource(); final Allele refAllele = determineReferenceAllele(VCs); - Byte referenceBaseForIndel = null; final Set alleles = new LinkedHashSet(); final Set filters = new HashSet(); diff --git a/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java index d8905ad35..e96aae07a 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.PrintReads; +import org.broadinstitute.sting.gatk.walkers.readutils.PrintReads; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java deleted file mode 100755 index 783a8d7fc..000000000 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLiteIntegrationTest.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.broadinstitute.sting.gatk.walkers.genotyper; - -import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; -import org.testng.SkipException; -import org.testng.annotations.Test; - -import java.util.Arrays; - -// ********************************************************************************** // -// Note that this class also serves as an integration test for the VariantAnnotator! // -// ********************************************************************************** // - -public class UnifiedGenotyperLiteIntegrationTest extends WalkerTest { - - private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129; - - // -------------------------------------------------------------------------------------------------------------- - // - // testing contamination down-sampling gets ignored - // - // -------------------------------------------------------------------------------------------------------------- - - @Test - public void testContaminationDownsampling() { - if ( !GATKLiteUtils.isGATKLite() ) - throw new SkipException("Only want to test for GATK lite"); - - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("9addd225a985178339a0c49dc5fdc220")); - executeTest("test contamination_percentage_to_filter gets ignored", spec); - } - -} diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/FlagStatIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/FlagStatIntegrationTest.java similarity index 92% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/FlagStatIntegrationTest.java rename to public/java/test/org/broadinstitute/sting/gatk/walkers/qc/FlagStatIntegrationTest.java index d2acaa588..aaebfc588 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/FlagStatIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/FlagStatIntegrationTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.qc; import org.broadinstitute.sting.WalkerTest; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java similarity index 98% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java rename to public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java index b457698e9..05c82806d 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.qc; import org.broadinstitute.sting.WalkerTest; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java similarity index 98% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java rename to public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java index ade9bda16..a19b3724f 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.readutils; import org.broadinstitute.sting.WalkerTest; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java similarity index 97% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java rename to public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java index 717d9d953..247000431 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.readutils; import org.broadinstitute.sting.WalkerTest; import org.testng.annotations.DataProvider; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsLargeScaleTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsLargeScaleTest.java similarity index 92% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsLargeScaleTest.java rename to public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsLargeScaleTest.java index ad7ac56f9..81a3082a2 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsLargeScaleTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsLargeScaleTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.readutils; import org.broadinstitute.sting.WalkerTest; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java similarity index 94% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java rename to public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java index 1aaa00aee..0da3b6b1f 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.gatk.walkers; +package org.broadinstitute.sting.gatk.walkers.readutils; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMRecord; @@ -59,7 +59,7 @@ public class PrintReadsUnitTest extends BaseTest { private ReferenceContext bases = null; //private ReferenceContext ref = new ReferenceContext() - PrintReads walker; + org.broadinstitute.sting.gatk.walkers.readutils.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 PrintReads(); + walker = new org.broadinstitute.sting.gatk.walkers.readutils.PrintReads(); writer = new ArtificialSAMFileWriter(); walker.out = writer; walker.initialize(); diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala deleted file mode 100755 index 165e6a4e9..000000000 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ /dev/null @@ -1,496 +0,0 @@ -package org.broadinstitute.sting.queue.qscripts - -import org.broadinstitute.sting.queue.extensions.gatk._ -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.extensions.picard._ -import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel -import org.broadinstitute.sting.utils.baq.BAQ.CalculationMode - -import collection.JavaConversions._ -import net.sf.samtools.SAMFileReader -import net.sf.samtools.SAMFileHeader.SortOrder - -import org.broadinstitute.sting.queue.util.QScriptUtils -import org.broadinstitute.sting.queue.function.ListWriterFunction -import org.broadinstitute.sting.commandline.Hidden -import org.broadinstitute.sting.commandline - -class DataProcessingPipeline extends QScript { - qscript => - - /**************************************************************************** - * Required Parameters - ****************************************************************************/ - - - @Input(doc="input BAM file - or list of BAM files", fullName="input", shortName="i", required=true) - var input: File = _ - - @Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true) - var reference: File = _ - - @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true) - var dbSNP: Seq[File] = Seq() - - /**************************************************************************** - * Optional Parameters - ****************************************************************************/ - - @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false) - var indels: Seq[File] = Seq() - - @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false) - var bwaPath: File = _ - - @Argument(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false) - var projectName: String = "project" - - @Argument(doc="Output path for the processed BAM files.", fullName="output_directory", shortName="outputDir", required=false) - var outputDir: String = "" - - @Argument(doc="the -L interval string to be used by GATK - output bams at interval only", fullName="gatk_interval_string", shortName="L", required=false) - var intervalString: String = "" - - @Input(doc="an intervals file to be used by GATK - output bams at intervals only", fullName="gatk_interval_file", shortName="intervals", required=false) - var intervals: File = _ - - @Argument(doc="Cleaning model: KNOWNS_ONLY, USE_READS or USE_SW", fullName="clean_model", shortName="cm", required=false) - var cleaningModel: String = "USE_READS" - - @Argument(doc="Decompose input BAM file and fully realign it using BWA and assume Single Ended reads", fullName="use_bwa_single_ended", shortName="bwase", required=false) - var useBWAse: Boolean = false - - @Argument(doc="Decompose input BAM file and fully realign it using BWA and assume Pair Ended reads", fullName="use_bwa_pair_ended", shortName="bwape", required=false) - var useBWApe: Boolean = false - - @Argument(doc="Decompose input BAM file and fully realign it using BWA SW", fullName="use_bwa_sw", shortName="bwasw", required=false) - var useBWAsw: Boolean = false - - @Argument(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false) - var bwaThreads: Int = 1 - - @Argument(doc="Perform validation on the BAM files", fullName="validation", shortName="vs", required=false) - var validation: Boolean = false - - - /**************************************************************************** - * Hidden Parameters - ****************************************************************************/ - @Hidden - @Argument(doc="How many ways to scatter/gather", fullName="scatter_gather", shortName="sg", required=false) - var nContigs: Int = -1 - - @Hidden - @Argument(doc="Define the default platform for Count Covariates -- useful for techdev purposes only.", fullName="default_platform", shortName="dp", required=false) - var defaultPlatform: String = "" - - @Hidden - @Argument(doc="Run the pipeline in test mode only", fullName = "test_mode", shortName = "test", required=false) - var testMode: Boolean = false - - - /**************************************************************************** - * Global Variables - ****************************************************************************/ - - val queueLogDir: String = ".qlog/" // Gracefully hide Queue's output - - var cleanModelEnum: ConsensusDeterminationModel = ConsensusDeterminationModel.USE_READS - - - - - /**************************************************************************** - * Helper classes and methods - ****************************************************************************/ - - class ReadGroup (val id: String, - val lb: String, - val pl: String, - val pu: String, - val sm: String, - val cn: String, - val ds: String) - {} - - // Utility function to merge all bam files of similar samples. Generates one BAM file per sample. - // It uses the sample information on the header of the input BAM files. - // - // Because the realignment only happens after these scripts are executed, in case you are using - // bwa realignment, this function will operate over the original bam files and output over the - // (to be realigned) bam files. - def createSampleFiles(bamFiles: Seq[File], realignedBamFiles: Seq[File]): Map[String, Seq[File]] = { - - // Creating a table with SAMPLE information from each input BAM file - val sampleTable = scala.collection.mutable.Map.empty[String, Seq[File]] - val realignedIterator = realignedBamFiles.iterator - for (bam <- bamFiles) { - val rBam = realignedIterator.next() // advance to next element in the realignedBam list so they're in sync. - - val samReader = new SAMFileReader(bam) - val header = samReader.getFileHeader - val readGroups = header.getReadGroups - - // only allow one sample per file. Bam files with multiple samples would require pre-processing of the file - // with PrintReads to separate the samples. Tell user to do it himself! - assert(!QScriptUtils.hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam) - - // Fill out the sample table with the readgroups in this file - for (rg <- readGroups) { - val sample = rg.getSample - if (!sampleTable.contains(sample)) - sampleTable(sample) = Seq(rBam) - else if ( !sampleTable(sample).contains(rBam)) - sampleTable(sample) :+= rBam - } - } - sampleTable.toMap - } - - // Rebuilds the Read Group string to give BWA - def addReadGroups(inBam: File, outBam: File, samReader: SAMFileReader) { - val readGroups = samReader.getFileHeader.getReadGroups - var index: Int = readGroups.length - for (rg <- readGroups) { - val intermediateInBam: File = if (index == readGroups.length) { inBam } else { swapExt(outBam, ".bam", index+1 + "-rg.bam") } - val intermediateOutBam: File = if (index > 1) {swapExt(outBam, ".bam", index + "-rg.bam") } else { outBam} - val readGroup = new ReadGroup(rg.getReadGroupId, rg.getLibrary, rg.getPlatform, rg.getPlatformUnit, rg.getSample, rg.getSequencingCenter, rg.getDescription) - add(addReadGroup(intermediateInBam, intermediateOutBam, readGroup)) - index = index - 1 - } - } - - // Takes a list of processed BAM files and realign them using the BWA option requested (bwase or bwape). - // Returns a list of realigned BAM files. - def performAlignment(bams: Seq[File]): Seq[File] = { - var realignedBams: Seq[File] = Seq() - var index = 1 - for (bam <- bams) { - // first revert the BAM file to the original qualities - val saiFile1 = swapExt(bam, ".bam", "." + index + ".1.sai") - val saiFile2 = swapExt(bam, ".bam", "." + index + ".2.sai") - val realignedSamFile = swapExt(bam, ".bam", "." + index + ".realigned.sam") - val realignedBamFile = swapExt(bam, ".bam", "." + index + ".realigned.bam") - val rgRealignedBamFile = swapExt(bam, ".bam", "." + index + ".realigned.rg.bam") - - if (useBWAse) { - val revertedBAM = revertBAM(bam, true) - add(bwa_aln_se(revertedBAM, saiFile1), - bwa_sam_se(revertedBAM, saiFile1, realignedSamFile)) - } - else if (useBWApe) { - val revertedBAM = revertBAM(bam, true) - add(bwa_aln_pe(revertedBAM, saiFile1, 1), - bwa_aln_pe(revertedBAM, saiFile2, 2), - bwa_sam_pe(revertedBAM, saiFile1, saiFile2, realignedSamFile)) - } - else if (useBWAsw) { - val revertedBAM = revertBAM(bam, false) - val fastQ = swapExt(revertedBAM, ".bam", ".fq") - add(convertToFastQ(revertedBAM, fastQ), - bwa_sw(fastQ, realignedSamFile)) - } - add(sortSam(realignedSamFile, realignedBamFile, SortOrder.coordinate)) - addReadGroups(realignedBamFile, rgRealignedBamFile, new SAMFileReader(bam)) - realignedBams :+= rgRealignedBamFile - index = index + 1 - } - realignedBams - } - - def getIndelCleaningModel: ConsensusDeterminationModel = { - if (cleaningModel == "KNOWNS_ONLY") - ConsensusDeterminationModel.KNOWNS_ONLY - else if (cleaningModel == "USE_SW") - ConsensusDeterminationModel.USE_SW - else - ConsensusDeterminationModel.USE_READS - } - - def revertBams(bams: Seq[File], removeAlignmentInformation: Boolean): Seq[File] = { - var revertedBAMList: Seq[File] = Seq() - for (bam <- bams) - revertedBAMList :+= revertBAM(bam, removeAlignmentInformation) - revertedBAMList - } - - def revertBAM(bam: File, removeAlignmentInformation: Boolean): File = { - val revertedBAM = swapExt(bam, ".bam", ".reverted.bam") - add(revert(bam, revertedBAM, removeAlignmentInformation)) - revertedBAM - } - - /**************************************************************************** - * Main script - ****************************************************************************/ - - - def script() { - // final output list of processed bam files - var cohortList: Seq[File] = Seq() - - // sets the model for the Indel Realigner - cleanModelEnum = getIndelCleaningModel - - // keep a record of the number of contigs in the first bam file in the list - val bams = QScriptUtils.createSeqFromFile(input) - if (nContigs < 0) - nContigs = QScriptUtils.getNumberOfContigs(bams(0)) - - val realignedBAMs = if (useBWApe || useBWAse || useBWAsw) {performAlignment(bams)} else {revertBams(bams, false)} - - // generate a BAM file per sample joining all per lane files if necessary - val sampleBAMFiles: Map[String, Seq[File]] = createSampleFiles(bams, realignedBAMs) - - // if this is a 'knowns only' indel realignment run, do it only once for all samples. - val globalIntervals = new File(outputDir + projectName + ".intervals") - if (cleaningModel == ConsensusDeterminationModel.KNOWNS_ONLY) - add(target(null, globalIntervals)) - - // put each sample through the pipeline - for ((sample, bamList) <- sampleBAMFiles) { - - // BAM files generated by the pipeline - val bam = new File(qscript.projectName + "." + sample + ".bam") - val cleanedBam = swapExt(bam, ".bam", ".clean.bam") - val dedupedBam = swapExt(bam, ".bam", ".clean.dedup.bam") - val recalBam = swapExt(bam, ".bam", ".clean.dedup.recal.bam") - - // Accessory files - val targetIntervals = if (cleaningModel == ConsensusDeterminationModel.KNOWNS_ONLY) {globalIntervals} else {swapExt(bam, ".bam", ".intervals")} - val metricsFile = swapExt(bam, ".bam", ".metrics") - val preRecalFile = swapExt(bam, ".bam", ".pre_recal.table") - val postRecalFile = swapExt(bam, ".bam", ".post_recal.table") - val preOutPath = swapExt(bam, ".bam", ".pre") - val postOutPath = swapExt(bam, ".bam", ".post") - val preValidateLog = swapExt(bam, ".bam", ".pre.validation") - val postValidateLog = swapExt(bam, ".bam", ".post.validation") - - - // Validation is an optional step for the BAM file generated after - // alignment and the final bam file of the pipeline. - if (validation) { - for (sampleFile <- bamList) - add(validate(sampleFile, preValidateLog), - validate(recalBam, postValidateLog)) - } - - if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY) - add(target(bamList, targetIntervals)) - - add(clean(bamList, targetIntervals, cleanedBam), - dedup(cleanedBam, dedupedBam, metricsFile), - cov(dedupedBam, preRecalFile), - recal(dedupedBam, preRecalFile, recalBam), - cov(recalBam, postRecalFile)) - - - cohortList :+= recalBam - } - - // output a BAM list with all the processed per sample files - val cohortFile = new File(qscript.outputDir + qscript.projectName + ".cohort.list") - add(writeList(cohortList, cohortFile)) - } - - - - /**************************************************************************** - * Classes (GATK Walkers) - ****************************************************************************/ - - - - // General arguments to non-GATK tools - trait ExternalCommonArgs extends CommandLineFunction { - this.memoryLimit = 4 - this.isIntermediate = true - } - - // General arguments to GATK walkers - trait CommandLineGATKArgs extends CommandLineGATK with ExternalCommonArgs { - this.reference_sequence = qscript.reference - } - - trait SAMargs extends PicardBamFunction with ExternalCommonArgs { - this.maxRecordsInRam = 100000 - } - - case class target (inBams: Seq[File], outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs { - if (cleanModelEnum != ConsensusDeterminationModel.KNOWNS_ONLY) - this.input_file = inBams - this.out = outIntervals - this.mismatchFraction = 0.0 - this.known ++= qscript.dbSNP - if (indels != null) - this.known ++= qscript.indels - this.scatterCount = nContigs - this.analysisName = queueLogDir + outIntervals + ".target" - this.jobName = queueLogDir + outIntervals + ".target" - } - - case class clean (inBams: Seq[File], tIntervals: File, outBam: File) extends IndelRealigner with CommandLineGATKArgs { - this.input_file = inBams - this.targetIntervals = tIntervals - this.out = outBam - this.known ++= qscript.dbSNP - if (qscript.indels != null) - this.known ++= qscript.indels - this.consensusDeterminationModel = cleanModelEnum - this.compress = 0 - this.noPGTag = qscript.testMode; - this.scatterCount = nContigs - this.analysisName = queueLogDir + outBam + ".clean" - this.jobName = queueLogDir + outBam + ".clean" - } - - case class cov (inBam: File, outRecalFile: File) extends BaseRecalibrator with CommandLineGATKArgs { - this.knownSites ++= qscript.dbSNP - this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate") - this.input_file :+= inBam - this.disable_indel_quals = true - this.out = outRecalFile - if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform - if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString) - else if (qscript.intervals != null) this.intervals :+= qscript.intervals - this.scatterCount = nContigs - this.analysisName = queueLogDir + outRecalFile + ".covariates" - this.jobName = queueLogDir + outRecalFile + ".covariates" - } - - case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs { - this.input_file :+= inBam - this.BQSR = inRecalFile - this.baq = CalculationMode.CALCULATE_AS_NECESSARY - this.out = outBam - if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString) - else if (qscript.intervals != null) this.intervals :+= qscript.intervals - this.scatterCount = nContigs - this.isIntermediate = false - this.analysisName = queueLogDir + outBam + ".recalibration" - this.jobName = queueLogDir + outBam + ".recalibration" - } - - - - /**************************************************************************** - * Classes (non-GATK programs) - ****************************************************************************/ - - - case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs { - this.input :+= inBam - this.output = outBam - this.metrics = metricsFile - this.memoryLimit = 16 - this.analysisName = queueLogDir + outBam + ".dedup" - this.jobName = queueLogDir + outBam + ".dedup" - } - - case class joinBams (inBams: Seq[File], outBam: File) extends MergeSamFiles with ExternalCommonArgs { - this.input = inBams - this.output = outBam - this.analysisName = queueLogDir + outBam + ".joinBams" - this.jobName = queueLogDir + outBam + ".joinBams" - } - - case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam with ExternalCommonArgs { - this.input :+= inSam - this.output = outBam - this.sortOrder = sortOrderP - this.analysisName = queueLogDir + outBam + ".sortSam" - this.jobName = queueLogDir + outBam + ".sortSam" - } - - case class validate (inBam: File, outLog: File) extends ValidateSamFile with ExternalCommonArgs { - this.input :+= inBam - this.output = outLog - this.REFERENCE_SEQUENCE = qscript.reference - this.isIntermediate = false - this.analysisName = queueLogDir + outLog + ".validate" - this.jobName = queueLogDir + outLog + ".validate" - } - - - case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups with ExternalCommonArgs { - this.input :+= inBam - this.output = outBam - this.RGID = readGroup.id - this.RGCN = readGroup.cn - this.RGDS = readGroup.ds - this.RGLB = readGroup.lb - this.RGPL = readGroup.pl - this.RGPU = readGroup.pu - this.RGSM = readGroup.sm - this.analysisName = queueLogDir + outBam + ".rg" - this.jobName = queueLogDir + outBam + ".rg" - } - - case class revert (inBam: File, outBam: File, removeAlignmentInfo: Boolean) extends RevertSam with ExternalCommonArgs { - this.output = outBam - this.input :+= inBam - this.removeAlignmentInformation = removeAlignmentInfo; - this.sortOrder = if (removeAlignmentInfo) {SortOrder.queryname} else {SortOrder.coordinate} - this.analysisName = queueLogDir + outBam + "revert" - this.jobName = queueLogDir + outBam + ".revert" - } - - case class convertToFastQ (inBam: File, outFQ: File) extends SamToFastq with ExternalCommonArgs { - this.input :+= inBam - this.fastq = outFQ - this.analysisName = queueLogDir + outFQ + "convert_to_fastq" - this.jobName = queueLogDir + outFQ + ".convert_to_fastq" - } - - case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with ExternalCommonArgs { - @Input(doc="bam file to be aligned") var bam = inBam - @Output(doc="output sai file") var sai = outSai - def commandLine = bwaPath + " aln -t " + bwaThreads + " -q 5 " + reference + " -b " + bam + " > " + sai - this.analysisName = queueLogDir + outSai + ".bwa_aln_se" - this.jobName = queueLogDir + outSai + ".bwa_aln_se" - } - - case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with ExternalCommonArgs { - @Input(doc="bam file to be aligned") var bam = inBam - @Output(doc="output sai file for 1st mating pair") var sai = outSai1 - def commandLine = bwaPath + " aln -t " + bwaThreads + " -q 5 " + reference + " -b" + index + " " + bam + " > " + sai - this.analysisName = queueLogDir + outSai1 + ".bwa_aln_pe1" - this.jobName = queueLogDir + outSai1 + ".bwa_aln_pe1" - } - - case class bwa_sam_se (inBam: File, inSai: File, outBam: File) extends CommandLineFunction with ExternalCommonArgs { - @Input(doc="bam file to be aligned") var bam = inBam - @Input(doc="bwa alignment index file") var sai = inSai - @Output(doc="output aligned bam file") var alignedBam = outBam - def commandLine = bwaPath + " samse " + reference + " " + sai + " " + bam + " > " + alignedBam - this.memoryLimit = 6 - this.analysisName = queueLogDir + outBam + ".bwa_sam_se" - this.jobName = queueLogDir + outBam + ".bwa_sam_se" - } - - case class bwa_sam_pe (inBam: File, inSai1: File, inSai2:File, outBam: File) extends CommandLineFunction with ExternalCommonArgs { - @Input(doc="bam file to be aligned") var bam = inBam - @Input(doc="bwa alignment index file for 1st mating pair") var sai1 = inSai1 - @Input(doc="bwa alignment index file for 2nd mating pair") var sai2 = inSai2 - @Output(doc="output aligned bam file") var alignedBam = outBam - def commandLine = bwaPath + " sampe " + reference + " " + sai1 + " " + sai2 + " " + bam + " " + bam + " > " + alignedBam - this.memoryLimit = 6 - this.analysisName = queueLogDir + outBam + ".bwa_sam_pe" - this.jobName = queueLogDir + outBam + ".bwa_sam_pe" - } - - case class bwa_sw (inFastQ: File, outBam: File) extends CommandLineFunction with ExternalCommonArgs { - @Input(doc="fastq file to be aligned") var fq = inFastQ - @Output(doc="output bam file") var bam = outBam - def commandLine = bwaPath + " bwasw -t " + bwaThreads + " " + reference + " " + fq + " > " + bam - this.analysisName = queueLogDir + outBam + ".bwasw" - this.jobName = queueLogDir + outBam + ".bwasw" - } - - case class writeList(inBams: Seq[File], outBamList: File) extends ListWriterFunction { - this.inputFiles = inBams - this.listFile = outBamList - this.analysisName = queueLogDir + outBamList + ".bamList" - this.jobName = queueLogDir + outBamList + ".bamList" - } -} diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala deleted file mode 100755 index b860358ca..000000000 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +++ /dev/null @@ -1,373 +0,0 @@ -package org.broadinstitute.sting.queue.qscripts - -import org.broadinstitute.sting.queue.extensions.gatk._ -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.gatk.phonehome.GATKRunReport - -class MethodsDevelopmentCallingPipeline extends QScript { - qscript => - - @Argument(shortName="outputDir", doc="output directory", required=false) - var outputDir: String = "./" - - @Argument(shortName="skipCalling", doc="skip the calling part of the pipeline and only run VQSR on preset, gold standard VCF files", required=false) - var skipCalling: Boolean = false - - @Argument(shortName="dataset", doc="selects the datasets to run. If not provided, all datasets will be used", required=false) - var datasets: List[String] = Nil - - @Argument(shortName="runGoldStandard", doc="run the pipeline with the goldstandard VCF files for comparison", required=false) - var runGoldStandard: Boolean = false - - @Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false) - var noBAQ: Boolean = false - - @Argument(shortName="noIndels", doc="do not call indels with the Unified Genotyper", required=false) - var noIndels: Boolean = false - - @Argument(shortName="mbq", doc="The minimum Phred-Scaled quality score threshold to be considered a good base.", required=false) - var minimumBaseQuality: Int = -1 - - @Argument(shortName="deletions", doc="Maximum deletion fraction allowed at a site to call a genotype.", required=false) - var deletions: Double = -1 - - @Argument(shortName="sample", doc="Samples to include in Variant Eval", required=false) - var samples: List[String] = Nil - - class Target( - val baseName: String, - val reference: File, - val dbsnpFile: String, - val hapmapFile: String, - val maskFile: String, - val bamList: File, - val goldStandard_VCF: File, - val intervals: String, - val indelTranchTarget: Double, - val snpTrancheTarget: Double, - val isLowpass: Boolean, - val isExome: Boolean, - val nSamples: Int) { - val name = qscript.outputDir + baseName - val clusterFile = new File(name + ".clusters") - val rawSnpVCF = new File(name + ".raw.vcf") - val rawIndelVCF = new File(name + ".raw.indel.vcf") - val filteredIndelVCF = new File(name + ".filtered.indel.vcf") - val recalibratedSnpVCF = new File(name + ".snp.recalibrated.vcf") - val recalibratedIndelVCF = new File(name + ".indel.recalibrated.vcf") - val tranchesSnpFile = new File(name + ".snp.tranches") - val tranchesIndelFile = new File(name + ".indel.tranches") - val vqsrSnpRscript = name + ".snp.vqsr.r" - val vqsrIndelRscript = name + ".indel.vqsr.r" - val recalSnpFile = new File(name + ".snp.tranches.recal") - val recalIndelFile = new File(name + ".indel.tranches.recal") - val goldStandardRecalibratedVCF = new File(name + "goldStandard.recalibrated.vcf") - val goldStandardTranchesFile = new File(name + "goldStandard.tranches") - val goldStandardRecalFile = new File(name + "goldStandard.tranches.recal") - val evalFile = new File(name + ".snp.eval") - val evalIndelFile = new File(name + ".indel.eval") - val goldStandardName = qscript.outputDir + "goldStandard/" + baseName - val goldStandardClusterFile = new File(goldStandardName + ".clusters") - } - - val b37_decoy = new File("/humgen/1kg/reference/human_g1k_v37_decoy.fasta") - val hg19 = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta") - val hg18 = new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta") - val b36 = new File("/humgen/1kg/reference/human_b36_both.fasta") - val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta") - val dbSNP_hg18_129 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_hg18.rod" // Special case for NA12878 collections that can't use 132 because they are part of it. - val dbSNP_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_132.b36.excluding_sites_after_129.vcf" - val dbSNP_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.leftAligned.vcf" // Special case for NA12878 collections that can't use 132 because they are part of it. - val hapmap_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.hg18_fwd.vcf" - val hapmap_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b36_fwd.vcf" - val hapmap_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" - val training_hapmap_b37 = "/humgen/1kg/processing/pipeline_test_bams/hapmap3.3_training_chr20.vcf" - val omni_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni25_sites_1525_samples.b36.vcf" - val omni_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" - val indelMask_b36 = "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.b36.bed" - val indelMask_b37 = "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.b37.bed" - val training_1000G = "/humgen/1kg/processing/official_release/phase1/projectConsensus/phase1.wgs.projectConsensus.v2b.recal.highQuality.vcf" - val badSites_1000G = "/humgen/1kg/processing/official_release/phase1/projectConsensus/phase1.wgs.projectConsensus.v2b.recal.terrible.vcf" - val projectConsensus_1000G = "/humgen/1kg/processing/official_release/phase1/projectConsensus/ALL.wgs.projectConsensus_v2b.20101123.snps.sites.vcf" - val indelGoldStandardCallset = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf" - - val lowPass: Boolean = true - val exome: Boolean = true - val indels: Boolean = true - - val queueLogDir = ".qlog/" - - // BUGBUG: We no longer support b36/hg18 because several of the necessary files aren't available aligned to those references - - val targetDataSets: Map[String, Target] = Map( - "NA12878_gold" -> new Target("NA12878.goldStandard", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/data/goldStandard.list"), - new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** There is no gold standard for the gold standard ** - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 90.0, 99.0, lowPass, !exome, 391), - "NA12878_wgs_b37" -> new Target("NA12878.HiSeq.WGS.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 1), - "NA12878_wgs_decoy" -> new Target("NA12878.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 1), - "NA12878_wgs_hg18" -> new Target("NA12878.HiSeq.WGS.hg18", hg18, dbSNP_hg18_129, hapmap_hg18, - "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask", - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"), - new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"), - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 90.0, 99.0, !lowPass, !exome, 1), - "NA12878_wex_b37" -> new Target("NA12878.HiSeq.WEx.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/seq/picard_aggregation/C339/NA12878/v3/NA12878.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** - "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 90.0, 98.0, !lowPass, exome, 1), - "NA12878_wex_hg18" -> new Target("NA12878.HiSeq.WEx.hg18", hg18, dbSNP_hg18_129, hapmap_hg18, - "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.indels.10.mask", - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.WEx.cleaned.recal.bam"), - new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"), - "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 90.0, 98.0, !lowPass, exome, 1), - "NA12878_wex_decoy" -> new Target("NA12878.HiSeq.WEx.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.b37_decoy.NA12878.clean.dedup.recal.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** - "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 90.0, 98.0, !lowPass, exome, 1), - "CEUTrio_wex_b37" -> new Target("CEUTrio.HiSeq.WEx.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), - "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 90.0, 98.0, !lowPass, exome, 3), - "CEUTrio_wgs_b37" -> new Target("CEUTrio.HiSeq.WGS.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.bwa.cleaned.recal.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 3), - "CEUTrio_wex_decoy" -> new Target("CEUTrio.HiSeq.WEx.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.b37_decoy.list"), - new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** - "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 90.0, 98.0, !lowPass, exome, 3), - "CEUTrio_wgs_decoy" -> new Target("CEUTrio.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.list"), - new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 3), - "GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"), - new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.GA2.hg19.filtered.vcf"), - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 1), - "FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"), - new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 90.0, 99.0, lowPass, !exome, 79), - "TGPWExGdA" -> new Target("1000G.WEx.GdA", b37, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"), // BUGBUG: reduce from 60 to 20 people - new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** - "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 90.0, 99.0, !lowPass, exome, 96), - "LowPassN60" -> new Target("lowpass.N60", b36, dbSNP_b36, hapmap_b36, indelMask_b36, - new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/lowpass.chr20.cleaned.matefixed.bam"), // the bam list to call from - new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"), // the gold standard VCF file to run through the VQSR - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 90.0, 99.0, lowPass, !exome, 60), // chunked interval list to use with Queue's scatter/gather functionality - "LowPassEUR363Nov" -> new Target("EUR.nov2010", b37, dbSNP_b37, hapmap_b37, indelMask_b37, - new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"), - new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** - "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 90.0, 99.0, lowPass, !exome, 363) - ) - - - def script = { - - // Selects the datasets in the -dataset argument and adds them to targets. - var targets: List[Target] = List() - if (!datasets.isEmpty) - for (ds <- datasets) - targets ::= targetDataSets(ds) - else // If -dataset is not specified, all datasets are used. - for (targetDS <- targetDataSets.valuesIterator) - targets ::= targetDS - - val goldStandard = true - for (target <- targets) { - if( !skipCalling ) { - if (!noIndels) add(new indelCall(target), new indelRecal(target), new indelCut(target), new indelEvaluation(target)) - add(new snpCall(target)) - add(new snpRecal(target, !goldStandard)) - add(new snpCut(target, !goldStandard)) - add(new snpEvaluation(target)) - } - if ( runGoldStandard ) { - add(new snpRecal(target, goldStandard)) - add(new snpCut(target, goldStandard)) - } - } - } - - - trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { - logging_level = "INFO"; - memoryLimit = 4; - phone_home = GATKRunReport.PhoneHomeOption.NO_ET - } - - def bai(bam: File) = new File(bam + ".bai") - - // 1.) Unified Genotyper Base - class GenotyperBase (t: Target) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS { - this.reference_sequence = t.reference - this.intervalsString ++= List(t.intervals) - this.scatterCount = 140 - this.nt = 2 - this.dcov = if ( t.isLowpass ) { 50 } else { 250 } - this.stand_call_conf = if ( t.isLowpass ) { 4.0 } else { 30.0 } - this.stand_emit_conf = if ( t.isLowpass ) { 4.0 } else { 30.0 } - this.input_file :+= t.bamList - this.D = new File(t.dbsnpFile) - } - - // 1a.) Call SNPs with UG - class snpCall (t: Target) extends GenotyperBase(t) { - if (minimumBaseQuality >= 0) - this.min_base_quality_score = minimumBaseQuality - if (qscript.deletions >= 0) - this.max_deletion_fraction = qscript.deletions - this.out = t.rawSnpVCF - this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP - this.baq = if (noBAQ || t.isExome) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY} - this.analysisName = t.name + "_UGs" - this.jobName = queueLogDir + t.name + ".snpcall" - } - - // 1b.) Call Indels with UG - class indelCall (t: Target) extends GenotyperBase(t) { - this.memoryLimit = 6 - this.out = t.rawIndelVCF - this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL - this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF - this.analysisName = t.name + "_UGi" - this.jobName = queueLogDir + t.name + ".indelcall" - } - - // 2.) Hard Filtering for indels - class indelFilter (t: Target) extends VariantFiltration with UNIVERSAL_GATK_ARGS { - this.memoryLimit = 2 - this.reference_sequence = t.reference - this.intervalsString ++= List(t.intervals) - this.scatterCount = 10 - this.V = t.rawIndelVCF - this.out = t.filteredIndelVCF - this.filterName ++= List("IndelQD", "IndelReadPosRankSum", "IndelFS") - this.filterExpression ++= List("QD < 2.0", "ReadPosRankSum < -20.0", "FS > 200.0") - if (t.nSamples >= 10) { - this.filterName ++= List("IndelInbreedingCoeff") - this.filterExpression ++= List("InbreedingCoeff < -0.8") - } - this.analysisName = t.name + "_VF" - this.jobName = queueLogDir + t.name + ".indelfilter" - } - - class VQSRBase(t: Target) extends VariantRecalibrator with UNIVERSAL_GATK_ARGS { - this.nt = 2 - this.reference_sequence = t.reference - this.intervalsString ++= List(t.intervals) - this.allPoly = true - this.tranche ++= List("100.0", "99.9", "99.5", "99.3", "99.0", "98.9", "98.8", "98.5", "98.4", "98.3", "98.2", "98.1", "98.0", "97.9", "97.8", "97.5", "97.0", "95.0", "90.0") - } - - class snpRecal(t: Target, goldStandard: Boolean) extends VQSRBase(t) with UNIVERSAL_GATK_ARGS { - this.input :+= ( if ( goldStandard ) { t.goldStandard_VCF } else { t.rawSnpVCF } ) - this.resource :+= new TaggedFile( t.hapmapFile, "known=false,training=true,truth=true,prior=15.0" ) - this.resource :+= new TaggedFile( omni_b37, "known=false,training=true,truth=true,prior=12.0" ) - this.resource :+= new TaggedFile( training_1000G, "known=false,training=true,prior=10.0" ) - this.resource :+= new TaggedFile( t.dbsnpFile, "known=true,prior=2.0" ) - this.resource :+= new TaggedFile( projectConsensus_1000G, "prior=8.0" ) - this.use_annotation ++= List("QD", "HaplotypeScore", "MQRankSum", "ReadPosRankSum", "MQ", "FS") - if(t.nSamples >= 10) - this.use_annotation ++= List("InbreedingCoeff") // InbreedingCoeff is a population-wide statistic that requires at least 10 samples to calculate - if(!t.isExome) - this.use_annotation ++= List("DP") - else { // exome specific parameters - this.resource :+= new TaggedFile( badSites_1000G, "bad=true,prior=2.0" ) - this.mG = 6 - if(t.nSamples <= 3) { // very few exome samples means very few variants - this.mG = 4 - this.percentBad = 0.04 - } - } - this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesSnpFile } - this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalSnpFile } - this.rscript_file = t.vqsrSnpRscript - this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP - this.analysisName = t.name + "_VQSRs" - this.jobName = queueLogDir + t.name + ".snprecal" - } - - class indelRecal(t: Target) extends VQSRBase(t) with UNIVERSAL_GATK_ARGS { - this.input :+= t.rawIndelVCF - this.resource :+= new TaggedFile(indelGoldStandardCallset, "known=false,training=true,truth=true,prior=12.0" ) - this.resource :+= new TaggedFile( t.dbsnpFile, "known=true,prior=2.0" ) - this.use_annotation ++= List("QD", "HaplotypeScore", "ReadPosRankSum", "FS") - if(t.nSamples >= 10) - this.use_annotation ++= List("InbreedingCoeff") // InbreedingCoeff is a population-wide statistic that requires at least 10 samples to calculate - this.tranches_file = t.tranchesIndelFile - this.recal_file = t.recalIndelFile - this.rscript_file = t.vqsrIndelRscript - this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL - this.analysisName = t.name + "_VQSRi" - this.jobName = queueLogDir + t.name + ".indelrecal" - } - - - // 4.) Apply the recalibration table to the appropriate tranches - class applyVQSRBase (t: Target) extends ApplyRecalibration with UNIVERSAL_GATK_ARGS { - this.memoryLimit = 6 - this.reference_sequence = t.reference - this.intervalsString ++= List(t.intervals) - } - - class snpCut (t: Target, goldStandard: Boolean) extends applyVQSRBase(t) { - this.input :+= ( if ( goldStandard ) { t.goldStandard_VCF } else { t.rawSnpVCF } ) - this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesSnpFile} - this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalSnpFile } - this.ts_filter_level = t.snpTrancheTarget - this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP - this.out = t.recalibratedSnpVCF - this.analysisName = t.name + "_AVQSRs" - this.jobName = queueLogDir + t.name + ".snpcut" - } - - class indelCut (t: Target) extends applyVQSRBase(t) { - this.input :+= t.rawIndelVCF - this.tranches_file = t.tranchesIndelFile - this.recal_file = t.recalIndelFile - this.ts_filter_level = t.indelTranchTarget - this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL - this.out = t.recalibratedIndelVCF - this.analysisName = t.name + "_AVQSRi" - this.jobName = queueLogDir + t.name + ".indelcut" - } - - - // 5.) Variant Evaluation Base(OPTIONAL) - class EvalBase(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS { - this.memoryLimit = 3 - this.comp :+= new TaggedFile(t.hapmapFile, "hapmap" ) - this.D = new File(t.dbsnpFile) - this.reference_sequence = t.reference - this.intervalsString ++= List(t.intervals) - this.sample = samples - } - - // 5a.) SNP Evaluation (OPTIONAL) based on the cut vcf - class snpEvaluation(t: Target) extends EvalBase(t) { - if (t.reference == b37 || t.reference == hg19) this.comp :+= new TaggedFile( omni_b37, "omni" ) - this.eval :+= t.recalibratedSnpVCF - this.out = t.evalFile - this.analysisName = t.name + "_VEs" - this.jobName = queueLogDir + t.name + ".snpeval" - } - - // 5b.) Indel Evaluation (OPTIONAL) - class indelEvaluation(t: Target) extends EvalBase(t) { - this.eval :+= t.recalibratedIndelVCF - this.comp :+= new TaggedFile(indelGoldStandardCallset, "indelGS" ) - this.noEV = true - this.evalModule = List("CompOverlap", "CountVariants", "TiTvVariantEvaluator", "ValidationReport", "IndelStatistics") - this.out = t.evalIndelFile - this.analysisName = t.name + "_VEi" - this.jobName = queueLogDir + queueLogDir + t.name + ".indeleval" - } -} diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala deleted file mode 100755 index ef73840b3..000000000 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala +++ /dev/null @@ -1,188 +0,0 @@ -package org.broadinstitute.sting.queue.qscripts - -import org.broadinstitute.sting.queue.QScript -import org.broadinstitute.sting.queue.util.QScriptUtils -import net.sf.samtools.SAMFileHeader.SortOrder -import org.broadinstitute.sting.utils.exceptions.UserException -import org.broadinstitute.sting.commandline.Hidden -import org.broadinstitute.sting.queue.extensions.picard.{ReorderSam, SortSam, AddOrReplaceReadGroups} -import org.broadinstitute.sting.queue.extensions.gatk._ - -/** - * Created by IntelliJ IDEA. - * User: carneiro - * Date: 4/20/11 - * Time: 16:29 PM - */ - - -class PacbioProcessingPipeline extends QScript { - - @Input(doc="input FASTA/FASTQ/BAM file - or list of FASTA/FASTQ/BAM files. ", shortName="i", required=true) - var input: File = _ - - @Input(doc="Reference fasta file", shortName="R", required=true) - var reference: File = _ - - @Input(doc="dbsnp VCF file to use ", shortName="D", required=true) - var dbSNP: File = _ - - @Argument(doc="Number of jobs to scatter/gather. Default: 0." , shortName = "sg", required=false) - var threads: Int = 0 - - @Argument(doc="Sample Name to fill in the Read Group information (only necessary if using fasta/fastq)" , shortName = "sn", required=false) - var sample: String = "NA" - - @Input(doc="The path to the binary of bwa to align fasta/fastq files", fullName="path_to_bwa", shortName="bwa", required=false) - var bwaPath: File = _ - - @Argument(doc="Input is a BLASR generated BAM file", shortName = "blasr", fullName="blasr_bam", required=false) - var BLASR_BAM: Boolean = false - - @Hidden - @Argument(doc="The default base qualities to use before recalibration. Default is Q20 (should be good for every dataset)." , shortName = "dbq", required=false) - var dbq: Int = 20 - - @Hidden - @Argument(shortName="bwastring", required=false) - var bwastring: String = "" - - @Hidden - @Argument(shortName = "test", fullName = "test_mode", required = false) - var testMode: Boolean = false - - val queueLogDir: String = ".qlog/" - - def script() { - - val fileList: Seq[File] = QScriptUtils.createSeqFromFile(input) - - for (file: File <- fileList) { - - var USE_BWA: Boolean = false - var resetQuals: Boolean = true - - if (file.endsWith(".fasta") || file.endsWith(".fq") || file.endsWith(".fastq")) { - if (bwaPath == null) { - throw new UserException("You provided a fasta/fastq file but didn't provide the path for BWA"); - } - USE_BWA = true - if (file.endsWith(".fq") || file.endsWith(".fastq")) - resetQuals = false - } - - // FASTA -> BAM steps - val alignedSam: File = file.getName + ".aligned.sam" - val sortedBam: File = swapExt(alignedSam, ".sam", ".bam") - val rgBam: File = swapExt(file, ".bam", ".rg.bam") - - val bamBase = if (USE_BWA) {rgBam} else {file} - - // BAM Steps - val mqBAM: File = swapExt(bamBase, ".bam", ".mq.bam") - val recalFile1: File = swapExt(bamBase, ".bam", ".recal1.table") - val recalFile2: File = swapExt(bamBase, ".bam", ".recal2.table") - val recalBam: File = swapExt(bamBase, ".bam", ".recal.bam") - val path1: String = recalBam + ".before" - val path2: String = recalBam + ".after" - - if (USE_BWA) { - add(align(file, alignedSam), - sortSam(alignedSam, sortedBam), - addReadGroup(sortedBam, rgBam, sample)) - } - - else if (BLASR_BAM) { - val reorderedBAM = swapExt(bamBase, ".bam", ".reordered.bam") - add(reorder(bamBase, reorderedBAM), - changeMQ(reorderedBAM, mqBAM)) - } - - val bam = if (BLASR_BAM) {mqBAM} else {bamBase} - - add(cov(bam, recalFile1, resetQuals), - recal(bam, recalFile1, recalBam), - cov(recalBam, recalFile2, false)) - } - } - - - // General arguments to non-GATK tools - trait ExternalCommonArgs extends CommandLineFunction { - this.memoryLimit = 4 - this.isIntermediate = true - } - - trait CommandLineGATKArgs extends CommandLineGATK with ExternalCommonArgs { - this.reference_sequence = reference - } - - - case class align(@Input inFastq: File, @Output outSam: File) extends ExternalCommonArgs { - def commandLine = bwaPath + " bwasw -b5 -q2 -r1 -z20 -t16 " + reference + " " + inFastq + " > " + outSam - this.memoryLimit = 8 - this.analysisName = queueLogDir + outSam + ".bwa_sam_se" - this.jobName = queueLogDir + outSam + ".bwa_sam_se" - } - - case class sortSam (inSam: File, outBam: File) extends SortSam with ExternalCommonArgs { - this.input = List(inSam) - this.output = outBam - this.memoryLimit = 8 - this.sortOrder = SortOrder.coordinate - this.analysisName = queueLogDir + outBam + ".sortSam" - this.jobName = queueLogDir + outBam + ".sortSam" - } - - case class reorder (inSam: File, outSam: File) extends ReorderSam with ExternalCommonArgs { - this.input = List(inSam) - this.output = outSam - this.sortReference = reference - } - - case class changeMQ(inBam: File, outBam: File) extends PrintReads with CommandLineGATKArgs { - this.input_file :+= inBam - this.out = outBam - this.read_filter :+= "ReassignMappingQuality" - } - - case class addReadGroup (inBam: File, outBam: File, sample: String) extends AddOrReplaceReadGroups with ExternalCommonArgs { - @Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai") - this.input = List(inBam) - this.output = outBam - this.RGID = "1" - this.RGCN = "BI" - this.RGPL = "PacBio_RS" - this.RGSM = sample - this.RGLB = "default_library" - this.RGPU = "default_pu" - this.analysisName = queueLogDir + outBam + ".rg" - this.jobName = queueLogDir + outBam + ".rg" - } - - case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends BaseRecalibrator with CommandLineGATKArgs { - if (resetQuals) - this.DBQ = dbq - this.knownSites :+= dbSNP - this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate") - this.input_file :+= inBam - this.disable_indel_quals = true - this.out = outRecalFile - this.analysisName = queueLogDir + outRecalFile + ".covariates" - this.jobName = queueLogDir + outRecalFile + ".covariates" - this.scatterCount = threads - this.read_filter :+= "BadCigar" - } - - case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs { - this.DBQ = dbq - this.input_file :+= inBam - this.BQSR = inRecalFile - this.out = outBam - this.isIntermediate = false - this.analysisName = queueLogDir + outBam + ".recalibration" - this.jobName = queueLogDir + outBam + ".recalibration" - this.read_filter :+= "BadCigar" - this.scatterCount = threads - } -} diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala deleted file mode 100644 index 60c9d9a59..000000000 --- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala +++ /dev/null @@ -1,67 +0,0 @@ -package org.broadinstitute.sting.queue.pipeline - -/* - * Copyright (c) 2011, 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. - */ - -import org.testng.annotations.Test -import org.broadinstitute.sting.BaseTest - -class DataProcessingPipelineTest { - @Test(timeOut=36000000) - def testSimpleBAM { - val projectName = "test1" - val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam" - val spec = new PipelineTestSpec - spec.name = "DataProcessingPipeline" - spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala", - " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", - " -i " + BaseTest.publicTestDir + "exampleBAM.bam", - " -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf", - " -test ", - " -p " + projectName).mkString - spec.fileMD5s += testOut -> "45d97df6d291695b92668e8a55c54cd0" - PipelineTest.executeTest(spec) - } - - @Test(timeOut=36000000) - def testBWAPEBAM { - val projectName = "test2" - val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam" - val spec = new PipelineTestSpec - spec.name = "DataProcessingPipeline" - spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala", - " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", - " -i " + BaseTest.publicTestDir + "exampleBAM.bam", - " -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf", - " -test ", - " -bwa /home/unix/carneiro/bin/bwa", - " -bwape ", - " -p " + projectName).mkString - spec.fileMD5s += testOut -> "9fca827ecc8436465b831bb6f879357a" - PipelineTest.executeTest(spec) - } - -} diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala deleted file mode 100644 index dd07cbfdc..000000000 --- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala +++ /dev/null @@ -1,46 +0,0 @@ -package org.broadinstitute.sting.queue.pipeline - -/* - * Copyright (c) 2011, 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. - */ - -import org.testng.annotations.Test -import org.broadinstitute.sting.BaseTest - -class PacbioProcessingPipelineTest { - @Test(timeOut=36000000) - def testPacbioProcessingPipeline { - val testOut = "exampleBAM.recal.bam" - val spec = new PipelineTestSpec - spec.name = "pacbioProcessingPipeline" - spec.args = Array( - " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala", - " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", - " -i " + BaseTest.publicTestDir + "exampleBAM.bam", - " -blasr ", - " -test ", - " -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf").mkString - spec.fileMD5s += testOut -> "b84f9c45e045685067ded681d5e6224c" - PipelineTest.executeTest(spec) - } -}