From 07b369ca7ec734a0dcbaf60d9412c9e60729075c Mon Sep 17 00:00:00 2001 From: David Roazen Date: Tue, 18 Dec 2012 14:56:48 -0500 Subject: [PATCH] Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move. --- build.xml | 34 +- .../AlleleBiasedDownsamplingUtils.java | 3 +- .../gatk/walkers/genotyper/ErrorModel.java | 4 +- .../GeneralPloidyGenotypeLikelihoods.java | 6 +- ...dyGenotypeLikelihoodsCalculationModel.java | 4 +- ...GeneralPloidyIndelGenotypeLikelihoods.java | 2 +- ...elGenotypeLikelihoodsCalculationModel.java | 2 +- .../GeneralPloidySNPGenotypeLikelihoods.java | 4 +- ...NPGenotypeLikelihoodsCalculationModel.java | 3 +- .../afcalc/AFCalcPerformanceTest.java | 8 +- .../genotyper/afcalc/AFCalcTestBuilder.java | 2 +- .../afcalc/GeneralPloidyExactAFCalc.java | 9 +- .../haplotypecaller/GenotypingEngine.java | 8 +- .../haplotypecaller/HaplotypeCaller.java | 12 +- .../haplotypecaller/HaplotypeResolver.java | 20 +- .../LikelihoodCalculationEngine.java | 5 +- .../haplotypecaller/LocalAssemblyEngine.java | 2 +- .../SimpleDeBruijnAssembler.java | 4 +- .../AdvancedPerReadAlleleLikelihoodMap.java | 2 +- ...eralPloidyGenotypeLikelihoodsUnitTest.java | 4 +- .../afcalc/AFCalcPerformanceUnitTest.java | 4 +- .../afcalc/AFCalcResultUnitTest.java | 2 +- .../genotyper/afcalc/AFCalcUnitTest.java | 2 +- ...neralPloidyAFCalculationModelUnitTest.java | 8 +- ...dentAllelesDiploidExactAFCalcUnitTest.java | 8 +- .../GenotypingEngineUnitTest.java | 6 +- .../SimpleDeBruijnAssemblerUnitTest.java | 5 - .../sting/utils/pairhmm/PairHMMUnitTest.java | 2 +- .../sting/alignment/Alignment.java | 2 +- .../sting/alignment/AlignmentValidation.java | 2 +- .../bwa/java/AlignerTestHarness.java | 2 +- .../alignment/bwa/java/BWAJavaAligner.java | 2 +- .../arguments/DbsnpArgumentCollection.java | 2 +- .../StandardCallerArgumentCollection.java | 2 +- ...VariantContextInputArgumentCollection.java | 2 +- .../sting/gatk/contexts/ReferenceContext.java | 2 +- .../storage/VariantContextWriterStorage.java | 12 +- .../VCFWriterArgumentTypeDescriptor.java | 2 +- .../io/stubs/VariantContextWriterStub.java | 16 +- .../gatk/refdata/VariantContextAdaptors.java | 2 +- .../gatk/refdata/tracks/FeatureManager.java | 4 +- .../gatk/refdata/tracks/RMDTrackBuilder.java | 1 - .../sting/gatk/samples/SampleDB.java | 2 +- .../sting/gatk/walkers/ClipReads.java | 2 +- .../gatk/walkers/annotator/AlleleBalance.java | 10 +- .../annotator/AlleleBalanceBySample.java | 12 +- .../gatk/walkers/annotator/BaseCounts.java | 8 +- .../annotator/BaseQualityRankSumTest.java | 6 +- .../walkers/annotator/ChromosomeCounts.java | 12 +- .../annotator/ClippingRankSumTest.java | 6 +- .../walkers/annotator/DepthOfCoverage.java | 10 +- .../annotator/DepthPerAlleleBySample.java | 14 +- .../gatk/walkers/annotator/FisherStrand.java | 8 +- .../gatk/walkers/annotator/GCContent.java | 8 +- .../walkers/annotator/HaplotypeScore.java | 12 +- .../gatk/walkers/annotator/HardyWeinberg.java | 10 +- .../walkers/annotator/HomopolymerRun.java | 6 +- .../walkers/annotator/InbreedingCoeff.java | 10 +- .../sting/gatk/walkers/annotator/LowMQ.java | 6 +- .../walkers/annotator/MVLikelihoodRatio.java | 6 +- .../annotator/MappingQualityRankSumTest.java | 6 +- .../walkers/annotator/MappingQualityZero.java | 8 +- .../annotator/MappingQualityZeroBySample.java | 12 +- .../annotator/MappingQualityZeroFraction.java | 6 +- .../gatk/walkers/annotator/NBaseCount.java | 8 +- .../gatk/walkers/annotator/QualByDepth.java | 10 +- .../walkers/annotator/RMSMappingQuality.java | 8 +- .../gatk/walkers/annotator/RankSumTest.java | 10 +- .../walkers/annotator/ReadPosRankSumTest.java | 6 +- .../gatk/walkers/annotator/SampleList.java | 10 +- .../sting/gatk/walkers/annotator/SnpEff.java | 7 +- .../walkers/annotator/SpanningDeletions.java | 6 +- .../annotator/TandemRepeatAnnotator.java | 12 +- .../annotator/TechnologyComposition.java | 6 +- .../TransmissionDisequilibriumTest.java | 8 +- .../walkers/annotator/VariantAnnotator.java | 13 +- .../annotator/VariantAnnotatorEngine.java | 4 +- .../gatk/walkers/annotator/VariantType.java | 6 +- .../ActiveRegionBasedAnnotation.java | 4 +- .../interfaces/AnnotatorCompatible.java | 2 +- .../interfaces/GenotypeAnnotation.java | 8 +- .../interfaces/InfoFieldAnnotation.java | 4 +- .../VariantAnnotatorAnnotation.java | 2 +- .../walkers/beagle/BeagleOutputToVCF.java | 9 +- .../walkers/beagle/ProduceBeagleInput.java | 17 +- .../beagle/VariantsToBeagleUnphased.java | 20 +- .../gatk/walkers/bqsr/BaseRecalibrator.java | 2 +- .../gatk/walkers/coverage/CallableLoci.java | 3 +- .../gatk/walkers/coverage/CoverageUtils.java | 2 +- .../walkers/coverage/DepthOfCoverage.java | 2 +- .../coverage/DepthOfCoverageStats.java | 2 +- .../walkers/coverage/GCContentByInterval.java | 2 +- .../diagnostics/ErrorRatePerCycle.java | 2 +- .../diagnostics/targets/DiagnoseTargets.java | 8 +- .../diagnostics/targets/ThresHolder.java | 2 +- .../walkers/diffengine/VCFDiffableReader.java | 6 +- .../fasta/FastaAlternateReferenceMaker.java | 2 +- .../sting/gatk/walkers/fasta/FastaStats.java | 2 +- .../gatk/walkers/filters/ClusteredSnps.java | 6 +- .../walkers/filters/FiltrationContext.java | 2 +- .../walkers/filters/VariantFiltration.java | 9 +- .../genotyper/ConsensusAlleleCounter.java | 4 +- .../walkers/genotyper/DiploidGenotype.java | 2 +- .../DiploidSNPGenotypeLikelihoods.java | 2 +- .../GenotypeLikelihoodsCalculationModel.java | 6 +- ...elGenotypeLikelihoodsCalculationModel.java | 4 +- ...NPGenotypeLikelihoodsCalculationModel.java | 4 +- .../genotyper/UnifiedArgumentCollection.java | 6 +- .../walkers/genotyper/UnifiedGenotyper.java | 14 +- .../genotyper/UnifiedGenotyperEngine.java | 12 +- .../walkers/genotyper/VariantCallContext.java | 2 +- .../gatk/walkers/genotyper/afcalc/AFCalc.java | 6 +- .../genotyper/afcalc/AFCalcResult.java | 2 +- .../genotyper/afcalc/DiploidExactAFCalc.java | 7 +- .../walkers/genotyper/afcalc/ExactAFCalc.java | 10 +- .../genotyper/afcalc/ExactCallLogger.java | 2 +- .../IndependentAllelesDiploidExactAFCalc.java | 2 +- .../afcalc/OriginalDiploidExactAFCalc.java | 4 +- .../genotyper/afcalc/StateTracker.java | 2 +- .../indels/HaplotypeIndelErrorModel.java | 2 +- .../gatk/walkers/indels/IndelRealigner.java | 3 +- .../indels/PairHMMIndelErrorModel.java | 2 +- .../indels/RealignerTargetCreator.java | 2 +- .../walkers/indels/SomaticIndelDetector.java | 6 +- .../gatk/walkers/phasing/AllelePair.java | 4 +- .../sting/gatk/walkers/phasing/BaseArray.java | 2 +- ...eSegregatingAlternateAllelesVCFWriter.java | 25 +- .../walkers/phasing/PhaseByTransmission.java | 11 +- .../gatk/walkers/phasing/PhasingRead.java | 2 +- .../gatk/walkers/phasing/PhasingUtils.java | 9 +- .../walkers/phasing/ReadBackedPhasing.java | 44 +- .../gatk/walkers/phasing/SNPallelePair.java | 6 +- .../gatk/walkers/qc/DocumentationTest.java | 4 +- .../sting/gatk/walkers/qc/QCRef.java | 2 +- .../gatk/walkers/qc/RodSystemValidation.java | 4 +- .../validation/GenotypeAndValidate.java | 17 +- .../validation/ValidationAmplicons.java | 4 +- .../FrequencyModeSelector.java | 5 +- .../GLBasedSampleSelector.java | 2 +- .../GTBasedSampleSelector.java | 6 +- .../validationsiteselector/GenomeEvent.java | 6 +- .../KeepAFSpectrumFrequencySelector.java | 6 +- .../NullSampleSelector.java | 2 +- .../SampleSelector.java | 2 +- .../UniformSamplingFrequencySelector.java | 6 +- .../ValidationSiteSelector.java | 14 +- .../gatk/walkers/varianteval/VariantEval.java | 17 +- .../varianteval/evaluators/CompOverlap.java | 4 +- .../varianteval/evaluators/CountVariants.java | 4 +- .../evaluators/GenotypeConcordance.java | 6 +- .../evaluators/IndelLengthHistogram.java | 4 +- .../varianteval/evaluators/IndelSummary.java | 6 +- .../MendelianViolationEvaluator.java | 2 +- .../evaluators/MultiallelicSummary.java | 6 +- .../evaluators/PrintMissingComp.java | 2 +- .../evaluators/ThetaVariantEvaluator.java | 6 +- .../evaluators/TiTvVariantEvaluator.java | 6 +- .../evaluators/ValidationReport.java | 6 +- .../evaluators/VariantEvaluator.java | 2 +- .../evaluators/VariantSummary.java | 8 +- .../GenotypePhasingEvaluator.java | 6 +- .../stratifications/AlleleCount.java | 6 +- .../stratifications/AlleleFrequency.java | 3 +- .../varianteval/stratifications/CompRod.java | 3 +- .../varianteval/stratifications/Contig.java | 3 +- .../varianteval/stratifications/CpG.java | 2 +- .../stratifications/Degeneracy.java | 2 +- .../DynamicStratification.java | 6 +- .../varianteval/stratifications/EvalRod.java | 3 +- .../varianteval/stratifications/Filter.java | 2 +- .../stratifications/FunctionalClass.java | 2 +- .../stratifications/IndelSize.java | 3 +- .../IntervalStratification.java | 2 +- .../stratifications/JexlExpression.java | 4 +- .../varianteval/stratifications/Novelty.java | 2 +- .../stratifications/OneBPIndel.java | 3 +- .../varianteval/stratifications/Sample.java | 2 +- .../stratifications/TandemRepeat.java | 7 +- .../stratifications/VariantStratifier.java | 2 +- .../stratifications/VariantType.java | 3 +- .../varianteval/util/EvaluationContext.java | 2 +- .../util/SortableJexlVCMatchExp.java | 2 +- .../varianteval/util/VariantEvalUtils.java | 8 +- .../ApplyRecalibration.java | 11 +- .../variantrecalibration/TrainingSet.java | 2 +- .../VQSRCalibrationCurve.java | 2 +- .../VariantDataManager.java | 10 +- .../VariantRecalibrator.java | 10 +- .../walkers/variantutils/CombineVariants.java | 19 +- .../variantutils/FilterLiftedVariants.java | 12 +- .../variantutils/LeftAlignVariants.java | 14 +- .../variantutils/LiftoverVariants.java | 15 +- .../variantutils/RandomlySplitVariants.java | 14 +- .../walkers/variantutils/SelectHeaders.java | 11 +- .../walkers/variantutils/SelectVariants.java | 12 +- .../variantutils/ValidateVariants.java | 6 +- .../VariantValidationAssessor.java | 15 +- .../variantutils/VariantsToBinaryPed.java | 11 +- .../walkers/variantutils/VariantsToTable.java | 14 +- .../walkers/variantutils/VariantsToVCF.java | 13 +- .../gatk/ArgumentDefinitionField.java | 2 +- .../queue/extensions/gatk/ArgumentField.java | 2 +- .../sting/utils/GenomeLocParser.java | 4 +- .../broadinstitute/sting/utils/Haplotype.java | 5 +- .../sting/utils/IndelUtils.java | 2 +- .../sting/utils/MendelianViolation.java | 6 +- .../sting/utils/SampleUtils.java | 14 +- .../utils/codecs/beagle/BeagleFeature.java | 2 +- .../utils/codecs/hapmap/RawHapMapFeature.java | 2 +- .../sting/utils/duplicates/DupUtils.java | 2 +- .../sting/utils/exceptions/UserException.java | 2 +- .../genotyper/PerReadAlleleLikelihoodMap.java | 2 +- .../StandardPerReadAlleleLikelihoodMap.java | 2 +- .../pileup/AbstractReadBackedPileup.java | 2 +- .../sting/utils/pileup/PileupElement.java | 2 +- .../sting/utils/recalibration/RecalUtils.java | 2 +- .../covariates/ContextCovariate.java | 2 +- .../covariates/CycleCovariate.java | 2 +- .../covariates/RepeatLengthCovariate.java | 10 +- .../sting/utils/sam/AlignmentUtils.java | 2 +- .../sting/utils/variant/GATKVCFUtils.java | 178 +++++++ .../variant/GATKVariantContextUtils.java | 450 ++++++++++++++++ .../codecs => variant}/bcf2/BCF2Codec.java | 19 +- .../codecs => variant}/bcf2/BCF2Decoder.java | 17 +- .../bcf2/BCF2GenotypeFieldDecoders.java | 10 +- .../bcf2/BCF2LazyGenotypesDecoder.java | 11 +- .../codecs => variant}/bcf2/BCF2Type.java | 2 +- .../codecs => variant}/bcf2/BCF2Utils.java | 12 +- .../codecs => variant}/bcf2/BCFVersion.java | 2 +- .../{sting => variant}/utils/BaseUtils.java | 12 +- .../broadinstitute/variant/utils/Utils.java | 130 +++++ .../variantcontext/Allele.java | 4 +- .../variantcontext/CommonInfo.java | 4 +- .../variantcontext/FastGenotype.java | 3 +- .../variantcontext/Genotype.java | 7 +- .../variantcontext/GenotypeBuilder.java | 4 +- .../variantcontext/GenotypeLikelihoods.java | 18 +- .../variantcontext/GenotypeType.java | 2 +- .../variantcontext/GenotypesContext.java | 2 +- .../variantcontext/LazyGenotypesContext.java | 2 +- .../variantcontext/VariantContext.java | 16 +- .../variantcontext/VariantContextBuilder.java | 26 +- .../variantcontext/VariantContextUtils.java | 495 +----------------- .../variantcontext/VariantJEXLContext.java | 9 +- .../variantcontext/writer/BCF2Encoder.java | 15 +- .../writer/BCF2FieldEncoder.java | 19 +- .../writer/BCF2FieldWriter.java | 21 +- .../writer/BCF2FieldWriterManager.java | 9 +- .../variantcontext/writer/BCF2Writer.java | 38 +- .../writer/IndexingVariantContextWriter.java | 25 +- .../writer/IntGenotypeFieldAccessors.java | 6 +- .../variantcontext/writer/Options.java | 2 +- .../writer/SortingVariantContextWriter.java | 4 +- .../SortingVariantContextWriterBase.java | 6 +- .../variantcontext/writer/VCFWriter.java | 23 +- .../writer/VariantContextWriter.java | 6 +- .../writer/VariantContextWriterFactory.java | 7 +- .../vcf/AbstractVCFCodec.java | 18 +- .../codecs => variant}/vcf/VCF3Codec.java | 4 +- .../codecs => variant}/vcf/VCFCodec.java | 2 +- .../vcf/VCFCompoundHeaderLine.java | 14 +- .../codecs => variant}/vcf/VCFConstants.java | 2 +- .../vcf/VCFContigHeaderLine.java | 2 +- .../vcf/VCFFilterHeaderLine.java | 2 +- .../vcf/VCFFormatHeaderLine.java | 2 +- .../codecs => variant}/vcf/VCFHeader.java | 8 +- .../codecs => variant}/vcf/VCFHeaderLine.java | 2 +- .../vcf/VCFHeaderLineCount.java | 2 +- .../vcf/VCFHeaderLineTranslator.java | 8 +- .../vcf/VCFHeaderLineType.java | 2 +- .../vcf/VCFHeaderVersion.java | 2 +- .../vcf/VCFIDHeaderLine.java | 2 +- .../vcf/VCFInfoHeaderLine.java | 2 +- .../vcf/VCFSimpleHeaderLine.java | 2 +- .../vcf/VCFStandardHeaderLines.java | 12 +- .../codecs => variant}/vcf/VCFUtils.java | 197 +------ .../org/broadinstitute/sting/WalkerTest.java | 6 +- .../commandline/ParsingEngineUnitTest.java | 2 +- .../sting/commandline/RodBindingUnitTest.java | 2 +- .../refdata/RefMetaDataTrackerUnitTest.java | 7 +- .../tracks/FeatureManagerUnitTest.java | 6 +- .../tracks/RMDTrackBuilderUnitTest.java | 4 +- .../FeatureToGATKFeatureIteratorUnitTest.java | 2 +- .../diffengine/DiffableReaderUnitTest.java | 4 +- .../ArtificialReadPileupTestProvider.java | 5 +- .../IndelGenotypeLikelihoodsUnitTest.java | 24 +- .../VariantEvalWalkerUnitTest.java | 6 +- .../variantutils/CombineVariantsUnitTest.java | 6 +- .../SelectVariantsIntegrationTest.java | 2 +- .../sting/utils/HaplotypeUnitTest.java | 6 +- .../VCFJarClassLoadingUnitTest.java | 107 ---- .../bcf2/BCF2EncoderDecoderUnitTest.java | 4 +- .../bcf2/BCF2UtilsUnitTest.java | 7 +- .../utils/BaseUtilsUnitTest.java | 3 +- .../variantcontext/AlleleUnitTest.java | 3 +- .../GenotypeLikelihoodsUnitTest.java | 7 +- .../variantcontext/GenotypeUnitTest.java | 5 +- .../GenotypesContextUnitTest.java | 3 +- .../VariantContextBenchmark.java | 83 ++- .../VariantContextTestProvider.java | 10 +- .../VariantContextUnitTest.java | 38 +- .../VariantContextUtilsUnitTest.java | 27 +- .../VariantJEXLContextUnitTest.java | 3 +- .../writer/VCFWriterUnitTest.java | 12 +- .../writer/VariantContextWritersUnitTest.java | 12 +- .../vcf/IndexFactoryUnitTest.java | 10 +- .../vcf/VCFHeaderUnitTest.java | 2 +- .../vcf/VCFIntegrationTest.java | 4 +- .../vcf/VCFStandardHeaderLinesUnitTest.java | 2 +- public/packages/GATKEngine.xml | 2 + .../sting/queue/util/VCF_BAM_utilities.scala | 4 +- 311 files changed, 1816 insertions(+), 1861 deletions(-) create mode 100755 public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java create mode 100644 public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/bcf2/BCF2Codec.java (95%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/bcf2/BCF2Decoder.java (94%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/bcf2/BCF2GenotypeFieldDecoders.java (97%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/bcf2/BCF2LazyGenotypesDecoder.java (89%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/bcf2/BCF2Type.java (99%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/bcf2/BCF2Utils.java (96%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/bcf2/BCFVersion.java (97%) rename public/java/src/org/broadinstitute/{sting => variant}/utils/BaseUtils.java (96%) create mode 100644 public/java/src/org/broadinstitute/variant/utils/Utils.java rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/Allele.java (99%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/CommonInfo.java (98%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/FastGenotype.java (98%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/Genotype.java (98%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/GenotypeBuilder.java (99%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/GenotypeLikelihoods.java (95%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/GenotypeType.java (96%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/GenotypesContext.java (99%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/LazyGenotypesContext.java (99%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/VariantContext.java (98%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/VariantContextBuilder.java (93%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/VariantContextUtils.java (66%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/VariantJEXLContext.java (97%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/BCF2Encoder.java (93%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/BCF2FieldEncoder.java (95%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/BCF2FieldWriter.java (94%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/BCF2FieldWriterManager.java (95%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/BCF2Writer.java (91%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/IndexingVariantContextWriter.java (85%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/IntGenotypeFieldAccessors.java (95%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/Options.java (95%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/SortingVariantContextWriter.java (95%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/SortingVariantContextWriterBase.java (97%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/VCFWriter.java (95%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/VariantContextWriter.java (56%) rename public/java/src/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/VariantContextWriterFactory.java (93%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/AbstractVCFCodec.java (97%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCF3Codec.java (97%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFCodec.java (99%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFCompoundHeaderLine.java (94%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFConstants.java (99%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFContigHeaderLine.java (97%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFFilterHeaderLine.java (95%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFFormatHeaderLine.java (95%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFHeader.java (97%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFHeaderLine.java (98%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFHeaderLineCount.java (72%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFHeaderLineTranslator.java (93%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFHeaderLineType.java (74%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFHeaderVersion.java (98%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFIDHeaderLine.java (96%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFInfoHeaderLine.java (94%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFSimpleHeaderLine.java (98%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFStandardHeaderLines.java (96%) rename public/java/src/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFUtils.java (57%) mode change 100755 => 100644 delete mode 100644 public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java rename public/java/test/org/broadinstitute/{sting/utils/codecs => variant}/bcf2/BCF2EncoderDecoderUnitTest.java (99%) rename public/java/test/org/broadinstitute/{sting/utils/codecs => variant}/bcf2/BCF2UtilsUnitTest.java (97%) rename public/java/test/org/broadinstitute/{sting => variant}/utils/BaseUtilsUnitTest.java (97%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/AlleleUnitTest.java (98%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/GenotypeLikelihoodsUnitTest.java (97%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/GenotypeUnitTest.java (97%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/GenotypesContextUnitTest.java (99%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/VariantContextBenchmark.java (76%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/VariantContextTestProvider.java (99%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/VariantContextUnitTest.java (96%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/VariantContextUtilsUnitTest.java (98%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/VariantJEXLContextUnitTest.java (97%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/VCFWriterUnitTest.java (95%) rename public/java/test/org/broadinstitute/{sting/utils => variant}/variantcontext/writer/VariantContextWritersUnitTest.java (93%) rename public/java/test/org/broadinstitute/{sting/utils/codecs => variant}/vcf/IndexFactoryUnitTest.java (88%) rename public/java/test/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFHeaderUnitTest.java (99%) rename public/java/test/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFIntegrationTest.java (97%) rename public/java/test/org/broadinstitute/{sting/utils/codecs => variant}/vcf/VCFStandardHeaderLinesUnitTest.java (99%) diff --git a/build.xml b/build.xml index 834aef3cd..49efd616d 100644 --- a/build.xml +++ b/build.xml @@ -644,12 +644,8 @@ - - - - - - + + @@ -659,7 +655,7 @@ - + @@ -667,14 +663,10 @@ - - + + - - - - - + @@ -685,7 +677,7 @@ - + @@ -703,12 +695,12 @@ - - + + - - + + @@ -719,7 +711,7 @@ - + @@ -755,7 +747,7 @@ - + diff --git a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java index 94f6ff649..53f206bfe 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java @@ -30,7 +30,8 @@ import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.variantcontext.Allele; import java.io.PrintStream; import java.util.*; 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 fc6d23382..30650e9c0 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 @@ -8,8 +8,8 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java index 303ab94d6..502853868 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java @@ -29,13 +29,13 @@ import net.sf.samtools.SAMUtils; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACcounts; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; 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.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; import java.util.*; 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 f6ad445c7..ce66ce8d0 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 @@ -31,11 +31,11 @@ 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.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java index 4bcaa5ff9..3b12fe475 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.*; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java index eb4cf1839..76a934091 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java @@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java index 0f0f85441..461329ad0 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import net.sf.samtools.SAMUtils; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.ArrayList; import java.util.Arrays; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java index 9f2fdc096..3250de2b2 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java @@ -31,7 +31,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java index 0a3512aa6..d6b3eb768 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java @@ -10,10 +10,10 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SimpleTimer; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import java.io.*; import java.util.*; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java index 6f3740ab3..f4f17f1e0 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java @@ -4,7 +4,7 @@ import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.ArrayList; import java.util.Arrays; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java index b248c8759..5f5d80fde 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java @@ -27,9 +27,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; @@ -532,7 +533,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc { } // if there is no mass on the (new) likelihoods, then just no-call the sample - if ( MathUtils.sum(newLikelihoods) > VariantContextUtils.SUM_GL_THRESH_NOCALL ) { + if ( MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) { newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES)); } else { @@ -544,7 +545,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc { gb.PL(newLikelihoods); // if we weren't asked to assign a genotype, then just no-call the sample - if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > VariantContextUtils.SUM_GL_THRESH_NOCALL ) + if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) gb.alleles(NO_CALL_ALLELES); else assignGenotype(gb, newLikelihoods, allelesToUse, ploidy); 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 a786a860c..3b90370bc 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 @@ -36,7 +36,9 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.variantcontext.*; import java.io.PrintStream; import java.util.*; @@ -158,7 +160,7 @@ public class GenotypingEngine { } // Merge the event to find a common reference representation - final VariantContext mergedVC = VariantContextUtils.simpleMerge(genomeLocParser, eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false); + 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 @@ -200,7 +202,7 @@ public class GenotypingEngine { VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, call); if( annotatedCall.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary! - annotatedCall = VariantContextUtils.reverseTrimAlleles(annotatedCall); + annotatedCall = GATKVariantContextUtils.reverseTrimAlleles(annotatedCall); } returnCalls.add( annotatedCall ); 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 9744c3dd8..2f733a01a 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 @@ -48,8 +48,8 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.clipping.ReadClipper; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fragments.FragmentCollection; @@ -61,8 +61,8 @@ import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.FileNotFoundException; import java.io.PrintStream; @@ -238,7 +238,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem samplesList.addAll( samples ); // initialize the UnifiedGenotyper Engine which is used to call into the exact model final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection( SCAC ); // this adapter is used so that the full set of unused UG arguments aren't exposed to the HC user - UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY); + UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY); // create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested UnifiedArgumentCollection simpleUAC = new UnifiedArgumentCollection(UAC); @@ -248,7 +248,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem simpleUAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling simpleUAC.CONTAMINATION_FRACTION = 0.0; simpleUAC.exactCallsLog = null; - UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY); + UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY); // initialize the output VCF header final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit()); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java index 8a401439b..0e4673497 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java @@ -39,18 +39,18 @@ import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.SWPairwiseAlignment; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; import java.util.*; 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 018102893..59f241cdb 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 @@ -29,16 +29,13 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.*; -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.pairhmm.*; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; -import java.io.PrintStream; import java.util.*; public class LikelihoodCalculationEngine { diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java index bf6c82d82..6d5d268a6 100755 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.activeregion.ActiveRegion; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; 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 3c5a1f79c..b0be5e757 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 @@ -11,8 +11,8 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import org.jgrapht.graph.DefaultDirectedGraph; import java.io.PrintStream; diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java index 77a7c3bd9..4a13fb615 100644 --- a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java +++ b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java @@ -29,7 +29,7 @@ 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.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.io.PrintStream; import java.util.*; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java index f95ba66b2..4d4dbbdb5 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java @@ -28,11 +28,11 @@ import net.sf.samtools.SAMUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java index 556b7451f..1b0ffbd26 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java @@ -4,8 +4,8 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java index ee5436264..4753ad07a 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java index 7ee909fe0..6b53d6188 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java index 3df2f7883..0f2dc84dc 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java @@ -2,10 +2,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; -import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeBuilder; +import org.broadinstitute.variant.variantcontext.GenotypesContext; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java index 663471106..1293c274b 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java @@ -3,10 +3,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java index 07e7b0d92..f44624a10 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java @@ -10,9 +10,9 @@ import net.sf.picard.reference.ReferenceSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java index 5652b118d..071c21f9e 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java @@ -10,16 +10,11 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.genotyper.ArtificialReadPileupTestProvider; import org.broadinstitute.sting.utils.Haplotype; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; import org.jgrapht.graph.DefaultDirectedGraph; import org.testng.Assert; -import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; -import java.io.File; -import java.io.FileNotFoundException; import java.io.PrintStream; import java.util.*; diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java index 6281054b1..4684d6d8a 100644 --- a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java @@ -29,7 +29,7 @@ package org.broadinstitute.sting.utils.pairhmm; // the imports for unit testing. import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/public/java/src/org/broadinstitute/sting/alignment/Alignment.java b/public/java/src/org/broadinstitute/sting/alignment/Alignment.java index c63f5615f..db21411b3 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/Alignment.java +++ b/public/java/src/org/broadinstitute/sting/alignment/Alignment.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.alignment; import net.sf.samtools.*; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java index b903b9f7d..ef50cf088 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java +++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java index 2d568a96a..67305ce78 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java +++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java @@ -4,7 +4,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.*; import org.broadinstitute.sting.alignment.Aligner; import org.broadinstitute.sting.alignment.Alignment; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java index fbeac9192..f29e639d6 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java +++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java @@ -6,7 +6,7 @@ import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.bwa.BWAAligner; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.reference.bwt.*; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java index e0c2ce72a..5a1c2a1b4 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.arguments; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; /** * @author ebanks diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java index 547f375bb..f8f1831f6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.File; import java.io.PrintStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java index 4c0257e6a..72b01df01 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.arguments; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; /** * @author ebanks diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java index 34627b973..88f4166ef 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.contexts; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java index 8e4633869..2a7c5c7b2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java @@ -30,14 +30,14 @@ import org.broad.tribble.AbstractFeatureReader; import org.broad.tribble.FeatureCodec; import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.variant.bcf2.BCF2Utils; +import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.writer.Options; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; +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.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java index f521c959d..8a989b040 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.io.stubs; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java index f92d78bb5..c512ba835 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java @@ -29,13 +29,13 @@ import org.broadinstitute.sting.gatk.CommandLineExecutable; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.utils.classloader.JVMUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.writer.Options; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +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.File; import java.io.OutputStream; @@ -232,7 +232,7 @@ public class VariantContextWriterStub implements Stub, Var } if ( UPDATE_CONTIG_HEADERS ) - vcfHeader = VCFUtils.withUpdatedContigs(vcfHeader, engine); + vcfHeader = GATKVCFUtils.withUpdatedContigs(vcfHeader, engine); } outputTracker.getStorage(this).writeHeader(vcfHeader); diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index 5c7da82d0..8713e9797 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java index a2fe94641..0e0e8017d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java @@ -33,9 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.AbstractVCFCodec; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.help.GATKDocUtils; diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java index 81fe73075..2bb6cbeee 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java @@ -39,7 +39,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java index 3de85028f..91439b65f 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java +++ b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.samples; import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.Genotype; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java index e63dbcabd..93eaee209 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java @@ -37,7 +37,7 @@ 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.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.clipping.ClippingOp; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index 18bdb02ed..943a1147a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -32,12 +32,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypesContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java index 4d79c4112..4bda9a6d4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java @@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAn import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeBuilder; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.Collection; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java index aef3e49cf..e19e82597 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java @@ -37,10 +37,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index e59fc827d..d234f3471 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java @@ -2,11 +2,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 0c78c0204..5b1a1e236 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -35,12 +35,12 @@ 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.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +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; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java index 1dff4d1a3..24da5e893 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java @@ -1,12 +1,12 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index c9481f244..97c61f056 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -8,13 +8,13 @@ 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.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index 89a239e54..05c36eda6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -7,17 +7,17 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; +import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeBuilder; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 52072d10c..f0d46cf35 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -34,13 +34,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 07391c78c..5994c1ab7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -8,11 +8,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index ca7180510..5ca3c9885 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -33,20 +33,20 @@ 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.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.Serializable; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java index 0340f457c..6a879db12 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java @@ -9,11 +9,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypesContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java index 037b357ae..ebeb10f43 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java @@ -7,9 +7,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java index dd058b469..826b45fa0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java @@ -10,11 +10,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypesContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java index c9a4d0ee6..cc42a7b35 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java @@ -6,10 +6,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java index c9d5ca261..0bc9fa37e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java @@ -11,10 +11,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MendelianViolation; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index 2679a169b..96e76ceab 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java @@ -2,12 +2,12 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java index 364bbdbb9..4b11a9698 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java @@ -8,13 +8,13 @@ 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.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java index afb4ceb60..057fbaf8a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java @@ -31,14 +31,14 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeBuilder; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java index 5f9f3416d..d0ea231a1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java @@ -7,11 +7,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java index 3e6aa62a2..1aaf3afcd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java @@ -6,11 +6,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index d75947879..af27d9c6f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -8,11 +8,11 @@ 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.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypesContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index 474b6b150..883e2ddce 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -10,12 +10,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index e7c0e6b14..adc661d66 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -10,14 +10,14 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MannWhitneyU; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypesContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index 334b89f01..de1fdf0d0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -7,14 +7,14 @@ import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java index 33e895187..090702e42 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java @@ -31,11 +31,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeaderLineCount; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java index b3b0be153..a19b77aae 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java @@ -35,9 +35,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; @@ -212,7 +213,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio // Make sure that the SnpEff version number and command-line header lines are present in the VCF header of // the SnpEff rod, and that the file was generated by a supported version of SnpEff: - VCFHeader snpEffVCFHeader = VCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName()); + VCFHeader snpEffVCFHeader = GATKVCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName()); VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY); VCFHeaderLine snpEffCommandLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_COMMAND_LINE_KEY); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java index 8e1140af1..7c113c188 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java @@ -7,10 +7,10 @@ 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.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java index c72ba1c5f..1862ab6c6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java @@ -31,12 +31,12 @@ 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.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.VCFHeaderLineCount; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; @@ -57,7 +57,7 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa if ( !vc.isIndel()) return null; - Pair,byte[]> result = VariantContextUtils.getNumTandemRepeatUnits(vc, ref.getForwardBases()); + Pair,byte[]> result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, ref.getForwardBases()); if (result == null) return null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java index 57b50c6e2..58cce6b30 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java @@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java index be7288a7e..40a442808 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java @@ -10,11 +10,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineCount; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 92060b4a3..09f01bd42 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -35,13 +35,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.util.*; @@ -225,7 +226,7 @@ public class VariantAnnotator extends RodWalker implements Ann // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones Set hInfo = new HashSet(); hInfo.addAll(engine.getVCFAnnotationDescriptions()); - for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) { + for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) { if ( isUniqueHeaderLine(line, hInfo) ) hInfo.add(line); } @@ -237,7 +238,7 @@ public class VariantAnnotator extends RodWalker implements Ann continue; } VCFInfoHeaderLine targetHeaderLine = null; - for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) { + for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) { if ( line instanceof VCFInfoHeaderLine ) { VCFInfoHeaderLine infoline = (VCFInfoHeaderLine)line; if ( infoline.getID().equals(expression.fieldName) ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 725097ddc..ddf5a6de1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -32,9 +32,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java index a5c2b32f0..944962d30 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java @@ -8,9 +8,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAn import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.IndelUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java index 03fcba760..632b60b02 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java @@ -1,8 +1,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.List; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java index f610a2ba8..0d599332d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java index 6970908b5..490bbdbde 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -4,10 +4,10 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeBuilder; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java index 5b2dc310d..ef717abd1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -4,8 +4,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.List; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java index 996d85a67..0ec7ef907 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index 83b10dd91..bdc129b8c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -35,10 +35,11 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.util.*; @@ -132,7 +133,7 @@ public class BeagleOutputToVCF extends RodWalker { // setup the header fields final Set hInfo = new HashSet(); - hInfo.addAll(VCFUtils.getHeaderFields(getToolkit())); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit())); hInfo.add(new VCFFormatHeaderLine("OG",1, VCFHeaderLineType.String, "Original Genotype input to Beagle")); hInfo.add(new VCFInfoHeaderLine("R2", 1, VCFHeaderLineType.Float, "r2 Value reported by Beagle on each site")); hInfo.add(new VCFInfoHeaderLine("NumGenotypesChanged", 1, VCFHeaderLineType.Integer, "The number of genotypes changed by Beagle")); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java index d11747766..e02b473b6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java @@ -38,14 +38,15 @@ import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibratio import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFFilterHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.VCFFilterHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.PrintStream; @@ -231,7 +232,7 @@ public class ProduceBeagleInput extends RodWalker { private final static double[] DIPLOID_FLAT_LOG10_LIKELIHOODS = MathUtils.toLog10(new double[]{ 0.33, 0.33, 0.33 }); public void writeBeagleOutput(VariantContext preferredVC, VariantContext otherVC, boolean isValidationSite, double prior) { - GenomeLoc currentLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),preferredVC); + GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), preferredVC); StringBuffer beagleOut = new StringBuffer(); String marker = String.format("%s:%d ",currentLoc.getContig(),currentLoc.getStart()); @@ -344,7 +345,7 @@ public class ProduceBeagleInput extends RodWalker { // setup the header fields Set hInfo = new HashSet(); - hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames)); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames)); hInfo.add(new VCFFilterHeaderLine("bootstrap","This site used for genotype bootstrapping with ProduceBeagleInputWalker")); bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames))); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java index a6a6d484e..fd552e12f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java @@ -36,16 +36,16 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.PrintStream; import java.util.Arrays; @@ -90,7 +90,7 @@ public class VariantsToBeagleUnphased extends RodWalker { throw new UserException.BadArgumentValue("bootstrap", "Bootstrap value must be fraction between 0 and 1"); if ( bootstrapVCFOutput != null ) { - Set hInfo = VCFUtils.getHeaderFields(getToolkit()); + Set hInfo = GATKVCFUtils.getHeaderFields(getToolkit()); bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit()))); } } @@ -141,7 +141,7 @@ public class VariantsToBeagleUnphased extends RodWalker { } public void writeUnphasedBeagleOutput(VariantContext vc, boolean makeMissing) { - GenomeLoc currentLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),vc); + GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc); StringBuffer beagleOut = new StringBuffer(); String marker = String.format("%s:%d ",currentLoc.getContig(), currentLoc.getStart()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 4d7dbc912..f4d192373 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -38,7 +38,7 @@ import org.broadinstitute.sting.gatk.filters.*; import org.broadinstitute.sting.gatk.iterators.ReadTransformer; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.BaseUtils; +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; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java index 48019efea..68084e606 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java @@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.variant.utils.BaseUtils; import java.io.File; import java.io.FileNotFoundException; @@ -305,7 +306,7 @@ public class CallableLoci extends LocusWalker { // setup the header fields Set hInfo = new HashSet(); - hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames)); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames)); if ( clusterWindow > 0 ) hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters")); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java index 7dcc95361..751418a61 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java @@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; @@ -283,7 +283,7 @@ public class ConsensusAlleleCounter { if (vcs.isEmpty()) return Collections.emptyList(); // nothing else to do, no alleles passed minimum count criterion - final VariantContext mergedVC = VariantContextUtils.simpleMerge(locParser, vcs, null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false); + final VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false); return mergedVC.getAlleles(); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java index 95b81e322..86047d30b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; public enum DiploidGenotype { AA ('A', 'A'), diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java index 2870b6629..290c33b2b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import net.sf.samtools.SAMUtils; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index a8ee4afde..ea09e17d8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -30,13 +30,13 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.List; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 0d9f443e2..56965c022 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -31,14 +31,14 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 791cdc325..c10f7264e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; @@ -40,7 +40,7 @@ import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 5f6ddf0f1..e7add3213 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -28,8 +28,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; import org.broadinstitute.sting.utils.pairhmm.PairHMM; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; public class UnifiedArgumentCollection extends StandardCallerArgumentCollection { @@ -151,7 +151,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection Sample ploidy - equivalent to number of chromosomes per pool. In pooled experiments this should be = # of samples in pool * individual sample ploidy */ @Argument(shortName="ploidy", fullName="sample_ploidy", doc="Plody (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).", required=false) - public int samplePloidy = VariantContextUtils.DEFAULT_PLOIDY; + public int samplePloidy = GATKVariantContextUtils.DEFAULT_PLOIDY; @Hidden @Argument(shortName="minqs", fullName="min_quality_score", doc="Min quality score to consider. Smaller numbers process faster. Default: Q1.", required=false) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 36be2e7c6..7b82403b5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -42,13 +42,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.PrintStream; import java.util.*; @@ -232,7 +232,7 @@ public class UnifiedGenotyper extends LocusWalker, Unif // Check for protected modes if (GATKLiteUtils.isGATKLite()) { // no polyploid/pooled mode in GATK Like - if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY || + 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"); @@ -303,7 +303,7 @@ public class UnifiedGenotyper extends LocusWalker, Unif headerInfo.add(new VCFInfoHeaderLine(UnifiedGenotyperEngine.NUMBER_OF_DISCOVERED_ALLELES_KEY, 1, VCFHeaderLineType.Integer, "Number of alternate alleles discovered (but not necessarily genotyped) at this site")); // add the pool values for each genotype - if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) { + if (UAC.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY) { headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_PER_SAMPLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the alternate allele count, in the same order as listed, for each individual sample")); headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the alternate allele fraction, in the same order as listed, for each individual sample")); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 8f2588679..1d5671857 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -40,11 +40,13 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.io.PrintStream; import java.lang.reflect.Constructor; @@ -112,7 +114,7 @@ public class UnifiedGenotyperEngine { // --------------------------------------------------------------------------------------------------------- @Requires({"toolkit != null", "UAC != null"}) public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) { - this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), VariantContextUtils.DEFAULT_PLOIDY); + this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), GATKVariantContextUtils.DEFAULT_PLOIDY); } @Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0","ploidy>0"}) @@ -503,7 +505,7 @@ public class UnifiedGenotyperEngine { // if we are subsetting alleles (either because there were too many or because some were not polymorphic) // then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext ) // limitedContext callers need to handle allele trimming on their own to keep their perReadAlleleLikelihoodMap alleles in sync - vcCall = VariantContextUtils.reverseTrimAlleles(vcCall); + vcCall = GATKVariantContextUtils.reverseTrimAlleles(vcCall); if ( annotationEngine != null && !limitedContext ) { // limitedContext callers need to handle annotations on their own by calling their own annotationEngine // Note: we want to use the *unfiltered* and *unBAQed* context for the annotations @@ -640,7 +642,7 @@ public class UnifiedGenotyperEngine { private void determineGLModelsToUse() { String modelPrefix = ""; - if ( !UAC.GLmodel.name().contains(GPSTRING) && UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY ) + if ( !UAC.GLmodel.name().contains(GPSTRING) && UAC.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY ) modelPrefix = GPSTRING; if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") ) { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java index 423c80112..a30ae0d34 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java index f783267bc..0e6c0762c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java @@ -29,9 +29,9 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.SimpleTimer; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.GenotypesContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.File; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java index 142469077..bd46c4b84 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java @@ -29,7 +29,7 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java index 4895c84d9..0c2e59d08 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java @@ -26,7 +26,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; @@ -84,7 +85,7 @@ public abstract class DiploidExactAFCalc extends ExactAFCalc { alleles.add(vc.getReference()); alleles.addAll(chooseMostLikelyAlternateAlleles(vc, getMaxAltAlleles())); builder.alleles(alleles); - builder.genotypes(VariantContextUtils.subsetDiploidAlleles(vc, alleles, false)); + builder.genotypes(GATKVariantContextUtils.subsetDiploidAlleles(vc, alleles, false)); return builder.make(); } else { return vc; @@ -330,6 +331,6 @@ public abstract class DiploidExactAFCalc extends ExactAFCalc { final List allelesToUse, final boolean assignGenotypes, final int ploidy) { - return VariantContextUtils.subsetDiploidAlleles(vc, allelesToUse, assignGenotypes); + return GATKVariantContextUtils.subsetDiploidAlleles(vc, allelesToUse, assignGenotypes); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java index ab230d398..8e8a2d8ce 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java @@ -26,10 +26,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypesContext; import java.util.ArrayList; @@ -71,7 +71,7 @@ abstract class ExactAFCalc extends AFCalc { if ( sample.hasLikelihoods() ) { double[] gls = sample.getLikelihoods().getAsVector(); - if ( MathUtils.sum(gls) < VariantContextUtils.SUM_GL_THRESH_NOCALL ) + if ( MathUtils.sum(gls) < GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) genotypeLikelihoods.add(gls); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java index b138ddf70..c9270a6a7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java @@ -4,7 +4,7 @@ import com.google.java.contract.Requires; import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.io.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java index 937ef2ffc..76017be4f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java index 67cc79646..f37e4e3d2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java @@ -2,8 +2,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Collections; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java index ad6361a3f..179b5d8ba 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java index 3a10620aa..795fc76ed 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.Arrays; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 345f79b2b..5d19ac5e8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -54,7 +54,8 @@ import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 848aaf8a3..15ced4f0b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.io.PrintStream; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index b14dc9cc9..ad97e3ddc 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -41,7 +41,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.PrintStream; import java.util.ArrayList; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java index 0165c6cf3..68be1629c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java @@ -53,7 +53,7 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec; import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature; import org.broadinstitute.sting.utils.codecs.refseq.Transcript; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.collections.CircularArray; import org.broadinstitute.sting.utils.collections.PrimitivePair; import org.broadinstitute.sting.utils.exceptions.StingException; @@ -64,8 +64,8 @@ import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.*; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java index c629bd313..985d0a9c9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java @@ -24,8 +24,8 @@ package org.broadinstitute.sting.gatk.walkers.phasing; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; import java.util.ArrayList; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java index 54838b55e..e131ea5e3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java @@ -23,7 +23,7 @@ */ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import java.util.Arrays; import java.util.LinkedList; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java index 5bbc6dacc..5515f2141 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java @@ -28,12 +28,13 @@ import net.sf.picard.reference.ReferenceSequenceFile; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.io.File; import java.io.FileNotFoundException; @@ -124,7 +125,7 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter return; } - logger.debug("Next VC input = " + VariantContextUtils.getLocation(genomeLocParser, vc)); + logger.debug("Next VC input = " + GATKVariantContextUtils.getLocation(genomeLocParser, vc)); boolean curVcIsNotFiltered = vc.isNotFiltered(); if (vcfrWaitingToMerge == null) { @@ -134,20 +135,20 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter throw new ReviewedStingException("filteredVcfrList should be empty if not waiting to merge a vc!"); if (curVcIsNotFiltered) { // still need to wait before can release vc - logger.debug("Waiting for new variant " + VariantContextUtils.getLocation(genomeLocParser, vc)); + logger.debug("Waiting for new variant " + GATKVariantContextUtils.getLocation(genomeLocParser, vc)); vcfrWaitingToMerge = new VCFRecord(vc, false); } else if (!emitOnlyMergedRecords) { // filtered records are never merged - logger.debug("DIRECTLY output " + VariantContextUtils.getLocation(genomeLocParser, vc)); + logger.debug("DIRECTLY output " + GATKVariantContextUtils.getLocation(genomeLocParser, vc)); innerWriter.add(vc); } } else { // waiting to merge vcfrWaitingToMerge - logger.debug("Waiting to merge " + VariantContextUtils.getLocation(genomeLocParser, vcfrWaitingToMerge.vc)); + logger.debug("Waiting to merge " + GATKVariantContextUtils.getLocation(genomeLocParser, vcfrWaitingToMerge.vc)); if (!curVcIsNotFiltered) { if (!emitOnlyMergedRecords) { // filtered records are never merged - logger.debug("Caching unprocessed output " + VariantContextUtils.getLocation(genomeLocParser, vc)); + logger.debug("Caching unprocessed output " + GATKVariantContextUtils.getLocation(genomeLocParser, vc)); filteredVcfrList.add(new VCFRecord(vc, false)); } } @@ -345,10 +346,10 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter if (!PhasingUtils.alleleSegregationIsKnown(gt1, gt2)) { aas.segregationUnknown++; - logger.debug("Unknown segregation of alleles [not phased] for " + samp + " at " + VariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + VariantContextUtils.getLocation(genomeLocParser, vc2)); + logger.debug("Unknown segregation of alleles [not phased] for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2)); } else if (gt1.isHomRef() || gt2.isHomRef()) { - logger.debug("gt1.isHomRef() || gt2.isHomRef() for " + samp + " at " + VariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + VariantContextUtils.getLocation(genomeLocParser, vc2)); + logger.debug("gt1.isHomRef() || gt2.isHomRef() for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2)); aas.eitherNotVariant++; } else { // BOTH gt1 and gt2 have at least one variant allele (so either hets, or homozygous variant): @@ -377,7 +378,7 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter // Check MNPs vs. CHets: if (containsRefAllele(site1Alleles) && containsRefAllele(site2Alleles)) { - logger.debug("HET-HET for " + samp + " at " + VariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + VariantContextUtils.getLocation(genomeLocParser, vc2)); + logger.debug("HET-HET for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2)); if (logger.isDebugEnabled() && !(gt1.isHet() && gt2.isHet())) throw new ReviewedStingException("Since !gt1.isHomRef() && !gt2.isHomRef(), yet both have ref alleles, they BOTH must be hets!"); @@ -463,7 +464,7 @@ class DistanceMergeRule extends VariantContextMergeRule { } public int minDistance(VariantContext vc1, VariantContext vc2) { - return VariantContextUtils.getLocation(genomeLocParser, vc1).minDistance(VariantContextUtils.getLocation(genomeLocParser, vc2)); + return GATKVariantContextUtils.getLocation(genomeLocParser, vc1).minDistance(GATKVariantContextUtils.getLocation(genomeLocParser, vc2)); } } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index 660942b5b..2b53dea43 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -12,11 +12,12 @@ import org.broadinstitute.sting.gatk.samples.Sample; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.io.PrintStream; import java.util.*; @@ -396,7 +397,7 @@ public class PhaseByTransmission extends RodWalker, HashMa public void initialize() { ArrayList rodNames = new ArrayList(); rodNames.add(variantCollection.variants.getName()); - Map vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); + Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); Set vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); //Get the trios from the families passed as ped @@ -406,7 +407,7 @@ public class PhaseByTransmission extends RodWalker, HashMa Set headerLines = new HashSet(); - headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit())); + headerLines.addAll(GATKVCFUtils.getHeaderFields(this.getToolkit())); headerLines.add(new VCFFormatHeaderLine(TRANSMISSION_PROBABILITY_TAG_NAME, 1, VCFHeaderLineType.Integer, "Phred score of the genotype combination and phase given that the genotypes are correct")); headerLines.add(new VCFHeaderLine("source", SOURCE_NAME)); vcfWriter.writeHeader(new VCFHeader(headerLines, vcfSamples)); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java index a95b13d68..4d764866d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java @@ -23,7 +23,7 @@ */ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java index 630d99ce9..5d819ccfd 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java @@ -29,9 +29,10 @@ import net.sf.samtools.util.StringUtil; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.util.*; @@ -161,8 +162,8 @@ class PhasingUtils { } static boolean mergeIntoMNPvalidationCheck(GenomeLocParser genomeLocParser, VariantContext vc1, VariantContext vc2) { - GenomeLoc loc1 = VariantContextUtils.getLocation(genomeLocParser, vc1); - GenomeLoc loc2 = VariantContextUtils.getLocation(genomeLocParser, vc2); + GenomeLoc loc1 = GATKVariantContextUtils.getLocation(genomeLocParser, vc1); + GenomeLoc loc2 = GATKVariantContextUtils.getLocation(genomeLocParser, vc2); if (!loc1.onSameContig(loc2)) throw new ReviewedStingException("Can only merge vc1, vc2 if on the same chromosome"); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index 7d848d0d4..68eab9889 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -34,24 +34,26 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.HasGenomeLocation; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.*; import java.util.*; -import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods; +import static org.broadinstitute.sting.utils.variant.GATKVCFUtils.getVCFHeadersFromRods; /** * Walks along all variant ROD loci, caching a user-defined window of VariantContext sites, and then finishes phasing them when they go out of range (using upstream and downstream reads). @@ -212,7 +214,7 @@ public class ReadBackedPhasing extends RodWalker hInfo = new HashSet(); - hInfo.addAll(VCFUtils.getHeaderFields(getToolkit())); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit())); hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName())); // Phasing-specific INFO fields: @@ -267,13 +269,13 @@ public class ReadBackedPhasing extends RodWalker header = VCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName()); + Map header = GATKVCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName()); samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); Set headerLines = VCFUtils.smartMergeHeaders(header.values(), logger); headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate")); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 9d96dedef..aaab1af83 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -16,11 +16,11 @@ import org.broadinstitute.sting.utils.codecs.table.TableFeature; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.File; import java.io.PrintStream; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java index 62305d3c0..6bd0cbc4b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java @@ -24,12 +24,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; -import java.util.HashMap; public abstract class FrequencyModeSelector implements Cloneable{ diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java index d71d0c9c8..6d7f2b672 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalc; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.TreeSet; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java index de832b108..c69325d00 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java @@ -24,12 +24,8 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; -import java.util.ArrayList; -import java.util.Map; -import java.util.Set; import java.util.TreeSet; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java index 67ddc47ff..c4c9b0e9d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java @@ -27,9 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import java.util.HashMap; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java index 7c1d63f02..a259544ca 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java @@ -26,9 +26,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.util.ArrayList; import java.util.Collections; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java index a48bcb8a1..0a3ae538a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java @@ -24,7 +24,7 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.TreeSet; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java index afbff93d0..2632716a9 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java @@ -23,7 +23,7 @@ */ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.TreeSet; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java index 4019c5631..7d03e8edb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.util.ArrayList; import java.util.Collections; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java index 9e5fd25a9..8a3efb50d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -31,13 +31,13 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.util.*; @@ -203,7 +203,7 @@ public class ValidationSiteSelector extends RodWalker { public void initialize() { // Get list of samples to include in the output - Map vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit()); + Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit()); TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); Collection samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index 201028d99..dc0f8f3fe 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -23,15 +23,16 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatc import org.broadinstitute.sting.gatk.walkers.varianteval.util.VariantEvalUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.io.File; import java.io.FileNotFoundException; @@ -172,7 +173,7 @@ public class VariantEval extends RodWalker implements TreeRedu protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 50; @Argument(shortName="ploidy", fullName="samplePloidy", doc="Per-sample ploidy (number of chromosomes per sample)", required=false) - protected int ploidy = VariantContextUtils.DEFAULT_PLOIDY; + protected int ploidy = GATKVariantContextUtils.DEFAULT_PLOIDY; @Argument(fullName="ancestralAlignments", shortName="aa", doc="Fasta file with ancestral alleles", required=false) private File ancestralAlignmentsFile = null; @@ -259,7 +260,7 @@ public class VariantEval extends RodWalker implements TreeRedu } // Now that we have all the rods categorized, determine the sample list from the eval rods. - Map vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), evals); + Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), evals); Set vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE); // Load the sample list, using an intermediate tree set to sort the samples diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java index c14754715..be1e300e2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -5,8 +5,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; /** * The Broad Institute diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index c7392cff0..3d5d5415c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -6,8 +6,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; @Analysis(description = "Counts different classes of variants in the sample") public class CountVariants extends VariantEvaluator implements StandardEval { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java index 15f791e9d..e51068431 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java @@ -7,9 +7,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypeType; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeType; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java index 0b17c7adb..2cfade223 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -30,8 +30,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java index dda7e8611..fc2e205c6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java @@ -32,9 +32,9 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; @Analysis(description = "Evaluation summary for indels") public class IndelSummary extends VariantEvaluator implements StandardEval { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 97a8b4dda..755fd1b03 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.MendelianViolation; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Map; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java index 09c8687eb..f0b4dd90d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java @@ -31,9 +31,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; @Analysis(description = "Evaluation summary for multi-allelic variants") public class MultiallelicSummary extends VariantEvaluator implements StandardEval { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java index a0cb662e0..b1ec79586 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java @@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites") public class PrintMissingComp extends VariantEvaluator { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index b87a8ee85..091eed217 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -5,9 +5,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index fe2437976..f761ce973 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -5,9 +5,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; @Analysis(description = "Ti/Tv Variant Evaluator") public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index a2bcdaf1d..323e67c75 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -5,10 +5,10 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Collection; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java index c08ff379b..162ca5df1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java @@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; public abstract class VariantEvaluator implements Comparable { private VariantEval walker; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java index 71ea6af98..151fb8fa5 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java @@ -34,11 +34,11 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java index 500ab8e65..9845318a0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java @@ -13,9 +13,9 @@ //import org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext; //import org.broadinstitute.sting.utils.GenomeLoc; //import org.broadinstitute.sting.utils.MathUtils; -//import org.broadinstitute.sting.utils.variantcontext.Genotype; -//import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; -//import org.broadinstitute.sting.utils.variantcontext.VariantContext; +//import org.broadinstitute.variant.variantcontext.Genotype; +//import org.broadinstitute.variant.variantcontext.GenotypesContext; +//import org.broadinstitute.variant.variantcontext.VariantContext; // //import java.util.HashMap; //import java.util.HashSet; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java index 7197fc14c..51552d552 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java @@ -4,10 +4,10 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java index 817663026..f35b33c47 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java @@ -3,9 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; -import java.util.ArrayList; import java.util.Collections; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java index 1274028d7..425aca43c 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java @@ -3,9 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; -import java.util.ArrayList; import java.util.Collections; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java index 328bab1db..b1b8d53a1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java @@ -2,9 +2,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; -import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java index 7536b0237..97aa45773 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java index eab59864f..ceefb8e43 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java index 21255f7b3..d4646a3ce 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java @@ -24,11 +24,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; - -import java.util.List; -import java.util.Map; -import java.util.Set; +import org.broadinstitute.variant.variantcontext.VariantContext; /** * Tag this stratification as dynamically determining the final strat based on the input data diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java index 6328d6a51..5aa47a0a5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java @@ -3,9 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; -import java.util.ArrayList; import java.util.Arrays; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java index 278ced713..72e3e2838 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java index 330451fff..2ebe49228 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java index 089351eaa..6bb738f7e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java @@ -2,9 +2,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; -import java.util.ArrayList; import java.util.Collections; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java index 4fc381b3f..bbb9ef9f4 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java index c89c4be66..d152b086e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java @@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.util.List; import java.util.ArrayList; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java index 2ad08d806..61bc3f0b4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java index 65633bc2b..7ffc3f56b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java @@ -26,10 +26,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; -import java.util.Collections; import java.util.List; /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java index 621f4337f..62f5282c7 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java @@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java index 834c02b83..aaa8e685a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java @@ -24,11 +24,10 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broad.tribble.util.ParsingUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.List; @@ -51,7 +50,7 @@ public class TandemRepeat extends VariantStratifier { public List getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) { if ( eval == null || ! eval.isIndel() ) return ALL; - else if ( VariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) { + else if ( GATKVariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) { print("REPEAT", eval, ref); return REPEAT; } else { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java index 90b6230ca..ffaa00b4a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java @@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.Stratifier; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Collections; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java index 09b89386f..081d09ded 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java @@ -26,9 +26,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; -import java.util.Arrays; import java.util.Collections; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java index c98c05a9a..07eb3ee7a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java @@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java index 38f7a7f40..737c49e43 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; import org.apache.commons.jexl2.Expression; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable { /** diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index e84b0b10e..3d22b7665 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -35,12 +35,12 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Require import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.StandardStratification; import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier; import org.broadinstitute.sting.utils.classloader.PluginManager; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index 158d1e78a..dbe6ce9e1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -38,12 +38,13 @@ import org.broadinstitute.sting.gatk.walkers.PartitionType; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.util.*; @@ -150,7 +151,7 @@ public class ApplyRecalibration extends RodWalker implements T // setup the header fields final Set hInfo = new HashSet(); - hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames)); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames)); addVQSRStandardHeaderLines(hInfo); final TreeSet samples = new TreeSet(); samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java index 5f688d001..a177ce904 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.commandline.Tags; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; /** * Created by IntelliJ IDEA. diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java index 04ba3ff14..361677e37 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java @@ -29,7 +29,7 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index f18db412f..016ce7372 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -30,15 +30,15 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.help.HelpUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index c670ad2fd..bdbcb8399 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -38,15 +38,15 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.R.RScriptExecutor; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.io.Resource; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.FileNotFoundException; 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 68fac7631..eb671ff4a 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 @@ -37,14 +37,15 @@ 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.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.Options; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.writer.Options; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.util.*; @@ -192,7 +193,7 @@ public class CombineVariants extends RodWalker implements Tree private Set samples; public void initialize() { - Map vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit()); + Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit()); if ( vcfWriter instanceof VariantContextWriterStub) { sitesOnlyVCF = ((VariantContextWriterStub)vcfWriter).getWriterOptions().contains(Options.DO_NOT_WRITE_GENOTYPES); @@ -289,13 +290,13 @@ public class CombineVariants extends RodWalker implements Tree // iterate over the types so that it's deterministic for (VariantContext.Type type : VariantContext.Type.values()) { if (VCsByType.containsKey(type)) - mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type), + mergedVCs.add(VariantContextUtils.simpleMerge(VCsByType.get(type), priority, rodNames.size() , filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges, SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC)); } } else if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.MIX_TYPES) { - mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), vcs, + mergedVCs.add(VariantContextUtils.simpleMerge(vcs, priority, rodNames.size(), filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges, SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC)); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index 92d6e686b..055e73b5a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -33,12 +33,12 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; @@ -62,7 +62,7 @@ public class FilterLiftedVariants extends RodWalker { public void initialize() { String trackName = variantCollection.variants.getName(); Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)); - Map vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); + Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.emptySet(), samples); writer.writeHeader(vcfHeader); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index 9fe499a03..fbb81fda0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -39,14 +39,14 @@ import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; import java.util.*; @@ -93,7 +93,7 @@ public class LeftAlignVariants extends RodWalker { public void initialize() { String trackName = variantCollection.variants.getName(); Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)); - Map vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); + Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); Set headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder(); baseWriter.writeHeader(new VCFHeader(headerLines, samples)); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 63209e98c..0afa4e46e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -38,14 +38,15 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.util.*; @@ -94,7 +95,7 @@ public class LiftoverVariants extends RodWalker { String trackName = variantCollection.variants.getName(); Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)); - Map vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); + Map vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName)); Set metaData = new HashSet(); if ( vcfHeaders.containsKey(trackName) ) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java index 2ab5136a7..2d8f9df8f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java @@ -35,14 +35,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.util.*; @@ -78,7 +78,7 @@ public class RandomlySplitVariants extends RodWalker { final List inputNames = Arrays.asList(variantCollection.variants.getName()); Set samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames); Set hInfo = new HashSet(); - hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames)); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames)); vcfWriter1.writeHeader(new VCFHeader(hInfo, samples)); vcfWriter2 = VariantContextWriterFactory.create(file2, getMasterSequenceDictionary()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java index 46a3a8cd1..f9453e7c4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java @@ -35,12 +35,13 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.text.ListFileUtils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.io.File; import java.util.*; @@ -148,7 +149,7 @@ public class SelectHeaders extends RodWalker implements TreeRe // Get list of samples to include in the output List rodNames = Arrays.asList(variantCollection.variants.getName()); - Map vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); + Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); Set headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger); headerLines.add(new VCFHeaderLine(VCFHeader.SOURCE_KEY, "SelectHeaders")); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 9253446c8..cffd405b1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -41,12 +41,14 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.utils.MendelianViolation; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.FileNotFoundException; @@ -349,7 +351,7 @@ public class SelectVariants extends RodWalker implements TreeR // Get list of samples to include in the output List rodNames = Arrays.asList(variantCollection.variants.getName()); - vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); + vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames); TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); Collection samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles); @@ -451,7 +453,7 @@ public class SelectVariants extends RodWalker implements TreeR UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH; UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES; UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES; - UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY); + UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY); headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null)); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index 189772f01..8e42f803b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -34,11 +34,11 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.File; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index 9236247f1..dfc9a8eea 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -34,13 +34,14 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.util.*; @@ -164,7 +165,7 @@ public class VariantValidationAssessor extends RodWalker // setup the header fields Set hInfo = new HashSet(); - hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames)); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames)); // set up the info and filter headers hInfo.add(new VCFInfoHeaderLine("NoCallPct", 1, VCFHeaderLineType.Float, "Percent of no-calls")); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index 4777b807f..98fe6636c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -1,7 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broad.tribble.TribbleException; -import org.broadinstitute.sting.alignment.bwa.java.AlignmentMatchSequence; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; @@ -10,18 +9,16 @@ 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.Reference; -import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.io.*; import java.util.*; @@ -117,7 +114,7 @@ public class VariantsToBinaryPed extends RodWalker { // family ID, individual ID, Paternal ID, Maternal ID, Sex, Phenotype int dummyID = 0; // increments for dummy parental and family IDs used // want to be especially careful to maintain order here - Map headers = VCFUtils.getVCFHeadersFromRods(getToolkit()); + Map headers = GATKVCFUtils.getVCFHeadersFromRods(getToolkit()); for ( Map.Entry header : headers.entrySet() ) { if ( ! header.getKey().equals(variantCollection.variants.getName()) && ! metaDataFile.getAbsolutePath().endsWith(".fam") ) { continue; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index dd5264a1b..ff65197b1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -27,19 +27,19 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; 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.Utils; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.io.PrintStream; import java.lang.reflect.Array; @@ -178,7 +178,7 @@ public class VariantsToTable extends RodWalker { public void initialize() { if ( !genotypeFieldsToTake.isEmpty() ) { - Map vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), variants); + Map vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), variants); TreeSet vcfSamples = new TreeSet(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE)); samples.addAll(vcfSamples); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index 059e9c5fb..7c44966d8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -39,16 +39,17 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.sting.utils.variantcontext.*; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.util.*; @@ -212,7 +213,7 @@ public class VariantsToVCF extends RodWalker { // setup the header fields Set hInfo = new HashSet(); - hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName()))); + hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName()))); hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY)); allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY); diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java index 2226c6458..597a916f1 100644 --- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java +++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java @@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileWriter; import org.broad.tribble.Tribble; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.lang.annotation.Annotation; diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java index 108a1c423..54eb67d8c 100644 --- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java +++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java @@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileWriter; import org.apache.commons.lang.StringEscapeUtils; import org.apache.commons.lang.StringUtils; import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.InputStream; diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index bf60b4a80..dbffacfbc 100644 --- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -34,10 +34,10 @@ import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import org.broad.tribble.Feature; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; /** * Factory class for creating GenomeLocs diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java index 4c708f2bf..2476a666e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java @@ -24,15 +24,14 @@ package org.broadinstitute.sting.utils; -import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.Cigar; import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.Serializable; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java index 9b1cc9733..8601f08b4 100755 --- a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java index a605a5596..ed55d2f97 100755 --- a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java +++ b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java @@ -1,9 +1,9 @@ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.gatk.samples.Sample; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypeType; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.GenotypeType; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java index 26c95bffd..2ccc145f9 100755 --- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java @@ -28,12 +28,12 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; +import org.broadinstitute.sting.utils.variant.GATKVCFUtils; +import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.text.ListFileUtils; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.variant.variantcontext.VariantContextUtils; import java.io.File; import java.io.FileNotFoundException; @@ -102,18 +102,18 @@ public class SampleUtils { public static Set getUniqueSamplesFromRods(GenomeAnalysisEngine toolkit, Collection rodNames) { Set samples = new LinkedHashSet(); - for ( VCFHeader header : VCFUtils.getVCFHeadersFromRods(toolkit, rodNames).values() ) + for ( VCFHeader header : GATKVCFUtils.getVCFHeadersFromRods(toolkit, rodNames).values() ) samples.addAll(header.getGenotypeSamples()); return samples; } public static Set getRodNamesWithVCFHeader(GenomeAnalysisEngine toolkit, Collection rodNames) { - return VCFUtils.getVCFHeadersFromRods(toolkit, rodNames).keySet(); + return GATKVCFUtils.getVCFHeadersFromRods(toolkit, rodNames).keySet(); } public static Set getSampleListWithVCFHeader(GenomeAnalysisEngine toolkit, Collection rodNames) { - return getSampleList(VCFUtils.getVCFHeadersFromRods(toolkit, rodNames)); + return getSampleList(GATKVCFUtils.getVCFHeadersFromRods(toolkit, rodNames)); } public static Set getSampleList(Map headers) { @@ -149,7 +149,7 @@ public class SampleUtils { // iterate to get all of the sample names - for ( Map.Entry pair : VCFUtils.getVCFHeadersFromRods(toolkit).entrySet() ) { + for ( Map.Entry pair : GATKVCFUtils.getVCFHeadersFromRods(toolkit).entrySet() ) { for ( String sample : pair.getValue().getGenotypeSamples() ) addUniqueSample(samples, sampleOverlapMap, rodNamesToSampleNames, sample, pair.getKey()); } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java index 0aa9ecba2..fc7df9f76 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.codecs.beagle; import org.broad.tribble.Feature; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.ArrayList; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java index d0480a90b..2a36e8ad3 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils.codecs.hapmap; import org.broad.tribble.Feature; import org.broad.tribble.annotation.Strand; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.HashMap; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java index 7ae575534..85e4a338a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.duplicates; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index 523fd5a97..b1410da27 100755 --- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpUtils; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.File; diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java index 9bb0e646f..10d35684b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java +++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java @@ -30,7 +30,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.io.PrintStream; import java.lang.reflect.Constructor; diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java index 7db818592..1a27c6ecb 100644 --- a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java +++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java @@ -28,7 +28,7 @@ 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.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Allele; import java.io.PrintStream; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java index ff274499b..7f323adae 100644 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.pileup; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.fragments.FragmentCollection; diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java index 8cba5ec23..429de4a0f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils.pileup; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java index 7e90d98b9..48b367ea7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.recalibration.covariates.*; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.R.RScriptExecutor; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.classloader.PluginManager; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java index b586a1607..6619c24eb 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java index a9b6c7152..6bff833e4 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates; import org.broadinstitute.sting.utils.recalibration.ReadCovariates; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java index d4e4ab65e..36352f806 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java @@ -1,11 +1,9 @@ package org.broadinstitute.sting.utils.recalibration.covariates; import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection; -import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.TandemRepeat; -import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.recalibration.ReadCovariates; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import java.util.Arrays; @@ -29,9 +27,9 @@ public class RepeatLengthCovariate implements ExperimentalCovariate { int maxRL = 0; for (int str = 1; str <= 8; str++) { if (i + str <= readBytes.length) { - maxRL = Math.max(maxRL, VariantContextUtils.findNumberofRepetitions( - Arrays.copyOfRange(readBytes,i,i + str), - Arrays.copyOfRange(readBytes,i,readBytes.length) + maxRL = Math.max(maxRL, GATKVariantContextUtils.findNumberofRepetitions( + Arrays.copyOfRange(readBytes, i, i + str), + Arrays.copyOfRange(readBytes, i, readBytes.length) )); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 585578958..7ef05edd8 100644 --- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -30,7 +30,7 @@ import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java new file mode 100755 index 000000000..4e394ace5 --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java @@ -0,0 +1,178 @@ +/* + * 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.variant; + +import org.broad.tribble.Feature; +import org.broad.tribble.FeatureCodecHeader; +import org.broad.tribble.readers.PositionalBufferedStream; +import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; +import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.*; + +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.util.*; + +/** + * A set of GATK-specific static utility methods for common operations on VCF files/records. + */ +public class GATKVCFUtils { + + /** + * Constructor access disallowed...static utility methods only! + */ + private GATKVCFUtils() { } + + public static Map getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List> rodBindings) { + // Collect the eval rod names + final Set names = new TreeSet(); + for ( final RodBinding evalRod : rodBindings ) + names.add(evalRod.getName()); + return getVCFHeadersFromRods(toolkit, names); + } + + public static Map getVCFHeadersFromRods(GenomeAnalysisEngine toolkit) { + return getVCFHeadersFromRods(toolkit, (Collection)null); + } + + public static Map getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, Collection rodNames) { + Map data = new HashMap(); + + // iterate to get all of the sample names + List dataSources = toolkit.getRodDataSources(); + for ( ReferenceOrderedDataSource source : dataSources ) { + // ignore the rod if it's not in our list + if ( rodNames != null && !rodNames.contains(source.getName()) ) + continue; + + if ( source.getHeader() != null && source.getHeader() instanceof VCFHeader ) + data.put(source.getName(), (VCFHeader)source.getHeader()); + } + + return data; + } + + public static Map getVCFHeadersFromRodPrefix(GenomeAnalysisEngine toolkit,String prefix) { + Map data = new HashMap(); + + // iterate to get all of the sample names + List dataSources = toolkit.getRodDataSources(); + for ( ReferenceOrderedDataSource source : dataSources ) { + // ignore the rod if lacks the prefix + if ( ! source.getName().startsWith(prefix) ) + continue; + + if ( source.getHeader() != null && source.getHeader() instanceof VCFHeader ) + data.put(source.getName(), (VCFHeader)source.getHeader()); + } + + return data; + } + + /** + * Gets the header fields from all VCF rods input by the user + * + * @param toolkit GATK engine + * + * @return a set of all fields + */ + public static Set getHeaderFields(GenomeAnalysisEngine toolkit) { + return getHeaderFields(toolkit, null); + } + + /** + * Gets the header fields from all VCF rods input by the user + * + * @param toolkit GATK engine + * @param rodNames names of rods to use, or null if we should use all possible ones + * + * @return a set of all fields + */ + public static Set getHeaderFields(GenomeAnalysisEngine toolkit, Collection rodNames) { + + // keep a map of sample name to occurrences encountered + TreeSet fields = new TreeSet(); + + // iterate to get all of the sample names + List dataSources = toolkit.getRodDataSources(); + for ( ReferenceOrderedDataSource source : dataSources ) { + // ignore the rod if it's not in our list + if ( rodNames != null && !rodNames.contains(source.getName()) ) + continue; + + if ( source.getRecordType().equals(VariantContext.class)) { + VCFHeader header = (VCFHeader)source.getHeader(); + if ( header != null ) + fields.addAll(header.getMetaDataInSortedOrder()); + } + } + + return fields; + } + + /** + * Add / replace the contig header lines in the VCFHeader with the information in the GATK engine + * + * @param header the header to update + * @param engine the GATK engine containing command line arguments and the master sequence dictionary + */ + public static VCFHeader withUpdatedContigs(final VCFHeader header, final GenomeAnalysisEngine engine) { + return VCFUtils.withUpdatedContigs(header, engine.getArguments().referenceFile, engine.getMasterSequenceDictionary()); + } + + /** + * Read all of the VCF records from source into memory, returning the header and the VariantContexts + * + * @param source the file to read, must be in VCF4 format + * @return + * @throws java.io.IOException + */ + public static Pair> readVCF(final File source) throws IOException { + // read in the features + final List vcs = new ArrayList(); + final VCFCodec codec = new VCFCodec(); + PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source)); + FeatureCodecHeader header = codec.readHeader(pbs); + pbs.close(); + + pbs = new PositionalBufferedStream(new FileInputStream(source)); + pbs.skip(header.getHeaderEnd()); + + final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue(); + + while ( ! pbs.isDone() ) { + final VariantContext vc = codec.decode(pbs); + if ( vc != null ) + vcs.add(vc); + } + + return new Pair>(vcfHeader, vcs); + } +} \ No newline at end of file diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java new file mode 100644 index 000000000..47f766d9b --- /dev/null +++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java @@ -0,0 +1,450 @@ +package org.broadinstitute.sting.utils.variant; + +import com.google.java.contract.Requires; +import org.apache.commons.lang.ArrayUtils; +import org.broadinstitute.sting.utils.GenomeLoc; +import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.variant.variantcontext.*; + +import java.util.*; + +public class GATKVariantContextUtils { + + public static final int DEFAULT_PLOIDY = 2; + public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call. + private static final List NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL); + + /** + * create a genome location, given a variant context + * @param genomeLocParser parser + * @param vc the variant context + * @return the genomeLoc + */ + public static final GenomeLoc getLocation(GenomeLocParser genomeLocParser,VariantContext vc) { + return genomeLocParser.createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd(), true); + } + + /** + * Returns true iff VC is an non-complex indel where every allele represents an expansion or + * contraction of a series of identical bases in the reference. + * + * For example, suppose the ref bases are CTCTCTGA, which includes a 3x repeat of CTCTCT + * + * If VC = -/CT, then this function returns true because the CT insertion matches exactly the + * upcoming reference. + * If VC = -/CTA then this function returns false because the CTA isn't a perfect match + * + * Now consider deletions: + * + * If VC = CT/- then again the same logic applies and this returns true + * The case of CTA/- makes no sense because it doesn't actually match the reference bases. + * + * The logic of this function is pretty simple. Take all of the non-null alleles in VC. For + * each insertion allele of n bases, check if that allele matches the next n reference bases. + * For each deletion allele of n bases, check if this matches the reference bases at n - 2 n, + * as it must necessarily match the first n bases. If this test returns true for all + * alleles you are a tandem repeat, otherwise you are not. + * + * @param vc + * @param refBasesStartingAtVCWithPad not this is assumed to include the PADDED reference + * @return + */ + @Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"}) + public static boolean isTandemRepeat(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) { + final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1); + if ( ! vc.isIndel() ) // only indels are tandem repeats + return false; + + final Allele ref = vc.getReference(); + + for ( final Allele allele : vc.getAlternateAlleles() ) { + if ( ! isRepeatAllele(ref, allele, refBasesStartingAtVCWithoutPad) ) + return false; + } + + // we've passed all of the tests, so we are a repeat + return true; + } + + /** + * + * @param vc + * @param refBasesStartingAtVCWithPad + * @return + */ + @Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"}) + public static Pair,byte[]> getNumTandemRepeatUnits(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) { + final boolean VERBOSE = false; + final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1); + if ( ! vc.isIndel() ) // only indels are tandem repeats + return null; + + final Allele refAllele = vc.getReference(); + final byte[] refAlleleBases = Arrays.copyOfRange(refAllele.getBases(), 1, refAllele.length()); + + byte[] repeatUnit = null; + final ArrayList lengths = new ArrayList(); + + for ( final Allele allele : vc.getAlternateAlleles() ) { + Pair result = getNumTandemRepeatUnits(refAlleleBases, Arrays.copyOfRange(allele.getBases(), 1, allele.length()), refBasesStartingAtVCWithoutPad.getBytes()); + + final int[] repetitionCount = result.first; + // repetition count = 0 means allele is not a tandem expansion of context + if (repetitionCount[0] == 0 || repetitionCount[1] == 0) + return null; + + if (lengths.size() == 0) { + lengths.add(repetitionCount[0]); // add ref allele length only once + } + lengths.add(repetitionCount[1]); // add this alt allele's length + + repeatUnit = result.second; + if (VERBOSE) { + System.out.println("RefContext:"+refBasesStartingAtVCWithoutPad); + System.out.println("Ref:"+refAllele.toString()+" Count:" + String.valueOf(repetitionCount[0])); + System.out.println("Allele:"+allele.toString()+" Count:" + String.valueOf(repetitionCount[1])); + System.out.println("RU:"+new String(repeatUnit)); + } + } + + return new Pair, byte[]>(lengths,repeatUnit); + } + + protected static Pair getNumTandemRepeatUnits(final byte[] refBases, final byte[] altBases, final byte[] remainingRefContext) { + /* we can't exactly apply same logic as in basesAreRepeated() to compute tandem unit and number of repeated units. + Consider case where ref =ATATAT and we have an insertion of ATAT. Natural description is (AT)3 -> (AT)5. + */ + + byte[] longB; + // find first repeat unit based on either ref or alt, whichever is longer + if (altBases.length > refBases.length) + longB = altBases; + else + longB = refBases; + + // see if non-null allele (either ref or alt, whichever is longer) can be decomposed into several identical tandem units + // for example, -*,CACA needs to first be decomposed into (CA)2 + final int repeatUnitLength = findRepeatedSubstring(longB); + final byte[] repeatUnit = Arrays.copyOf(longB, repeatUnitLength); + + final int[] repetitionCount = new int[2]; +// repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext)); +// repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext)); + int repetitionsInRef = findNumberofRepetitions(repeatUnit,refBases); + repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext))-repetitionsInRef; + repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext))-repetitionsInRef; + + return new Pair(repetitionCount, repeatUnit); + + } + + /** + * Find out if a string can be represented as a tandem number of substrings. + * For example ACTACT is a 2-tandem of ACT, + * but ACTACA is not. + * + * @param bases String to be tested + * @return Length of repeat unit, if string can be represented as tandem of substring (if it can't + * be represented as one, it will be just the length of the input string) + */ + public static int findRepeatedSubstring(byte[] bases) { + + int repLength; + for (repLength=1; repLength <=bases.length; repLength++) { + final byte[] candidateRepeatUnit = Arrays.copyOf(bases,repLength); + boolean allBasesMatch = true; + for (int start = repLength; start < bases.length; start += repLength ) { + // check that remaining of string is exactly equal to repeat unit + final byte[] basePiece = Arrays.copyOfRange(bases,start,start+candidateRepeatUnit.length); + if (!Arrays.equals(candidateRepeatUnit, basePiece)) { + allBasesMatch = false; + break; + } + } + if (allBasesMatch) + return repLength; + } + + return repLength; + } + + /** + * Helper routine that finds number of repetitions a string consists of. + * For example, for string ATAT and repeat unit AT, number of repetitions = 2 + * @param repeatUnit Substring + * @param testString String to test + * @return Number of repetitions (0 if testString is not a concatenation of n repeatUnit's + */ + public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) { + int numRepeats = 0; + for (int start = 0; start < testString.length; start += repeatUnit.length) { + int end = start + repeatUnit.length; + byte[] unit = Arrays.copyOfRange(testString,start, end); + if(Arrays.equals(unit,repeatUnit)) + numRepeats++; + else + return numRepeats; + } + return numRepeats; + } + + /** + * Helper function for isTandemRepeat that checks that allele matches somewhere on the reference + * @param ref + * @param alt + * @param refBasesStartingAtVCWithoutPad + * @return + */ + protected static boolean isRepeatAllele(final Allele ref, final Allele alt, final String refBasesStartingAtVCWithoutPad) { + if ( ! Allele.oneIsPrefixOfOther(ref, alt) ) + return false; // we require one allele be a prefix of another + + if ( ref.length() > alt.length() ) { // we are a deletion + return basesAreRepeated(ref.getBaseString(), alt.getBaseString(), refBasesStartingAtVCWithoutPad, 2); + } else { // we are an insertion + return basesAreRepeated(alt.getBaseString(), ref.getBaseString(), refBasesStartingAtVCWithoutPad, 1); + } + } + + protected static boolean basesAreRepeated(final String l, final String s, final String ref, final int minNumberOfMatches) { + final String potentialRepeat = l.substring(s.length()); // skip s bases + + for ( int i = 0; i < minNumberOfMatches; i++) { + final int start = i * potentialRepeat.length(); + final int end = (i+1) * potentialRepeat.length(); + if ( ref.length() < end ) + return false; // we ran out of bases to test + final String refSub = ref.substring(start, end); + if ( ! refSub.equals(potentialRepeat) ) + return false; // repeat didn't match, fail + } + + return true; // we passed all tests, we matched + } + + /** + * Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs + * + * @param vc variant context with genotype likelihoods + * @return genotypes context + */ + public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) { + return subsetDiploidAlleles(vc, vc.getAlleles(), true); + } + + /** + * Split variant context into its biallelic components if there are more than 2 alleles + * + * For VC has A/B/C alleles, returns A/B and A/C contexts. + * Genotypes are all no-calls now (it's not possible to fix them easily) + * Alleles are right trimmed to satisfy VCF conventions + * + * If vc is biallelic or non-variant it is just returned + * + * Chromosome counts are updated (but they are by definition 0) + * + * @param vc a potentially multi-allelic variant context + * @return a list of bi-allelic (or monomorphic) variant context + */ + public static List splitVariantContextToBiallelics(final VariantContext vc) { + if ( ! vc.isVariant() || vc.isBiallelic() ) + // non variant or biallelics already satisfy the contract + return Collections.singletonList(vc); + else { + final List biallelics = new LinkedList(); + + for ( final Allele alt : vc.getAlternateAlleles() ) { + VariantContextBuilder builder = new VariantContextBuilder(vc); + final List alleles = Arrays.asList(vc.getReference(), alt); + builder.alleles(alleles); + builder.genotypes(subsetDiploidAlleles(vc, alleles, false)); + VariantContextUtils.calculateChromosomeCounts(builder, true); + biallelics.add(reverseTrimAlleles(builder.make())); + } + + return biallelics; + } + } + + /** + * subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately) + * + * @param vc variant context with genotype likelihoods + * @param allelesToUse which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC *** + * @param assignGenotypes true if we should update the genotypes based on the (subsetted) PLs + * @return genotypes + */ + public static GenotypesContext subsetDiploidAlleles(final VariantContext vc, + final List allelesToUse, + final boolean assignGenotypes) { + + // the genotypes with PLs + final GenotypesContext oldGTs = vc.getGenotypes(); + + // samples + final List sampleIndices = oldGTs.getSampleNamesOrderedByName(); + + // the new genotypes to create + final GenotypesContext newGTs = GenotypesContext.create(); + + // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward + final int numOriginalAltAlleles = vc.getAlternateAlleles().size(); + final int numNewAltAlleles = allelesToUse.size() - 1; + + // which PLs should be carried forward? + ArrayList likelihoodIndexesToUse = null; + + // an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles, + // then we can keep the PLs as is; otherwise, we determine which ones to keep + if ( numNewAltAlleles != numOriginalAltAlleles && numNewAltAlleles > 0 ) { + likelihoodIndexesToUse = new ArrayList(30); + + final boolean[] altAlleleIndexToUse = new boolean[numOriginalAltAlleles]; + for ( int i = 0; i < numOriginalAltAlleles; i++ ) { + if ( allelesToUse.contains(vc.getAlternateAllele(i)) ) + altAlleleIndexToUse[i] = true; + } + + // numLikelihoods takes total # of alleles. Use default # of chromosomes (ploidy) = 2 + final int numLikelihoods = GenotypeLikelihoods.numLikelihoods(1 + numOriginalAltAlleles, DEFAULT_PLOIDY); + for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) { + final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex); + // consider this entry only if both of the alleles are good + if ( (alleles.alleleIndex1 == 0 || altAlleleIndexToUse[alleles.alleleIndex1 - 1]) && (alleles.alleleIndex2 == 0 || altAlleleIndexToUse[alleles.alleleIndex2 - 1]) ) + likelihoodIndexesToUse.add(PLindex); + } + } + + // create the new genotypes + for ( int k = 0; k < oldGTs.size(); k++ ) { + final Genotype g = oldGTs.get(sampleIndices.get(k)); + if ( !g.hasLikelihoods() ) { + newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES)); + continue; + } + + // create the new likelihoods array from the alleles we are allowed to use + final double[] originalLikelihoods = g.getLikelihoods().getAsVector(); + double[] newLikelihoods; + if ( likelihoodIndexesToUse == null ) { + newLikelihoods = originalLikelihoods; + } else { + newLikelihoods = new double[likelihoodIndexesToUse.size()]; + int newIndex = 0; + for ( int oldIndex : likelihoodIndexesToUse ) + newLikelihoods[newIndex++] = originalLikelihoods[oldIndex]; + + // might need to re-normalize + newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true); + } + + // if there is no mass on the (new) likelihoods, then just no-call the sample + if ( MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) { + newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES)); + } + else { + final GenotypeBuilder gb = new GenotypeBuilder(g); + + if ( numNewAltAlleles == 0 ) + gb.noPL(); + else + gb.PL(newLikelihoods); + + // if we weren't asked to assign a genotype, then just no-call the sample + if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) { + gb.alleles(NO_CALL_ALLELES); + } + else { + // find the genotype with maximum likelihoods + int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods); + GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex); + + gb.alleles(Arrays.asList(allelesToUse.get(alleles.alleleIndex1), allelesToUse.get(alleles.alleleIndex2))); + if ( numNewAltAlleles != 0 ) gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods)); + } + newGTs.add(gb.make()); + } + } + + return newGTs; + } + + public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) { + + // see whether we need to trim common reference base from all alleles + final int trimExtent = computeReverseClipping(inputVC.getAlleles(), inputVC.getReference().getDisplayString().getBytes(), 0, false); + if ( trimExtent <= 0 || inputVC.getAlleles().size() <= 1 ) + return inputVC; + + final List alleles = new ArrayList(); + final GenotypesContext genotypes = GenotypesContext.create(); + final Map originalToTrimmedAlleleMap = new HashMap(); + + for (final Allele a : inputVC.getAlleles()) { + if (a.isSymbolic()) { + alleles.add(a); + originalToTrimmedAlleleMap.put(a, a); + } else { + // get bases for current allele and create a new one with trimmed bases + final byte[] newBases = Arrays.copyOfRange(a.getBases(), 0, a.length()-trimExtent); + final Allele trimmedAllele = Allele.create(newBases, a.isReference()); + alleles.add(trimmedAllele); + originalToTrimmedAlleleMap.put(a, trimmedAllele); + } + } + + // now we can recreate new genotypes with trimmed alleles + for ( final Genotype genotype : inputVC.getGenotypes() ) { + final List originalAlleles = genotype.getAlleles(); + final List trimmedAlleles = new ArrayList(); + for ( final Allele a : originalAlleles ) { + if ( a.isCalled() ) + trimmedAlleles.add(originalToTrimmedAlleleMap.get(a)); + else + trimmedAlleles.add(Allele.NO_CALL); + } + genotypes.add(new GenotypeBuilder(genotype).alleles(trimmedAlleles).make()); + } + + return new VariantContextBuilder(inputVC).stop(inputVC.getStart() + alleles.get(0).length() - 1).alleles(alleles).genotypes(genotypes).make(); + } + + public static int computeReverseClipping(final List unclippedAlleles, + final byte[] ref, + final int forwardClipping, + final boolean allowFullClip) { + int clipping = 0; + boolean stillClipping = true; + + while ( stillClipping ) { + for ( final Allele a : unclippedAlleles ) { + if ( a.isSymbolic() ) + continue; + + // we need to ensure that we don't reverse clip out all of the bases from an allele because we then will have the wrong + // position set for the VariantContext (although it's okay to forward clip it all out, because the position will be fine). + if ( a.length() - clipping == 0 ) + return clipping - (allowFullClip ? 0 : 1); + + if ( a.length() - clipping <= forwardClipping || a.length() - forwardClipping == 0 ) { + stillClipping = false; + } + else if ( ref.length == clipping ) { + if ( allowFullClip ) + stillClipping = false; + else + return -1; + } + else if ( a.getBases()[a.length()-clipping-1] != ref[ref.length-clipping-1] ) { + stillClipping = false; + } + } + if ( stillClipping ) + clipping++; + } + + return clipping; + } +} diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java index c221b8fba..b8bc1be6b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.bcf2; +package org.broadinstitute.variant.bcf2; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; @@ -30,12 +30,11 @@ import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodecHeader; +import org.broad.tribble.TribbleException; import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.vcf.*; +import org.broadinstitute.variant.variantcontext.*; import java.io.ByteArrayInputStream; import java.io.FileInputStream; @@ -127,7 +126,7 @@ public final class BCF2Codec implements FeatureCodec { createLazyGenotypesDecoder(info, builder); return builder.fullyDecoded(true).make(); } catch ( IOException e ) { - throw new UserException.CouldNotReadInputFile("Failed to read BCF file", e); + throw new TribbleException("Failed to read BCF file", e); } } @@ -166,7 +165,7 @@ public final class BCF2Codec implements FeatureCodec { this.header = (VCFHeader)headerParser.readHeader(headerReader); bps.close(); } catch ( IOException e ) { - throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 header"); + throw new TribbleException("I/O error while reading BCF2 header"); } // create the config offsets @@ -271,8 +270,8 @@ public final class BCF2Codec implements FeatureCodec { final int nSamples = nFormatSamples & 0x00FFFFF; if ( header.getNGenotypeSamples() != nSamples ) - error("GATK currently doesn't support reading BCF2 files with " + - "different numbers of samples per record. Saw " + header.getNGenotypeSamples() + + error("Reading BCF2 files with different numbers of samples per record " + + "is not currently supported. Saw " + header.getNGenotypeSamples() + " samples in header but have a record with " + nSamples + " samples"); decodeID(builder); @@ -494,6 +493,6 @@ public final class BCF2Codec implements FeatureCodec { } private void error(final String message) throws RuntimeException { - throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos)); + throw new TribbleException(String.format("%s, at record %d with position %d:", message, recordNo, pos)); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java index 05ba2aa1f..ca5975ab0 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java @@ -22,14 +22,13 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.bcf2; +package org.broadinstitute.variant.bcf2; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; import org.broad.tribble.FeatureCodec; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broad.tribble.TribbleException; import java.io.ByteArrayInputStream; import java.io.IOException; @@ -69,7 +68,7 @@ public final class BCF2Decoder { * @return */ public void readNextBlock(final int blockSizeInBytes, final InputStream stream) { - if ( blockSizeInBytes < 0 ) throw new UserException.MalformedBCF2("Invalid block size " + blockSizeInBytes); + if ( blockSizeInBytes < 0 ) throw new TribbleException("Invalid block size " + blockSizeInBytes); setRecordBytes(readRecordBytes(blockSizeInBytes, stream)); } @@ -84,7 +83,7 @@ public final class BCF2Decoder { final int bytesRead = (int)stream.skip(blockSizeInBytes); validateReadBytes(bytesRead, 1, blockSizeInBytes); } catch ( IOException e ) { - throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e); + throw new TribbleException("I/O error while reading BCF2 file", e); } this.recordBytes = null; this.recordStream = null; @@ -175,7 +174,7 @@ public final class BCF2Decoder { case INT32: return value; case FLOAT: return rawFloatToFloat(value); case CHAR: return value & 0xFF; // TODO -- I cannot imagine why we'd get here, as string needs to be special cased - default: throw new ReviewedStingException("BCF2 codec doesn't know how to decode type " + type ); + default: throw new TribbleException("BCF2 codec doesn't know how to decode type " + type ); } } } @@ -205,7 +204,7 @@ public final class BCF2Decoder { return BCF2Utils.isCollapsedString(s) ? BCF2Utils.explodeStringList(s) : s; } } catch ( IOException e ) { - throw new ReviewedStingException("readByte failure", e); + throw new TribbleException("readByte failure", e); } } @@ -348,7 +347,7 @@ public final class BCF2Decoder { validateReadBytes(bytesRead, nReadAttempts, blockSizeInBytes); } catch ( IOException e ) { - throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e); + throw new TribbleException("I/O error while reading BCF2 file", e); } return record; @@ -365,7 +364,7 @@ public final class BCF2Decoder { assert expected >= 0; if ( actuallyRead < expected ) { - throw new UserException.MalformedBCF2( + throw new TribbleException( String.format("Failed to read next complete record: expected %d bytes but read only %d after %d iterations", expected, actuallyRead, nReadAttempts)); } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java index e4ae96262..9355d56de 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java @@ -22,15 +22,15 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.bcf2; +package org.broadinstitute.variant.bcf2; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.GenotypeBuilder; import java.io.IOException; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java similarity index 89% rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java index 46b1fa6c1..c2d893b7f 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java @@ -22,13 +22,12 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.bcf2; +package org.broadinstitute.variant.bcf2; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broad.tribble.TribbleException; +import org.broadinstitute.variant.variantcontext.*; import java.io.IOException; import java.util.*; @@ -85,7 +84,7 @@ public class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser try { fieldDecoder.decode(siteAlleles, field, decoder, typeDescriptor, numElements, builders); } catch ( ClassCastException e ) { - throw new UserException.MalformedBCF2("BUG: expected encoding of field " + field + throw new TribbleException("BUG: expected encoding of field " + field + " inconsistent with the value observed in the decoded value"); } } @@ -96,7 +95,7 @@ public class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser return new LazyGenotypesContext.LazyData(genotypes, codec.getHeader().getSampleNamesInOrder(), codec.getHeader().getSampleNameToOffset()); } catch ( IOException e ) { - throw new ReviewedStingException("Unexpected IOException parsing already read genotypes data block", e); + throw new TribbleException("Unexpected IOException parsing already read genotypes data block", e); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Type.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2Type.java index 1162a5d1e..b24f2a582 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Type.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.bcf2; +package org.broadinstitute.variant.bcf2; import com.google.java.contract.Requires; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Utils.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2Utils.java index 2ac916db1..30d6b4ee4 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Utils.java @@ -22,12 +22,12 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.bcf2; +package org.broadinstitute.variant.bcf2; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broad.tribble.TribbleException; +import org.broadinstitute.variant.vcf.*; import java.io.*; import java.util.*; @@ -214,7 +214,7 @@ public final class BCF2Utils { return potentialType; } - throw new ReviewedStingException("Integer cannot be encoded in allowable range of even INT32: " + value); + throw new TribbleException("Integer cannot be encoded in allowable range of even INT32: " + value); } @Ensures("result.isIntegerType()") @@ -249,7 +249,7 @@ public final class BCF2Utils { case INT8: return t2; case INT16: return t2 == BCF2Type.INT32 ? t2 : t1; case INT32: return t1; - default: throw new ReviewedStingException("BUG: unexpected BCF2Type " + t1); + default: throw new TribbleException("BUG: unexpected BCF2Type " + t1); } } @@ -262,7 +262,7 @@ public final class BCF2Utils { case INT8: break; case INT16: maxType = BCF2Type.INT16; break; case INT32: return BCF2Type.INT32; // fast path for largest possible value - default: throw new ReviewedStingException("Unexpected integer type " + type1 ); + default: throw new TribbleException("Unexpected integer type " + type1 ); } } return maxType; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java b/public/java/src/org/broadinstitute/variant/bcf2/BCFVersion.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java rename to public/java/src/org/broadinstitute/variant/bcf2/BCFVersion.java index 742da7c0c..5e1915c22 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java +++ b/public/java/src/org/broadinstitute/variant/bcf2/BCFVersion.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.bcf2; +package org.broadinstitute.variant.bcf2; import java.io.IOException; import java.io.InputStream; diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/variant/utils/BaseUtils.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/utils/BaseUtils.java rename to public/java/src/org/broadinstitute/variant/utils/BaseUtils.java index 53a49d8b2..4786622b0 100644 --- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java +++ b/public/java/src/org/broadinstitute/variant/utils/BaseUtils.java @@ -1,10 +1,9 @@ -package org.broadinstitute.sting.utils; +package org.broadinstitute.variant.utils; import net.sf.samtools.util.StringUtil; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.Arrays; +import java.util.Random; /** * BaseUtils contains some basic utilities for manipulating nucleotides. @@ -47,6 +46,9 @@ public class BaseUtils { public static final int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G'); public static final int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T'); + // Use a fixed random seed to allow for deterministic results when using random bases + private static final Random randomNumberGen = new Random(47382911L); + /// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or // a pyrimidine to another pyrimidine nucleotide (C <-> T). // Approximately two out of every three single nucleotide polymorphisms (SNPs) are transitions. @@ -185,7 +187,7 @@ public class BaseUtils { */ static public int simpleBaseToBaseIndex(final byte base) { if ( base < 0 || base >= 256 ) - throw new UserException.BadInput("Non-standard bases were encountered in either the input reference or BAM file(s)"); + throw new IllegalArgumentException("Non-standard bases were encountered in either the input reference or BAM file(s)"); return baseIndexMap[base]; } @@ -425,7 +427,7 @@ public class BaseUtils { int randomBaseIndex = excludeBaseIndex; while (randomBaseIndex == excludeBaseIndex) { - randomBaseIndex = GenomeAnalysisEngine.getRandomGenerator().nextInt(4); + randomBaseIndex = randomNumberGen.nextInt(4); } return randomBaseIndex; diff --git a/public/java/src/org/broadinstitute/variant/utils/Utils.java b/public/java/src/org/broadinstitute/variant/utils/Utils.java new file mode 100644 index 000000000..1272429cb --- /dev/null +++ b/public/java/src/org/broadinstitute/variant/utils/Utils.java @@ -0,0 +1,130 @@ +package org.broadinstitute.variant.utils; + +import java.util.Collection; +import java.util.Iterator; + +public class Utils { + + /** + * The smallest log10 value we'll emit from normalizeFromLog10 and other functions + * where the real-space value is 0.0. + */ + public final static double LOG10_P_OF_ZERO = -1000000.0; + + /** + * Returns a string of the form elt1.toString() [sep elt2.toString() ... sep elt.toString()] for a collection of + * elti objects (note there's no actual space between sep and the elti elements). Returns + * "" if collection is empty. If collection contains just elt, then returns elt.toString() + * + * @param separator the string to use to separate objects + * @param objects a collection of objects. the element order is defined by the iterator over objects + * @param the type of the objects + * @return a non-null string + */ + public static String join(final String separator, final Collection objects) { + if (objects.isEmpty()) { // fast path for empty collection + return ""; + } else { + final Iterator iter = objects.iterator(); + final T first = iter.next(); + + if ( ! iter.hasNext() ) // fast path for singleton collections + return first.toString(); + else { // full path for 2+ collection that actually need a join + final StringBuilder ret = new StringBuilder(first.toString()); + while(iter.hasNext()) { + ret.append(separator); + ret.append(iter.next().toString()); + } + return ret.toString(); + } + } + } + + + /** + * normalizes the log10-based array. ASSUMES THAT ALL ARRAY ENTRIES ARE <= 0 (<= 1 IN REAL-SPACE). + * + * @param array the array to be normalized + * @return a newly allocated array corresponding the normalized values in array + */ + public static double[] normalizeFromLog10(double[] array) { + return normalizeFromLog10(array, false); + } + + /** + * normalizes the log10-based array. ASSUMES THAT ALL ARRAY ENTRIES ARE <= 0 (<= 1 IN REAL-SPACE). + * + * @param array the array to be normalized + * @param takeLog10OfOutput if true, the output will be transformed back into log10 units + * @return a newly allocated array corresponding the normalized values in array, maybe log10 transformed + */ + public static double[] normalizeFromLog10(double[] array, boolean takeLog10OfOutput) { + return normalizeFromLog10(array, takeLog10OfOutput, false); + } + + /** + * See #normalizeFromLog10 but with the additional option to use an approximation that keeps the calculation always in log-space + * + * @param array + * @param takeLog10OfOutput + * @param keepInLogSpace + * + * @return + */ + public static double[] normalizeFromLog10(double[] array, boolean takeLog10OfOutput, boolean keepInLogSpace) { + // for precision purposes, we need to add (or really subtract, since they're + // all negative) the largest value; also, we need to convert to normal-space. + double maxValue = arrayMax(array); + + // we may decide to just normalize in log space without converting to linear space + if (keepInLogSpace) { + for (int i = 0; i < array.length; i++) { + array[i] -= maxValue; + } + return array; + } + + // default case: go to linear space + double[] normalized = new double[array.length]; + + for (int i = 0; i < array.length; i++) + normalized[i] = Math.pow(10, array[i] - maxValue); + + // normalize + double sum = 0.0; + for (int i = 0; i < array.length; i++) + sum += normalized[i]; + for (int i = 0; i < array.length; i++) { + double x = normalized[i] / sum; + if (takeLog10OfOutput) { + x = Math.log10(x); + if ( x < LOG10_P_OF_ZERO || Double.isInfinite(x) ) + x = array[i] - maxValue; + } + + normalized[i] = x; + } + + return normalized; + } + + public static double arrayMax(final double[] array) { + return array[maxElementIndex(array, array.length)]; + } + + public static int maxElementIndex(final double[] array, final int endIndex) { + if (array == null || array.length == 0) + throw new IllegalArgumentException("Array cannot be null!"); + + int maxI = 0; + for (int i = 1; i < endIndex; i++) { + if (array[i] > array[maxI]) + maxI = i; + } + + return maxI; + } +} + + diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/variant/variantcontext/Allele.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java rename to public/java/src/org/broadinstitute/variant/variantcontext/Allele.java index 85c925204..b231019b8 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/Allele.java @@ -1,6 +1,6 @@ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import java.util.Arrays; import java.util.Collection; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java b/public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java rename to public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java index 127f91677..3cc54384f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java @@ -1,7 +1,7 @@ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java b/public/java/src/org/broadinstitute/variant/variantcontext/FastGenotype.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java rename to public/java/src/org/broadinstitute/variant/variantcontext/FastGenotype.java index 4a7df9da4..8d8a8bbfb 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/FastGenotype.java @@ -22,11 +22,10 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/variant/variantcontext/Genotype.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java rename to public/java/src/org/broadinstitute/variant/variantcontext/Genotype.java index 67e80cf3c..4f83fa7be 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/Genotype.java @@ -1,12 +1,11 @@ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; import com.google.java.contract.Requires; import org.broad.tribble.util.ParsingUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.vcf.VCFConstants; import java.util.*; @@ -209,7 +208,7 @@ public abstract class Genotype implements Comparable { } if ( observedAllele == null ) - throw new ReviewedStingException("BUG: there are no alleles present in this genotype but the alleles list is not null"); + throw new IllegalStateException("BUG: there are no alleles present in this genotype but the alleles list is not null"); return sawMultipleAlleles ? GenotypeType.HET : observedAllele.isReference() ? GenotypeType.HOM_REF : GenotypeType.HOM_VAR; } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeBuilder.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java rename to public/java/src/org/broadinstitute/variant/variantcontext/GenotypeBuilder.java index 8fd792d3b..b8af1a305 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeBuilder.java @@ -22,14 +22,14 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; import com.google.java.contract.Requires; import org.broad.tribble.util.ParsingUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFConstants; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java rename to public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java index 641eb5449..287105dde 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java @@ -22,15 +22,13 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.broad.tribble.TribbleException; -import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.variant.utils.Utils; +import org.broadinstitute.variant.vcf.VCFConstants; import java.util.Arrays; import java.util.EnumMap; @@ -156,7 +154,7 @@ public class GenotypeLikelihoods { //Returns null in case of missing likelihoods public EnumMap getAsMap(boolean normalizeFromLog10){ //Make sure that the log10likelihoods are set - double[] likelihoods = normalizeFromLog10 ? MathUtils.normalizeFromLog10(getAsVector()) : getAsVector(); + double[] likelihoods = normalizeFromLog10 ? Utils.normalizeFromLog10(getAsVector()) : getAsVector(); if(likelihoods == null) return null; EnumMap likelihoodsMap = new EnumMap(GenotypeType.class); @@ -216,7 +214,7 @@ public class GenotypeLikelihoods { if (qual < 0) { // QUAL can be negative if the chosen genotype is not the most likely one individually. // In this case, we compute the actual genotype probability and QUAL is the likelihood of it not being the chosen one - double[] normalized = MathUtils.normalizeFromLog10(likelihoods); + double[] normalized = Utils.normalizeFromLog10(likelihoods); double chosenGenotype = normalized[iOfChoosenGenotype]; return Math.log10(1.0 - chosenGenotype); } else { @@ -234,7 +232,7 @@ public class GenotypeLikelihoods { likelihoodsAsVector[i] = Integer.parseInt(strings[i]) / -10.0; } } catch (NumberFormatException e) { - throw new UserException.MalformedVCF("The GL/PL tag contains non-integer values: " + likelihoodsAsString_PLs); + throw new TribbleException("The GL/PL tag contains non-integer values: " + likelihoodsAsString_PLs); } return likelihoodsAsVector; } else @@ -335,7 +333,7 @@ public class GenotypeLikelihoods { // a bit of sanity checking for ( int i = 0; i < cache.length; i++ ) { if ( cache[i] == null ) - throw new ReviewedStingException("BUG: cache entry " + i + " is unexpected null"); + throw new IllegalStateException("BUG: cache entry " + i + " is unexpected null"); } return cache; @@ -422,7 +420,7 @@ public class GenotypeLikelihoods { public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) { // make sure that we've cached enough data if ( PLindex >= PLIndexToAlleleIndex.length ) - throw new ReviewedStingException("GATK limitation: cannot genotype more than " + MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles"); + throw new IllegalStateException("Internal limitation: cannot genotype more than " + MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles"); return PLIndexToAlleleIndex[PLindex]; } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeType.java b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeType.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeType.java rename to public/java/src/org/broadinstitute/variant/variantcontext/GenotypeType.java index 1e3f43065..53798015e 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeType.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeType.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; /** * Summary types for Genotype objects diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypesContext.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java rename to public/java/src/org/broadinstitute/variant/variantcontext/GenotypesContext.java index f306bac4d..d7239b2f3 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypesContext.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/LazyGenotypesContext.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java rename to public/java/src/org/broadinstitute/variant/variantcontext/LazyGenotypesContext.java index 1f73ecabd..8ecca17ca 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/LazyGenotypesContext.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java rename to public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java index 12f9cb20c..f0588f840 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java @@ -1,12 +1,10 @@ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import org.apache.log4j.Logger; import org.broad.tribble.Feature; import org.broad.tribble.TribbleException; import org.broad.tribble.util.ParsingUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.variant.vcf.*; import java.util.*; @@ -1156,7 +1154,7 @@ public class VariantContext implements Feature { // to enable tribble integratio if ( WARN_ABOUT_BAD_END ) logger.warn(message); else - throw new ReviewedStingException(message); + throw new TribbleException(message); } } else { final long length = (stop - start) + 1; @@ -1387,7 +1385,7 @@ public class VariantContext implements Feature { // to enable tribble integratio final int obsSize = decoded instanceof List ? ((List) decoded).size() : 1; final int expSize = format.getCount(this); if ( obsSize != expSize ) { - throw new UserException.MalformedVCFHeader("Discordant field size detected for field " + + throw new TribbleException.InvalidHeader("Discordant field size detected for field " + field + " at " + getChr() + ":" + getStart() + ". Field had " + obsSize + " values " + "but the header says this should have " + expSize + " values based on header record " + format); @@ -1437,17 +1435,17 @@ public class VariantContext implements Feature { // to enable tribble integratio case Flag: final boolean b = Boolean.valueOf(string) || string.equals("1"); if ( b == false ) - throw new UserException.MalformedVCF("VariantContext FLAG fields " + field + " cannot contain false values" + throw new TribbleException("VariantContext FLAG fields " + field + " cannot contain false values" + " as seen at " + getChr() + ":" + getStart()); return b; case String: return string; case Integer: return Integer.valueOf(string); case Float: return Double.valueOf(string); - default: throw new ReviewedStingException("Unexpected type for field" + field); + default: throw new TribbleException("Unexpected type for field" + field); } } } catch (NumberFormatException e) { - throw new UserException.MalformedVCF("Could not decode field " + field + " with value " + string + " of declared type " + format.getType()); + throw new TribbleException("Could not decode field " + field + " with value " + string + " of declared type " + format.getType()); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextBuilder.java similarity index 93% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java rename to public/java/src/org/broadinstitute/variant/variantcontext/VariantContextBuilder.java index 40ac089ef..bd12b8be5 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextBuilder.java @@ -22,12 +22,10 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import com.google.java.contract.*; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.vcf.VCFConstants; import java.util.*; @@ -105,7 +103,7 @@ public class VariantContextBuilder { * @param parent Cannot be null */ public VariantContextBuilder(VariantContext parent) { - if ( parent == null ) throw new ReviewedStingException("BUG: VariantContextBuilder parent argument cannot be null in VariantContextBuilder"); + if ( parent == null ) throw new IllegalArgumentException("BUG: VariantContextBuilder parent argument cannot be null in VariantContextBuilder"); this.alleles = parent.alleles; this.attributes = parent.getAttributes(); this.attributesCanBeModified = false; @@ -121,7 +119,7 @@ public class VariantContextBuilder { } public VariantContextBuilder(VariantContextBuilder parent) { - if ( parent == null ) throw new ReviewedStingException("BUG: VariantContext parent argument cannot be null in VariantContextBuilder"); + if ( parent == null ) throw new IllegalArgumentException("BUG: VariantContext parent argument cannot be null in VariantContextBuilder"); this.alleles = parent.alleles; this.attributesCanBeModified = false; this.contig = parent.contig; @@ -384,20 +382,6 @@ public class VariantContextBuilder { return this; } - /** - * Tells us that the resulting VariantContext should have the specified location - * @param loc - * @return - */ - @Requires({"loc.getContig() != null", "loc.getStart() >= 0", "loc.getStop() >= 0"}) - public VariantContextBuilder loc(final GenomeLoc loc) { - this.contig = loc.getContig(); - this.start = loc.getStart(); - this.stop = loc.getStop(); - toValidate.add(VariantContext.Validation.ALLELES); - return this; - } - /** * Tells us that the resulting VariantContext should have the specified contig chr * @param contig @@ -442,8 +426,6 @@ public class VariantContextBuilder { /** * Compute the end position for this VariantContext from the alleles themselves * - * @see VariantContextUtils.computeEndFromAlleles() - * * assigns this builder the stop position computed. * * @param alleles the list of alleles to consider. The reference allele must be the first one diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java similarity index 66% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java rename to public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java index 8b360eb5e..5d9a6d476 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java @@ -21,21 +21,18 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.commons.jexl2.Expression; import org.apache.commons.jexl2.JexlEngine; -import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; +import org.broad.tribble.TribbleException; import org.broad.tribble.util.popgen.HardyWeinbergCalculation; -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.variant.utils.BaseUtils; +import org.broadinstitute.variant.utils.Utils; +import org.broadinstitute.variant.vcf.*; import java.io.Serializable; import java.util.*; @@ -50,7 +47,6 @@ public class VariantContextUtils { private static Set MISSING_KEYS_WARNED_ABOUT = new HashSet(); final public static JexlEngine engine = new JexlEngine(); - public static final int DEFAULT_PLOIDY = 2; private final static boolean ASSUME_MISSING_FIELDS_ARE_STRINGS = false; static { @@ -173,7 +169,7 @@ public class VariantContextUtils { return new VCFInfoHeaderLine(field, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Auto-generated string header for " + field); } else - throw new UserException.MalformedVCF("Fully decoding VariantContext requires header line for all fields, but none was found for " + field); + throw new TribbleException("Fully decoding VariantContext requires header line for all fields, but none was found for " + field); } return metaData; } @@ -208,10 +204,10 @@ public class VariantContextUtils { */ public static List initializeMatchExps(String[] names, String[] exps) { if ( names == null || exps == null ) - throw new ReviewedStingException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) ); + throw new IllegalArgumentException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) ); if ( names.length != exps.length ) - throw new UserException("Inconsistent number of provided filter names and expressions: names=" + Arrays.toString(names) + " exps=" + Arrays.toString(exps)); + throw new IllegalArgumentException("Inconsistent number of provided filter names and expressions: names=" + Arrays.toString(names) + " exps=" + Arrays.toString(exps)); Map map = new HashMap(); for ( int i = 0; i < names.length; i++ ) { map.put(names[i], exps[i]); } @@ -247,7 +243,7 @@ public class VariantContextUtils { Expression exp = engine.createExpression(expStr); exps.add(new JexlVCMatchExp(name, exp)); } catch (Exception e) { - throw new UserException.BadArgumentValue(name, "Invalid expression used (" + expStr + "). Please see the JEXL docs for correct syntax.") ; + throw new IllegalArgumentException("Argument " + name + "has a bad value. Invalid expression used (" + expStr + "). Please see the JEXL docs for correct syntax.") ; } } @@ -409,7 +405,6 @@ public class VariantContextUtils { KEEP_UNCONDITIONAL } - @Hidden public enum MultipleAllelesMergeType { /** * Combine only alleles of the same type (SNP, indel, etc.) into a single VCF record. @@ -426,7 +421,6 @@ public class VariantContextUtils { * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with * the sample name * - * @param genomeLocParser loc parser * @param unsortedVCs collection of unsorted VCs * @param priorityListOfVCs priority list detailing the order in which we should grab the VCs * @param filteredRecordMergeType merge type for filtered records @@ -438,8 +432,7 @@ public class VariantContextUtils { * @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count? * @return new VariantContext representing the merge of unsortedVCs */ - public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, - final Collection unsortedVCs, + public static VariantContext simpleMerge(final Collection unsortedVCs, final List priorityListOfVCs, final FilteredRecordMergeType filteredRecordMergeType, final GenotypeMergeType genotypeMergeOptions, @@ -449,7 +442,7 @@ public class VariantContextUtils { final boolean filteredAreUncalled, final boolean mergeInfoWithMaxAC ) { int originalNumOfVCs = priorityListOfVCs == null ? 0 : priorityListOfVCs.size(); - return simpleMerge(genomeLocParser,unsortedVCs,priorityListOfVCs,originalNumOfVCs,filteredRecordMergeType,genotypeMergeOptions,annotateOrigin,printMessages,setKey,filteredAreUncalled,mergeInfoWithMaxAC); + return simpleMerge(unsortedVCs,priorityListOfVCs,originalNumOfVCs,filteredRecordMergeType,genotypeMergeOptions,annotateOrigin,printMessages,setKey,filteredAreUncalled,mergeInfoWithMaxAC); } /** @@ -457,7 +450,6 @@ public class VariantContextUtils { * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with * the sample name * - * @param genomeLocParser loc parser * @param unsortedVCs collection of unsorted VCs * @param priorityListOfVCs priority list detailing the order in which we should grab the VCs * @param filteredRecordMergeType merge type for filtered records @@ -469,8 +461,7 @@ public class VariantContextUtils { * @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count? * @return new VariantContext representing the merge of unsortedVCs */ - public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, - final Collection unsortedVCs, + public static VariantContext simpleMerge(final Collection unsortedVCs, final List priorityListOfVCs, final int originalNumOfVCs, final FilteredRecordMergeType filteredRecordMergeType, @@ -517,7 +508,7 @@ public class VariantContextUtils { final Set variantSources = new HashSet(); // contains the set of sources we found in our set of VCs that are variant final Set rsIDs = new LinkedHashSet(1); // most of the time there's one id - GenomeLoc loc = getLocation(genomeLocParser,first); + VariantContext longestVC = first; int depth = 0; int maxAC = -1; final Map attributesWithMaxAC = new LinkedHashMap(); @@ -533,11 +524,11 @@ public class VariantContextUtils { // cycle through and add info from the other VCs, making sure the loc/reference matches for ( final VariantContext vc : VCs ) { - if ( loc.getStart() != vc.getStart() ) - throw new ReviewedStingException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString()); + if ( longestVC.getStart() != vc.getStart() ) + throw new IllegalStateException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString()); - if ( getLocation(genomeLocParser,vc).size() > loc.size() ) - loc = getLocation(genomeLocParser,vc); // get the longest location + if ( getSize(vc) > getSize(longestVC) ) + longestVC = vc; // get the longest location nFiltered += vc.isFiltered() ? 1 : 0; if ( vc.isVariant() ) variantSources.add(vc.getSource()); @@ -612,8 +603,8 @@ public class VariantContextUtils { continue; if ( hasPLIncompatibleAlleles(alleles, vc.alleles)) { if ( ! genotypes.isEmpty() ) - logger.debug(String.format("Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s", - genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles)); + logger.debug(String.format("Stripping PLs at %s:%d-%d due to incompatible alleles merged=%s vs. single=%s", + vc.getChr(), vc.getStart(), vc.getEnd(), alleles, vc.alleles)); genotypes = stripPLsAndAD(genotypes); // this will remove stale AC,AF attributed from vc calculateChromosomeCounts(vc, attributes, true); @@ -661,7 +652,7 @@ public class VariantContextUtils { final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs); final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID); - builder.loc(loc.getContig(), loc.getStart(), loc.getStop()); + builder.loc(longestVC.getChr(), longestVC.getStart(), longestVC.getEnd()); builder.alleles(alleles); builder.genotypes(genotypes); builder.log10PError(log10PError); @@ -788,7 +779,7 @@ public class VariantContextUtils { for ( String name : vc.getSampleNames() ) { //System.out.printf("Checking %s %b%n", name, names.contains(name)); if ( names.contains(name) ) - throw new UserException("REQUIRE_UNIQUE sample names is true but duplicate names were discovered " + name); + throw new IllegalStateException("REQUIRE_UNIQUE sample names is true but duplicate names were discovered " + name); } names.addAll(vc.getSampleNames()); @@ -804,7 +795,7 @@ public class VariantContextUtils { if ( ref == null || ref.length() < myRef.length() ) ref = myRef; else if ( ref.length() == myRef.length() && ! ref.equals(myRef) ) - throw new UserException.BadInput(String.format("The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s", vc.getChr(), vc.getStart(), ref, myRef)); + throw new TribbleException(String.format("The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s", vc.getChr(), vc.getStart(), ref, myRef)); } return ref; @@ -826,7 +817,7 @@ public class VariantContextUtils { // Allele myRef = vc.getReference(); - if ( refAllele.length() <= myRef.length() ) throw new ReviewedStingException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele); + if ( refAllele.length() <= myRef.length() ) throw new IllegalStateException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele); byte[] extraBases = Arrays.copyOfRange(refAllele.getBases(), myRef.length(), refAllele.length()); // System.out.printf("Remapping allele at %s%n", vc); @@ -863,7 +854,7 @@ public class VariantContextUtils { private int getIndex(VariantContext vc) { int i = priorityListOfVCs.indexOf(vc.getSource()); - if ( i == -1 ) throw new UserException.BadArgumentValue(Utils.join(",", priorityListOfVCs), "Priority list " + priorityListOfVCs + " doesn't contain variant context " + vc.getSource()); + if ( i == -1 ) throw new IllegalArgumentException("Priority list " + priorityListOfVCs + " doesn't contain variant context " + vc.getSource()); return i; } @@ -985,14 +976,8 @@ public class VariantContextUtils { return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSVERSION; } - /** - * create a genome location, given a variant context - * @param genomeLocParser parser - * @param vc the variant context - * @return the genomeLoc - */ - public static final GenomeLoc getLocation(GenomeLocParser genomeLocParser,VariantContext vc) { - return genomeLocParser.createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd(), true); + public static int getSize( VariantContext vc ) { + return vc.getEnd() - vc.getStart() + 1; } public static final Set genotypeNames(final Collection genotypes) { @@ -1002,354 +987,6 @@ public class VariantContextUtils { return names; } - /** - * Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs - * - * @param vc variant context with genotype likelihoods - * @return genotypes context - */ - public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) { - return subsetDiploidAlleles(vc, vc.getAlleles(), true); - } - - private static final List NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL); - public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call. - - /** - * Split variant context into its biallelic components if there are more than 2 alleles - * - * For VC has A/B/C alleles, returns A/B and A/C contexts. - * Genotypes are all no-calls now (it's not possible to fix them easily) - * Alleles are right trimmed to satisfy VCF conventions - * - * If vc is biallelic or non-variant it is just returned - * - * Chromosome counts are updated (but they are by definition 0) - * - * @param vc a potentially multi-allelic variant context - * @return a list of bi-allelic (or monomorphic) variant context - */ - public static List splitVariantContextToBiallelics(final VariantContext vc) { - if ( ! vc.isVariant() || vc.isBiallelic() ) - // non variant or biallelics already satisfy the contract - return Collections.singletonList(vc); - else { - final List biallelics = new LinkedList(); - - for ( final Allele alt : vc.getAlternateAlleles() ) { - VariantContextBuilder builder = new VariantContextBuilder(vc); - final List alleles = Arrays.asList(vc.getReference(), alt); - builder.alleles(alleles); - builder.genotypes(VariantContextUtils.subsetDiploidAlleles(vc, alleles, false)); - calculateChromosomeCounts(builder, true); - biallelics.add(reverseTrimAlleles(builder.make())); - } - - return biallelics; - } - } - - /** - * subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately) - * - * @param vc variant context with genotype likelihoods - * @param allelesToUse which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC *** - * @param assignGenotypes true if we should update the genotypes based on the (subsetted) PLs - * @return genotypes - */ - public static GenotypesContext subsetDiploidAlleles(final VariantContext vc, - final List allelesToUse, - final boolean assignGenotypes) { - - // the genotypes with PLs - final GenotypesContext oldGTs = vc.getGenotypes(); - - // samples - final List sampleIndices = oldGTs.getSampleNamesOrderedByName(); - - // the new genotypes to create - final GenotypesContext newGTs = GenotypesContext.create(); - - // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward - final int numOriginalAltAlleles = vc.getAlternateAlleles().size(); - final int numNewAltAlleles = allelesToUse.size() - 1; - - // which PLs should be carried forward? - ArrayList likelihoodIndexesToUse = null; - - // an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles, - // then we can keep the PLs as is; otherwise, we determine which ones to keep - if ( numNewAltAlleles != numOriginalAltAlleles && numNewAltAlleles > 0 ) { - likelihoodIndexesToUse = new ArrayList(30); - - final boolean[] altAlleleIndexToUse = new boolean[numOriginalAltAlleles]; - for ( int i = 0; i < numOriginalAltAlleles; i++ ) { - if ( allelesToUse.contains(vc.getAlternateAllele(i)) ) - altAlleleIndexToUse[i] = true; - } - - // numLikelihoods takes total # of alleles. Use default # of chromosomes (ploidy) = 2 - final int numLikelihoods = GenotypeLikelihoods.numLikelihoods(1 + numOriginalAltAlleles, DEFAULT_PLOIDY); - for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) { - final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex); - // consider this entry only if both of the alleles are good - if ( (alleles.alleleIndex1 == 0 || altAlleleIndexToUse[alleles.alleleIndex1 - 1]) && (alleles.alleleIndex2 == 0 || altAlleleIndexToUse[alleles.alleleIndex2 - 1]) ) - likelihoodIndexesToUse.add(PLindex); - } - } - - // create the new genotypes - for ( int k = 0; k < oldGTs.size(); k++ ) { - final Genotype g = oldGTs.get(sampleIndices.get(k)); - if ( !g.hasLikelihoods() ) { - newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES)); - continue; - } - - // create the new likelihoods array from the alleles we are allowed to use - final double[] originalLikelihoods = g.getLikelihoods().getAsVector(); - double[] newLikelihoods; - if ( likelihoodIndexesToUse == null ) { - newLikelihoods = originalLikelihoods; - } else { - newLikelihoods = new double[likelihoodIndexesToUse.size()]; - int newIndex = 0; - for ( int oldIndex : likelihoodIndexesToUse ) - newLikelihoods[newIndex++] = originalLikelihoods[oldIndex]; - - // might need to re-normalize - newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true); - } - - // if there is no mass on the (new) likelihoods, then just no-call the sample - if ( MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) { - newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES)); - } - else { - final GenotypeBuilder gb = new GenotypeBuilder(g); - - if ( numNewAltAlleles == 0 ) - gb.noPL(); - else - gb.PL(newLikelihoods); - - // if we weren't asked to assign a genotype, then just no-call the sample - if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) { - gb.alleles(NO_CALL_ALLELES); - } - else { - // find the genotype with maximum likelihoods - int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods); - GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex); - - gb.alleles(Arrays.asList(allelesToUse.get(alleles.alleleIndex1), allelesToUse.get(alleles.alleleIndex2))); - if ( numNewAltAlleles != 0 ) gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods)); - } - newGTs.add(gb.make()); - } - } - - return newGTs; - } - - /** - * Returns true iff VC is an non-complex indel where every allele represents an expansion or - * contraction of a series of identical bases in the reference. - * - * For example, suppose the ref bases are CTCTCTGA, which includes a 3x repeat of CTCTCT - * - * If VC = -/CT, then this function returns true because the CT insertion matches exactly the - * upcoming reference. - * If VC = -/CTA then this function returns false because the CTA isn't a perfect match - * - * Now consider deletions: - * - * If VC = CT/- then again the same logic applies and this returns true - * The case of CTA/- makes no sense because it doesn't actually match the reference bases. - * - * The logic of this function is pretty simple. Take all of the non-null alleles in VC. For - * each insertion allele of n bases, check if that allele matches the next n reference bases. - * For each deletion allele of n bases, check if this matches the reference bases at n - 2 n, - * as it must necessarily match the first n bases. If this test returns true for all - * alleles you are a tandem repeat, otherwise you are not. - * - * @param vc - * @param refBasesStartingAtVCWithPad not this is assumed to include the PADDED reference - * @return - */ - @Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"}) - public static boolean isTandemRepeat(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) { - final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1); - if ( ! vc.isIndel() ) // only indels are tandem repeats - return false; - - final Allele ref = vc.getReference(); - - for ( final Allele allele : vc.getAlternateAlleles() ) { - if ( ! isRepeatAllele(ref, allele, refBasesStartingAtVCWithoutPad) ) - return false; - } - - // we've passed all of the tests, so we are a repeat - return true; - } - - /** - * - * @param vc - * @param refBasesStartingAtVCWithPad - * @return - */ - @Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"}) - public static Pair,byte[]> getNumTandemRepeatUnits(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) { - final boolean VERBOSE = false; - final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1); - if ( ! vc.isIndel() ) // only indels are tandem repeats - return null; - - final Allele refAllele = vc.getReference(); - final byte[] refAlleleBases = Arrays.copyOfRange(refAllele.getBases(), 1, refAllele.length()); - - byte[] repeatUnit = null; - final ArrayList lengths = new ArrayList(); - - for ( final Allele allele : vc.getAlternateAlleles() ) { - Pair result = getNumTandemRepeatUnits(refAlleleBases, Arrays.copyOfRange(allele.getBases(), 1, allele.length()), refBasesStartingAtVCWithoutPad.getBytes()); - - final int[] repetitionCount = result.first; - // repetition count = 0 means allele is not a tandem expansion of context - if (repetitionCount[0] == 0 || repetitionCount[1] == 0) - return null; - - if (lengths.size() == 0) { - lengths.add(repetitionCount[0]); // add ref allele length only once - } - lengths.add(repetitionCount[1]); // add this alt allele's length - - repeatUnit = result.second; - if (VERBOSE) { - System.out.println("RefContext:"+refBasesStartingAtVCWithoutPad); - System.out.println("Ref:"+refAllele.toString()+" Count:" + String.valueOf(repetitionCount[0])); - System.out.println("Allele:"+allele.toString()+" Count:" + String.valueOf(repetitionCount[1])); - System.out.println("RU:"+new String(repeatUnit)); - } - } - - return new Pair, byte[]>(lengths,repeatUnit); - } - - protected static Pair getNumTandemRepeatUnits(final byte[] refBases, final byte[] altBases, final byte[] remainingRefContext) { - /* we can't exactly apply same logic as in basesAreRepeated() to compute tandem unit and number of repeated units. - Consider case where ref =ATATAT and we have an insertion of ATAT. Natural description is (AT)3 -> (AT)5. - */ - - byte[] longB; - // find first repeat unit based on either ref or alt, whichever is longer - if (altBases.length > refBases.length) - longB = altBases; - else - longB = refBases; - - // see if non-null allele (either ref or alt, whichever is longer) can be decomposed into several identical tandem units - // for example, -*,CACA needs to first be decomposed into (CA)2 - final int repeatUnitLength = findRepeatedSubstring(longB); - final byte[] repeatUnit = Arrays.copyOf(longB, repeatUnitLength); - - final int[] repetitionCount = new int[2]; -// repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext)); -// repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext)); - int repetitionsInRef = findNumberofRepetitions(repeatUnit,refBases); - repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext))-repetitionsInRef; - repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext))-repetitionsInRef; - - return new Pair(repetitionCount, repeatUnit); - - } - - /** - * Find out if a string can be represented as a tandem number of substrings. - * For example ACTACT is a 2-tandem of ACT, - * but ACTACA is not. - * - * @param bases String to be tested - * @return Length of repeat unit, if string can be represented as tandem of substring (if it can't - * be represented as one, it will be just the length of the input string) - */ - protected static int findRepeatedSubstring(byte[] bases) { - - int repLength; - for (repLength=1; repLength <=bases.length; repLength++) { - final byte[] candidateRepeatUnit = Arrays.copyOf(bases,repLength); - boolean allBasesMatch = true; - for (int start = repLength; start < bases.length; start += repLength ) { - // check that remaining of string is exactly equal to repeat unit - final byte[] basePiece = Arrays.copyOfRange(bases,start,start+candidateRepeatUnit.length); - if (!Arrays.equals(candidateRepeatUnit, basePiece)) { - allBasesMatch = false; - break; - } - } - if (allBasesMatch) - return repLength; - } - - return repLength; - } - - /** - * Helper routine that finds number of repetitions a string consists of. - * For example, for string ATAT and repeat unit AT, number of repetitions = 2 - * @param repeatUnit Substring - * @param testString String to test - * @return Number of repetitions (0 if testString is not a concatenation of n repeatUnit's - */ - public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) { - int numRepeats = 0; - for (int start = 0; start < testString.length; start += repeatUnit.length) { - int end = start + repeatUnit.length; - byte[] unit = Arrays.copyOfRange(testString,start, end); - if(Arrays.equals(unit,repeatUnit)) - numRepeats++; - else - return numRepeats; - } - return numRepeats; - } - - /** - * Helper function for isTandemRepeat that checks that allele matches somewhere on the reference - * @param ref - * @param alt - * @param refBasesStartingAtVCWithoutPad - * @return - */ - protected static boolean isRepeatAllele(final Allele ref, final Allele alt, final String refBasesStartingAtVCWithoutPad) { - if ( ! Allele.oneIsPrefixOfOther(ref, alt) ) - return false; // we require one allele be a prefix of another - - if ( ref.length() > alt.length() ) { // we are a deletion - return basesAreRepeated(ref.getBaseString(), alt.getBaseString(), refBasesStartingAtVCWithoutPad, 2); - } else { // we are an insertion - return basesAreRepeated(alt.getBaseString(), ref.getBaseString(), refBasesStartingAtVCWithoutPad, 1); - } - } - - protected static boolean basesAreRepeated(final String l, final String s, final String ref, final int minNumberOfMatches) { - final String potentialRepeat = l.substring(s.length()); // skip s bases - - for ( int i = 0; i < minNumberOfMatches; i++) { - final int start = i * potentialRepeat.length(); - final int end = (i+1) * potentialRepeat.length(); - if ( ref.length() < end ) - return false; // we ran out of bases to test - final String refSub = ref.substring(start, end); - if ( ! refSub.equals(potentialRepeat) ) - return false; // repeat didn't match, fail - } - - return true; // we passed all tests, we matched - } - /** * Compute the end position for this VariantContext from the alleles themselves * @@ -1368,11 +1005,11 @@ public class VariantContextUtils { final Allele ref = alleles.get(0); if ( ref.isNonReference() ) - throw new ReviewedStingException("computeEndFromAlleles requires first allele to be reference"); + throw new IllegalStateException("computeEndFromAlleles requires first allele to be reference"); if ( VariantContext.hasSymbolicAlleles(alleles) ) { if ( endForSymbolicAlleles == -1 ) - throw new ReviewedStingException("computeEndFromAlleles found a symbolic allele but endForSymbolicAlleles was provided"); + throw new IllegalStateException("computeEndFromAlleles found a symbolic allele but endForSymbolicAlleles was provided"); return endForSymbolicAlleles; } else { return start + Math.max(ref.length() - 1, 0); @@ -1408,80 +1045,4 @@ public class VariantContextUtils { } } - public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) { - - // see whether we need to trim common reference base from all alleles - final int trimExtent = computeReverseClipping(inputVC.getAlleles(), inputVC.getReference().getDisplayString().getBytes(), 0, false); - if ( trimExtent <= 0 || inputVC.getAlleles().size() <= 1 ) - return inputVC; - - final List alleles = new ArrayList(); - final GenotypesContext genotypes = GenotypesContext.create(); - final Map originalToTrimmedAlleleMap = new HashMap(); - - for (final Allele a : inputVC.getAlleles()) { - if (a.isSymbolic()) { - alleles.add(a); - originalToTrimmedAlleleMap.put(a, a); - } else { - // get bases for current allele and create a new one with trimmed bases - final byte[] newBases = Arrays.copyOfRange(a.getBases(), 0, a.length()-trimExtent); - final Allele trimmedAllele = Allele.create(newBases, a.isReference()); - alleles.add(trimmedAllele); - originalToTrimmedAlleleMap.put(a, trimmedAllele); - } - } - - // now we can recreate new genotypes with trimmed alleles - for ( final Genotype genotype : inputVC.getGenotypes() ) { - final List originalAlleles = genotype.getAlleles(); - final List trimmedAlleles = new ArrayList(); - for ( final Allele a : originalAlleles ) { - if ( a.isCalled() ) - trimmedAlleles.add(originalToTrimmedAlleleMap.get(a)); - else - trimmedAlleles.add(Allele.NO_CALL); - } - genotypes.add(new GenotypeBuilder(genotype).alleles(trimmedAlleles).make()); - } - - return new VariantContextBuilder(inputVC).stop(inputVC.getStart() + alleles.get(0).length() - 1).alleles(alleles).genotypes(genotypes).make(); - } - - public static int computeReverseClipping(final List unclippedAlleles, - final byte[] ref, - final int forwardClipping, - final boolean allowFullClip) { - int clipping = 0; - boolean stillClipping = true; - - while ( stillClipping ) { - for ( final Allele a : unclippedAlleles ) { - if ( a.isSymbolic() ) - continue; - - // we need to ensure that we don't reverse clip out all of the bases from an allele because we then will have the wrong - // position set for the VariantContext (although it's okay to forward clip it all out, because the position will be fine). - if ( a.length() - clipping == 0 ) - return clipping - (allowFullClip ? 0 : 1); - - if ( a.length() - clipping <= forwardClipping || a.length() - forwardClipping == 0 ) { - stillClipping = false; - } - else if ( ref.length == clipping ) { - if ( allowFullClip ) - stillClipping = false; - else - return -1; - } - else if ( a.getBases()[a.length()-clipping-1] != ref[ref.length-clipping-1] ) { - stillClipping = false; - } - } - if ( stillClipping ) - clipping++; - } - - return clipping; - } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java rename to public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java index abe85e383..96643b9e9 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java @@ -21,13 +21,12 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import org.apache.commons.jexl2.JexlContext; import org.apache.commons.jexl2.MapContext; -import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.variant.utils.Utils; +import org.broadinstitute.variant.vcf.VCFConstants; import java.util.Collection; import java.util.HashMap; @@ -275,7 +274,7 @@ class JEXLMap implements Map { if (e.getMessage().contains("undefined variable")) jexl.put(exp,false); else - throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage())); + throw new IllegalArgumentException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage())); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Encoder.java similarity index 93% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Encoder.java index 22acc4787..f71f4e577 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Encoder.java @@ -22,13 +22,12 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.bcf2.BCF2Type; +import org.broadinstitute.variant.bcf2.BCF2Utils; import java.io.ByteArrayOutputStream; import java.io.IOException; @@ -80,7 +79,7 @@ public final class BCF2Encoder { case INT32: encodeTypedInt((Integer)value, type); break; case FLOAT: encodeTypedFloat((Double) value); break; case CHAR: encodeTypedString((String) value); break; - default: throw new ReviewedStingException("Illegal type encountered " + type); + default: throw new IllegalArgumentException("Illegal type encountered " + type); } } } @@ -155,7 +154,7 @@ public final class BCF2Encoder { case INT32: encodeRawBytes((Integer) value, type); break; case FLOAT: encodeRawFloat((Double) value); break; case CHAR: encodeRawChar((Byte) value); break; - default: throw new ReviewedStingException("Illegal type encountered " + type); + default: throw new IllegalArgumentException("Illegal type encountered " + type); } } } catch ( ClassCastException e ) { @@ -238,7 +237,7 @@ public final class BCF2Encoder { */ @Requires("o != null") public final BCF2Type encode(final Object o) throws IOException { - if ( o == null ) throw new ReviewedStingException("Generic encode cannot deal with null values"); + if ( o == null ) throw new IllegalArgumentException("Generic encode cannot deal with null values"); if ( o instanceof List ) { final BCF2Type type = determineBCFType(((List) o).get(0)); @@ -262,7 +261,7 @@ public final class BCF2Encoder { else if ( toType instanceof Double ) return BCF2Type.FLOAT; else - throw new ReviewedStingException("No native encoding for Object of type " + arg.getClass().getSimpleName()); + throw new IllegalArgumentException("No native encoding for Object of type " + arg.getClass().getSimpleName()); } private final List stringToBytes(final String v) throws IOException { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldEncoder.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldEncoder.java index a91eb216d..5f3e66c2a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldEncoder.java @@ -22,17 +22,16 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.bcf2.BCF2Type; +import org.broadinstitute.variant.bcf2.BCF2Utils; +import org.broadinstitute.variant.vcf.VCFCompoundHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderLineCount; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.IOException; import java.util.Collections; @@ -85,7 +84,7 @@ public abstract class BCF2FieldEncoder { this.staticType = staticType; final Integer offset = dict.get(getField()); - if ( offset == null ) throw new ReviewedStingException("Format error: could not find string " + getField() + " in header as required by BCF"); + if ( offset == null ) throw new IllegalStateException("Format error: could not find string " + getField() + " in header as required by BCF"); this.dictionaryOffset = offset; dictionaryOffsetType = BCF2Utils.determineIntegerType(offset); } @@ -260,7 +259,7 @@ public abstract class BCF2FieldEncoder { @Requires("isDynamicallyTyped()") @Ensures("result != null") public BCF2Type getDynamicType(final Object value) { - throw new ReviewedStingException("BUG: cannot get dynamic type for statically typed BCF2 field " + getField()); + throw new IllegalStateException("BUG: cannot get dynamic type for statically typed BCF2 field " + getField()); } // ---------------------------------------------------------------------- @@ -351,7 +350,7 @@ public abstract class BCF2FieldEncoder { public Flag(final VCFCompoundHeaderLine headerLine, final Map dict ) { super(headerLine, dict, BCF2Type.INT8); if ( ! headerLine.isFixedCount() || headerLine.getCount() != 0 ) - throw new ReviewedStingException("Flag encoder only suppports atomic flags for field " + getField()); + throw new IllegalStateException("Flag encoder only supports atomic flags for field " + getField()); } @Override diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriter.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriter.java index 61c0129bb..c75242e8b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriter.java @@ -22,17 +22,16 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.bcf2.BCF2Type; +import org.broadinstitute.variant.bcf2.BCF2Utils; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.Genotype; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.IOException; import java.util.ArrayList; @@ -208,7 +207,7 @@ public abstract class BCF2FieldWriter { this.ige = ige; if ( ! (fieldEncoder instanceof BCF2FieldEncoder.IntArray) ) - throw new ReviewedStingException("BUG: IntGenotypesWriter requires IntArray encoder for field " + getField()); + throw new IllegalArgumentException("BUG: IntGenotypesWriter requires IntArray encoder for field " + getField()); } @Override @@ -266,7 +265,7 @@ public abstract class BCF2FieldWriter { @Override public void start(final BCF2Encoder encoder, final VariantContext vc) throws IOException { if ( vc.getNAlleles() > BCF2Utils.MAX_ALLELES_IN_GENOTYPES ) - throw new ReviewedStingException("Current BCF2 encoder cannot handle sites " + + throw new IllegalStateException("Current BCF2 encoder cannot handle sites " + "with > " + BCF2Utils.MAX_ALLELES_IN_GENOTYPES + " alleles, but you have " + vc.getNAlleles() + " at " + vc.getChr() + ":" + vc.getStart()); @@ -312,7 +311,7 @@ public abstract class BCF2FieldWriter { else if ( a == Allele.NO_CALL ) return -1; else { final Integer o = alleleMapForTriPlus.get(a); - if ( o == null ) throw new ReviewedStingException("BUG: Couldn't find allele offset for allele " + a); + if ( o == null ) throw new IllegalStateException("BUG: Couldn't find allele offset for allele " + a); return o; } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java index 9c63a69e7..e8d58f2f2 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java @@ -22,13 +22,12 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.vcf.*; import java.util.HashMap; import java.util.Map; @@ -74,7 +73,7 @@ public class BCF2FieldWriterManager { @Ensures("map.containsKey(field)") private final void add(final Map map, final String field, final T writer) { if ( map.containsKey(field) ) - throw new ReviewedStingException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders"); + throw new IllegalStateException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders"); map.put(field, writer); } @@ -118,7 +117,7 @@ public class BCF2FieldWriterManager { else return new BCF2FieldEncoder.GenericInts(line, dict); default: - throw new ReviewedStingException("Unexpected type for field " + line.getID()); + throw new IllegalArgumentException("Unexpected type for field " + line.getID()); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java similarity index 91% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java index 536f07f90..3e37ade25 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java @@ -22,23 +22,21 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils; -import org.broadinstitute.sting.utils.codecs.bcf2.BCFVersion; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.codecs.vcf.VCFContigHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.bcf2.BCF2Codec; +import org.broadinstitute.variant.bcf2.BCF2Type; +import org.broadinstitute.variant.bcf2.BCF2Utils; +import org.broadinstitute.variant.bcf2.BCFVersion; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.vcf.VCFContigHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.variantcontext.*; +import org.broadinstitute.variant.vcf.VCFUtils; import java.io.*; import java.util.*; @@ -133,7 +131,7 @@ class BCF2Writer extends IndexingVariantContextWriter { logger.warn("No contig dictionary found in header, falling back to reference sequence dictionary"); createContigDictionary(VCFUtils.makeContigHeaderLines(getRefDict(), null)); } else { - throw new UserException.MalformedBCF2("Cannot write BCF2 file with missing contig lines"); + throw new IllegalStateException("Cannot write BCF2 file with missing contig lines"); } } else { createContigDictionary(header.getContigLines()); @@ -163,7 +161,7 @@ class BCF2Writer extends IndexingVariantContextWriter { BCF2Type.INT32.write(headerBytes.length, outputStream); outputStream.write(headerBytes); } catch (IOException e) { - throw new UserException.CouldNotCreateOutputFile("BCF2 stream", "Got IOException while trying to write BCF2 header", e); + throw new RuntimeException("BCF2 stream: Got IOException while trying to write BCF2 header", e); } } @@ -183,7 +181,7 @@ class BCF2Writer extends IndexingVariantContextWriter { writeBlock(infoBlock, genotypesBlock); } catch ( IOException e ) { - throw new UserException("Error writing record to BCF2 file: " + vc.toString(), e); + throw new RuntimeException("Error writing record to BCF2 file: " + vc.toString(), e); } } @@ -194,7 +192,7 @@ class BCF2Writer extends IndexingVariantContextWriter { outputStream.close(); } catch ( IOException e ) { - throw new UserException("Failed to close BCF2 file"); + throw new RuntimeException("Failed to close BCF2 file"); } super.close(); } @@ -214,7 +212,7 @@ class BCF2Writer extends IndexingVariantContextWriter { private byte[] buildSitesData( VariantContext vc ) throws IOException { final int contigIndex = contigDictionary.get(vc.getChr()); if ( contigIndex == -1 ) - throw new UserException(String.format("Contig %s not found in sequence dictionary from reference", vc.getChr())); + throw new IllegalStateException(String.format("Contig %s not found in sequence dictionary from reference", vc.getChr())); // note use of encodeRawValue to not insert the typing byte encoder.encodeRawValue(contigIndex, BCF2Type.INT32); @@ -309,7 +307,7 @@ class BCF2Writer extends IndexingVariantContextWriter { for ( Allele allele : vc.getAlleles() ) { final byte[] s = allele.getDisplayBases(); if ( s == null ) - throw new ReviewedStingException("BUG: BCF2Writer encountered null padded allele" + allele); + throw new IllegalStateException("BUG: BCF2Writer encountered null padded allele" + allele); encoder.encodeTypedString(s); } } @@ -370,7 +368,7 @@ class BCF2Writer extends IndexingVariantContextWriter { * @param fieldType */ private final void errorUnexpectedFieldToWrite(final VariantContext vc, final String field, final String fieldType) { - throw new UserException("Found field " + field + " in the " + fieldType + " fields of VariantContext at " + + throw new IllegalStateException("Found field " + field + " in the " + fieldType + " fields of VariantContext at " + vc.getChr() + ":" + vc.getStart() + " from " + vc.getSource() + " but this hasn't been defined in the VCFHeader"); } @@ -403,7 +401,7 @@ class BCF2Writer extends IndexingVariantContextWriter { // iterate over strings until we find one that needs 16 bits, and break for ( final String string : strings ) { final Integer got = stringDictionaryMap.get(string); - if ( got == null ) throw new ReviewedStingException("Format error: could not find string " + string + " in header as required by BCF"); + if ( got == null ) throw new IllegalStateException("Format error: could not find string " + string + " in header as required by BCF"); final int offset = got; offsets.add(offset); } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java similarity index 85% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java index 298f12da3..6311d9e9a 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java @@ -22,21 +22,19 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import net.sf.samtools.SAMSequenceDictionary; +import net.sf.samtools.SAMSequenceRecord; import org.broad.tribble.Tribble; import org.broad.tribble.index.DynamicIndexCreator; import org.broad.tribble.index.Index; import org.broad.tribble.index.IndexFactory; import org.broad.tribble.util.LittleEndianOutputStream; -import org.broadinstitute.sting.gatk.refdata.tracks.IndexDictionaryUtils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.*; @@ -97,7 +95,7 @@ abstract class IndexingVariantContextWriter implements VariantContextWriter { // try to close the index stream (keep it separate to help debugging efforts) if ( indexer != null ) { Index index = indexer.finalizeIndex(positionalOutputStream.getPosition()); - IndexDictionaryUtils.setIndexSequenceDictionary(index, refDict); + setIndexSequenceDictionary(index, refDict); index.write(idxStream); idxStream.close(); } @@ -105,7 +103,7 @@ abstract class IndexingVariantContextWriter implements VariantContextWriter { // close the underlying output stream as well outputStream.close(); } catch (IOException e) { - throw new ReviewedStingException("Unable to close index for " + getStreamName(), e); + throw new RuntimeException("Unable to close index for " + getStreamName(), e); } } @@ -137,6 +135,17 @@ abstract class IndexingVariantContextWriter implements VariantContextWriter { protected static final String writerName(final File location, final OutputStream stream) { return location == null ? stream.toString() : location.getAbsolutePath(); } + + // a constant we use for marking sequence dictionary entries in the Tribble index property list + private static final String SequenceDictionaryPropertyPredicate = "DICT:"; + + private static void setIndexSequenceDictionary(Index index, SAMSequenceDictionary dict) { + for ( SAMSequenceRecord seq : dict.getSequences() ) { + final String contig = SequenceDictionaryPropertyPredicate + seq.getSequenceName(); + final String length = String.valueOf(seq.getSequenceLength()); + index.addProperty(contig,length); + } + } } final class PositionalOutputStream extends OutputStream { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IntGenotypeFieldAccessors.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IntGenotypeFieldAccessors.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java index fc117e5e1..e1d07d6f7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IntGenotypeFieldAccessors.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java @@ -22,10 +22,10 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.variantcontext.Genotype; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.variantcontext.Genotype; import java.util.HashMap; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/Options.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/Options.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/Options.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/Options.java index 3a5cb23b0..7aa7fb123 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/Options.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/Options.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; /** * Available writer options for VariantContextWriters diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriter.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriter.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriter.java index b51892b31..4de130514 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriter.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriter.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; /** * this class writes VCF files, allowing records to be passed in unsorted (up to a certain genomic distance away) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriterBase.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriterBase.java index 1f3cdd0fe..413afa0fd 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriterBase.java @@ -23,10 +23,10 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.*; import java.util.concurrent.PriorityBlockingQueue; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java index 4c35d6181..175434853 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java @@ -22,15 +22,13 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; import net.sf.samtools.SAMSequenceDictionary; import org.broad.tribble.TribbleException; import org.broad.tribble.util.ParsingUtils; -import org.broadinstitute.sting.utils.codecs.vcf.*; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.vcf.*; +import org.broadinstitute.variant.variantcontext.*; import java.io.*; import java.lang.reflect.Array; @@ -119,7 +117,7 @@ class VCFWriter extends IndexingVariantContextWriter { mHeader = writeHeader(header, writer, doNotWriteGenotypes, getVersionLine(), getStreamName()); flushBuffer(); } catch ( IOException e ) { - throw new UserException.CouldNotCreateOutputFile(getStreamName(), e); + throw new RuntimeException("Couldn't write file " + getStreamName(), e); } } @@ -171,7 +169,7 @@ class VCFWriter extends IndexingVariantContextWriter { writer.flush(); // necessary so that writing to an output stream will work } catch (IOException e) { - throw new ReviewedStingException("IOException writing the VCF header to " + streamNameForError, e); + throw new RuntimeException("IOException writing the VCF header to " + streamNameForError, e); } return header; @@ -187,7 +185,7 @@ class VCFWriter extends IndexingVariantContextWriter { // TODO -- would it be useful to null out the line buffer so we don't have it around unnecessarily? writer.close(); } catch (IOException e) { - throw new ReviewedStingException("Unable to close " + getStreamName(), e); + throw new RuntimeException("Unable to close " + getStreamName(), e); } super.close(); @@ -398,7 +396,7 @@ class VCFWriter extends IndexingVariantContextWriter { for ( String field : genotypeFormatKeys ) { if ( field.equals(VCFConstants.GENOTYPE_KEY) ) { if ( !g.isAvailable() ) { - throw new ReviewedStingException("GTs cannot be missing for some samples if they are available for others in the record"); + throw new IllegalStateException("GTs cannot be missing for some samples if they are available for others in the record"); } writeAllele(g.getAllele(0), alleleMap); @@ -599,10 +597,9 @@ class VCFWriter extends IndexingVariantContextWriter { private final void fieldIsMissingFromHeaderError(final VariantContext vc, final String id, final String field) { if ( !allowMissingFieldsInHeader) - throw new UserException.MalformedVCFHeader("Key " + id + " found in VariantContext field " + field + throw new IllegalStateException("Key " + id + " found in VariantContext field " + field + " at " + vc.getChr() + ":" + vc.getStart() - + " but this key isn't defined in the VCFHeader. The GATK now requires all VCFs to have" - + " complete VCF headers by default. This error can be disabled with the engine argument" - + " -U LENIENT_VCF_PROCESSING"); + + " but this key isn't defined in the VCFHeader. We require all VCFs to have" + + " complete VCF headers by default."); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriter.java similarity index 56% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriter.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriter.java index 0ad78c7e0..4313b044d 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriter.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriter.java @@ -1,7 +1,7 @@ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.variantcontext.VariantContext; /** * this class writes VCF files diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java similarity index 93% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java index 035aff7d6..0c98567a1 100644 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java +++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java @@ -22,10 +22,9 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; import net.sf.samtools.SAMSequenceDictionary; -import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; import java.io.FileNotFoundException; @@ -107,7 +106,7 @@ public class VariantContextWriterFactory { } /** - * Returns a output stream writing to location, or throws a UserException if this fails + * Returns a output stream writing to location, or throws an exception if this fails * @param location * @return */ @@ -115,7 +114,7 @@ public class VariantContextWriterFactory { try { return new FileOutputStream(location); } catch (FileNotFoundException e) { - throw new UserException.CouldNotCreateOutputFile(location, "Unable to create VCF writer", e); + throw new RuntimeException(location + ": Unable to create VCF writer", e); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java rename to public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java index 652f7f96f..3bad6b064 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.apache.log4j.Logger; import org.broad.tribble.AsciiFeatureCodec; @@ -8,9 +8,7 @@ import org.broad.tribble.TribbleException; import org.broad.tribble.readers.LineReader; import org.broad.tribble.util.BlockCompressedInputStream; import org.broad.tribble.util.ParsingUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import java.io.FileInputStream; import java.io.FileNotFoundException; @@ -148,7 +146,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec sampleNames.add(strings[arrayIndex++]); if ( sawFormatTag && sampleNames.size() == 0 ) - throw new UserException.MalformedVCFHeader("The FORMAT field was provided but there is no genotype/sample data"); + throw new TribbleException.InvalidHeader("The FORMAT field was provided but there is no genotype/sample data"); } else { if ( str.startsWith(VCFConstants.INFO_HEADER_START) ) { @@ -203,7 +201,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null; // our header cannot be null, we need the genotype sample names and counts - if (header == null) throw new ReviewedStingException("VCF Header cannot be null when decoding a record"); + if (header == null) throw new TribbleException("VCF Header cannot be null when decoding a record"); if (parts == null) parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)]; @@ -213,8 +211,8 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns. Otherwise check that we have nine (normal colummns + genotyping data) if (( (header == null || !header.hasGenotypingData()) && nParts != NUM_STANDARD_FIELDS) || (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) ) - throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) + - " tokens, and saw " + nParts + " )", lineNo); + throw new TribbleException("Line " + lineNo + ": there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) + + " tokens, and saw " + nParts + " )"); return parseVCFLine(parts, includeGenotypes); } @@ -692,10 +690,10 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec protected void generateException(String message) { - throw new UserException.MalformedVCF(message, lineNo); + throw new TribbleException(String.format("The provided VCF file is malformed at approximately line number %d: %s", lineNo, message)); } protected static void generateException(String message, int lineNo) { - throw new UserException.MalformedVCF(message, lineNo); + throw new TribbleException(String.format("The provided VCF file is malformed at approximately line number %d: %s", lineNo, message)); } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/public/java/src/org/broadinstitute/variant/vcf/VCF3Codec.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java rename to public/java/src/org/broadinstitute/variant/vcf/VCF3Codec.java index 2c103b473..6cbd26de9 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCF3Codec.java @@ -22,12 +22,10 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.broad.tribble.TribbleException; import org.broad.tribble.readers.LineReader; -import org.broad.tribble.util.ParsingUtils; -import org.broadinstitute.sting.utils.variantcontext.*; import java.io.IOException; import java.util.*; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/variant/vcf/VCFCodec.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFCodec.java index f12f13dc7..6a31727ee 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFCodec.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.broad.tribble.TribbleException; import org.broad.tribble.readers.LineReader; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java index 5273806a7..68252f01b 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java @@ -22,14 +22,12 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.apache.log4j.Logger; import org.broad.tribble.TribbleException; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.LinkedHashMap; @@ -65,7 +63,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF public boolean isFixedCount() { return countType == VCFHeaderLineCount.INTEGER; } public int getCount() { if ( ! isFixedCount() ) - throw new ReviewedStingException("Asking for header line count when type is not an integer"); + throw new TribbleException("Asking for header line count when type is not an integer"); return count; } @@ -91,7 +89,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF final int ploidy = vc.getMaxPloidy(2); return GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), ploidy); default: - throw new ReviewedStingException("Unknown count type: " + countType); + throw new TribbleException("Unknown count type: " + countType); } } @@ -172,7 +170,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF } if ( count < 0 && countType == VCFHeaderLineCount.INTEGER ) - throw new UserException.MalformedVCFHeader("Count < 0 for fixed size VCF header field " + name); + throw new TribbleException.InvalidHeader("Count < 0 for fixed size VCF header field " + name); try { type = VCFHeaderLineType.valueOf(mapping.get("Type")); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java b/public/java/src/org/broadinstitute/variant/vcf/VCFConstants.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFConstants.java index dac58eb10..09e74cff6 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFConstants.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import java.util.Locale; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java index 35cc75af2..f4bcd69bf 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import java.util.Map; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFFilterHeaderLine.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFFilterHeaderLine.java index bfc484a7e..ff5352404 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFFilterHeaderLine.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import java.util.Arrays; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFFormatHeaderLine.java similarity index 95% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFFormatHeaderLine.java index 5fc3187c5..5d749f37d 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFFormatHeaderLine.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; /** diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java similarity index 97% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java index 44a3e9af3..46f9187a1 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java @@ -22,11 +22,11 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.apache.log4j.Logger; +import org.broad.tribble.TribbleException; import org.broad.tribble.util.ParsingUtils; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.*; @@ -124,7 +124,7 @@ public class VCFHeader { this(metaData); if ( genotypeSampleNames.size() != new HashSet(genotypeSampleNames).size() ) - throw new ReviewedStingException("BUG: VCF header has duplicate sample names"); + throw new TribbleException.InvalidHeader("BUG: VCF header has duplicate sample names"); mGenotypeSampleNames.addAll(genotypeSampleNames); samplesWereAlreadySorted = ParsingUtils.isSorted(genotypeSampleNames); @@ -234,7 +234,7 @@ public class VCFHeader { if ( hasFormatLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && ! hasFormatLine(VCFConstants.GENOTYPE_PL_KEY) ) { logger.warn("Found " + VCFConstants.GENOTYPE_LIKELIHOODS_KEY + " format, but no " - + VCFConstants.GENOTYPE_PL_KEY + " field. As the GATK now only manages PL fields internally" + + VCFConstants.GENOTYPE_PL_KEY + " field. We now only manage PL fields internally" + " automatically adding a corresponding PL field to your VCF header"); addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification")); } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLine.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLine.java index 9b5886c65..3333fd455 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLine.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.broad.tribble.TribbleException; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineCount.java similarity index 72% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineCount.java index d615c7c78..2bef149a2 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineCount.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; /** * the count encodings we use for fields in VCF header lines diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineTranslator.java similarity index 93% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineTranslator.java index dcc38a6f9..1b20c52ff 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineTranslator.java @@ -1,6 +1,6 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; -import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broad.tribble.TribbleException; import java.util.*; @@ -77,10 +77,10 @@ class VCF4Parser implements VCFLineParser { index = 0; if ( expectedTagOrder != null ) { if ( ret.size() > expectedTagOrder.size() ) - throw new UserException.MalformedVCFHeader("unexpected tag count " + ret.size() + " in line " + valueLine); + throw new TribbleException.InvalidHeader("unexpected tag count " + ret.size() + " in line " + valueLine); for ( String str : ret.keySet() ) { if ( !expectedTagOrder.get(index).equals(str) ) - throw new UserException.MalformedVCFHeader("Unexpected tag " + str + " in line " + valueLine); + throw new TribbleException.InvalidHeader("Unexpected tag " + str + " in line " + valueLine); index++; } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineType.java similarity index 74% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineType.java index 83e272415..0defd09c5 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineType.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; /** * the type encodings we use for fields in VCF header lines diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderVersion.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderVersion.java index c65ce17b9..16229857e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderVersion.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.broad.tribble.TribbleException; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFIDHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFIDHeaderLine.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFIDHeaderLine.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFIDHeaderLine.java index 65321881a..c18c1b6ea 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFIDHeaderLine.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFIDHeaderLine.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; /** an interface for ID-based header lines **/ public interface VCFIDHeaderLine { diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFInfoHeaderLine.java similarity index 94% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFInfoHeaderLine.java index 9f249c531..7db527efe 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFInfoHeaderLine.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; /** diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFSimpleHeaderLine.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFSimpleHeaderLine.java index c9699e7b5..94a1bd20b 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFSimpleHeaderLine.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import java.util.LinkedHashMap; import java.util.List; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java b/public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java similarity index 96% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java index b2e8cc100..5b00cfa37 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java @@ -22,12 +22,12 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broad.tribble.TribbleException; import java.util.*; @@ -76,7 +76,7 @@ public class VCFStandardHeaderLines { /** * Adds header lines for each of the format fields in IDs to header, returning the set of * IDs without standard descriptions, unless throwErrorForMissing is true, in which - * case this situation results in a ReviewedStingException + * case this situation results in a TribbleException * * @param IDs * @return @@ -126,7 +126,7 @@ public class VCFStandardHeaderLines { /** * Adds header lines for each of the info fields in IDs to header, returning the set of * IDs without standard descriptions, unless throwErrorForMissing is true, in which - * case this situation results in a ReviewedStingException + * case this situation results in a TribbleException * * @param IDs * @return @@ -246,7 +246,7 @@ public class VCFStandardHeaderLines { @Ensures({"standards.containsKey(line.getID())"}) public void add(final T line) { if ( standards.containsKey(line.getID()) ) - throw new ReviewedStingException("Attempting to add multiple standard header lines for ID " + line.getID()); + throw new TribbleException("Attempting to add multiple standard header lines for ID " + line.getID()); standards.put(line.getID(), line); } @@ -255,7 +255,7 @@ public class VCFStandardHeaderLines { public T get(final String ID, final boolean throwErrorForMissing) { final T x = standards.get(ID); if ( throwErrorForMissing && x == null ) - throw new ReviewedStingException("Couldn't find a standard VCF header line for field " + ID); + throw new TribbleException("Couldn't find a standard VCF header line for field " + ID); return x; } } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java old mode 100755 new mode 100644 similarity index 57% rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java rename to public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java index a8aefb703..ccb9935cb --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java +++ b/public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java @@ -1,160 +1,15 @@ -/* - * 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.codecs.vcf; +package org.broadinstitute.variant.vcf; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; import org.apache.commons.io.FilenameUtils; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodecHeader; -import org.broad.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import java.io.File; -import java.io.FileInputStream; -import java.io.IOException; import java.util.*; -/** - * A set of static utility methods for common operations on VCF files/records. - */ public class VCFUtils { - /** - * Constructor access disallowed...static utility methods only! - */ - private VCFUtils() { } - - public static Map getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List> rodBindings) { - // Collect the eval rod names - final Set names = new TreeSet(); - for ( final RodBinding evalRod : rodBindings ) - names.add(evalRod.getName()); - return getVCFHeadersFromRods(toolkit, names); - } - - public static Map getVCFHeadersFromRods(GenomeAnalysisEngine toolkit) { - return getVCFHeadersFromRods(toolkit, (Collection)null); - } - - public static Map getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, Collection rodNames) { - Map data = new HashMap(); - - // iterate to get all of the sample names - List dataSources = toolkit.getRodDataSources(); - for ( ReferenceOrderedDataSource source : dataSources ) { - // ignore the rod if it's not in our list - if ( rodNames != null && !rodNames.contains(source.getName()) ) - continue; - - if ( source.getHeader() != null && source.getHeader() instanceof VCFHeader ) - data.put(source.getName(), (VCFHeader)source.getHeader()); - } - - return data; - } - - public static Map getVCFHeadersFromRodPrefix(GenomeAnalysisEngine toolkit,String prefix) { - Map data = new HashMap(); - - // iterate to get all of the sample names - List dataSources = toolkit.getRodDataSources(); - for ( ReferenceOrderedDataSource source : dataSources ) { - // ignore the rod if lacks the prefix - if ( ! source.getName().startsWith(prefix) ) - continue; - - if ( source.getHeader() != null && source.getHeader() instanceof VCFHeader ) - data.put(source.getName(), (VCFHeader)source.getHeader()); - } - - return data; - } - - /** - * Gets the header fields from all VCF rods input by the user - * - * @param toolkit GATK engine - * - * @return a set of all fields - */ - public static Set getHeaderFields(GenomeAnalysisEngine toolkit) { - return getHeaderFields(toolkit, null); - } - - /** - * Gets the header fields from all VCF rods input by the user - * - * @param toolkit GATK engine - * @param rodNames names of rods to use, or null if we should use all possible ones - * - * @return a set of all fields - */ - public static Set getHeaderFields(GenomeAnalysisEngine toolkit, Collection rodNames) { - - // keep a map of sample name to occurrences encountered - TreeSet fields = new TreeSet(); - - // iterate to get all of the sample names - List dataSources = toolkit.getRodDataSources(); - for ( ReferenceOrderedDataSource source : dataSources ) { - // ignore the rod if it's not in our list - if ( rodNames != null && !rodNames.contains(source.getName()) ) - continue; - - if ( source.getRecordType().equals(VariantContext.class)) { - VCFHeader header = (VCFHeader)source.getHeader(); - if ( header != null ) - fields.addAll(header.getMetaDataInSortedOrder()); - } - } - - return fields; - } - - /** Only displays a warning if a logger is provided and an identical warning hasn't been already issued */ - private static final class HeaderConflictWarner { - Logger logger; - Set alreadyIssued = new HashSet(); - - private HeaderConflictWarner(final Logger logger) { - this.logger = logger; - } - - public void warn(final VCFHeaderLine line, final String msg) { - if ( logger != null && ! alreadyIssued.contains(line.getKey()) ) { - alreadyIssued.add(line.getKey()); - logger.warn(msg); - } - } - } public static Set smartMergeHeaders(Collection headers, Logger logger) throws IllegalStateException { HashMap map = new HashMap(); // from KEY.NAME -> line @@ -236,16 +91,6 @@ public class VCFUtils { return rsID; } - /** - * Add / replace the contig header lines in the VCFHeader with the information in the GATK engine - * - * @param header the header to update - * @param engine the GATK engine containing command line arguments and the master sequence dictionary - */ - public static VCFHeader withUpdatedContigs(final VCFHeader header, final GenomeAnalysisEngine engine) { - return VCFUtils.withUpdatedContigs(header, engine.getArguments().referenceFile, engine.getMasterSequenceDictionary()); - } - /** * Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary * @@ -323,32 +168,20 @@ public class VCFUtils { return assembly; } - /** - * Read all of the VCF records from source into memory, returning the header and the VariantContexts - * - * @param source the file to read, must be in VCF4 format - * @return - * @throws IOException - */ - public static Pair> readVCF(final File source) throws IOException { - // read in the features - final List vcs = new ArrayList(); - final VCFCodec codec = new VCFCodec(); - PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source)); - FeatureCodecHeader header = codec.readHeader(pbs); - pbs.close(); + /** Only displays a warning if a logger is provided and an identical warning hasn't been already issued */ + private static final class HeaderConflictWarner { + Logger logger; + Set alreadyIssued = new HashSet(); - pbs = new PositionalBufferedStream(new FileInputStream(source)); - pbs.skip(header.getHeaderEnd()); - - final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue(); - - while ( ! pbs.isDone() ) { - final VariantContext vc = codec.decode(pbs); - if ( vc != null ) - vcs.add(vc); + private HeaderConflictWarner(final Logger logger) { + this.logger = logger; } - return new Pair>(vcfHeader, vcs); + public void warn(final VCFHeaderLine line, final String msg) { + if ( logger != null && ! alreadyIssued.contains(line.getKey()) ) { + alreadyIssued.add(line.getKey()); + logger.warn(msg); + } + } } -} \ No newline at end of file +} diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java index fa9f9e8a7..b36400a92 100755 --- a/public/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java @@ -34,12 +34,12 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; +import org.broadinstitute.variant.bcf2.BCF2Utils; +import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.variantcontext.VariantContextTestProvider; +import org.broadinstitute.variant.variantcontext.VariantContextTestProvider; import org.testng.Assert; import org.testng.annotations.AfterSuite; import org.testng.annotations.BeforeMethod; diff --git a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java index be2e91557..67031a586 100755 --- a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.commandline; import org.apache.commons.io.FileUtils; import org.broad.tribble.Feature; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java b/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java index 206f32532..307bf41a3 100644 --- a/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.Test; import org.testng.annotations.BeforeMethod; diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java index 2f73e373c..c520399e4 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java @@ -36,11 +36,10 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.*; import java.util.*; diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java index 48e4ff4ed..c01ed61c0 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java @@ -32,11 +32,11 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.codecs.table.BedTableCodec; import org.broadinstitute.sting.utils.codecs.table.TableFeature; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; +import org.broadinstitute.variant.vcf.VCF3Codec; +import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java index 6264758ad..60a941a9e 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java @@ -29,8 +29,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.SAMSequenceDictionary; import org.broad.tribble.Tribble; import org.broad.tribble.index.Index; -import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; +import org.broadinstitute.variant.vcf.VCF3Codec; +import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java index c00fbbcdb..c4e566135 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java @@ -29,7 +29,7 @@ import org.broad.tribble.Feature; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; +import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java index c1c22aceb..d50a8f0ae 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java @@ -30,8 +30,8 @@ package org.broadinstitute.sting.gatk.walkers.diffengine; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; -import org.broadinstitute.sting.utils.variantcontext.Allele; +import org.broadinstitute.variant.vcf.VCFConstants; +import org.broadinstitute.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java index f7f7999be..e48c4d197 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -29,7 +29,7 @@ import net.sf.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.QualityUtils; @@ -38,9 +38,6 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import java.util.*; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java index 85528f58b..12662c748 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java @@ -1,39 +1,17 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; -import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel; -import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; -import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; -import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; -import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.Allele; import java.util.*; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; import org.testng.Assert; -import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeSuite; -import org.testng.annotations.DataProvider; import org.testng.annotations.Test; /** diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java index f6c12f443..24903bba4 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java @@ -37,9 +37,9 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Variant import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager; import org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java index 21d49638f..a400a004a 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java @@ -2,12 +2,8 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.PositionalBufferedStream; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; +import org.broadinstitute.variant.vcf.*; import org.testng.Assert; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderUnitTest; -import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java index a1d673b56..f21b662e2 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -262,7 +262,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { @Test() public void testFileWithoutInfoLineInHeader() { - testFileWithoutInfoLineInHeader("testFileWithoutInfoLineInHeader", UserException.class); + testFileWithoutInfoLineInHeader("testFileWithoutInfoLineInHeader", IllegalStateException.class); } @Test() diff --git a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java index 13db1d39e..7350e0076 100644 --- a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java @@ -30,9 +30,9 @@ import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.CigarOperator; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; +import org.broadinstitute.variant.variantcontext.Allele; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java deleted file mode 100644 index 50fbea708..000000000 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java +++ /dev/null @@ -1,107 +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.variantcontext; - -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.testng.annotations.Test; - -import java.io.File; -import java.io.FileNotFoundException; -import java.net.MalformedURLException; -import java.net.URL; -import java.net.URLClassLoader; - -/** - * Test to ensure that, given only the VCF jar and its expected dependencies, core VCF classes will load. - */ -public class VCFJarClassLoadingUnitTest { - @Test - public void testVCFJarClassLoading() throws ClassNotFoundException, MalformedURLException { - URL[] jarURLs; - - try { - jarURLs = new URL[] { getVCFJarFile().toURI().toURL(), getTribbleJarFile().toURI().toURL() }; - } - catch ( FileNotFoundException e ) { - throw new ReviewedStingException("Could not find the VCF jar and/or its dependencies", e); - } - - ClassLoader classLoader = new URLClassLoader(jarURLs, null); - classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.VariantContext"); - classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec"); - classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFCodec"); - classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec"); - classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter"); - classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VCFWriter"); - classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.BCF2Writer"); - } - - /** - * Locates the tribble jar within the dist directory. - * - * Makes the horrible assumption that tests will always be run from the root of a Sting clone, - * but this is much less problematic than using the classpath to locate tribble, since - * the classpath won't explicitly contain tribble when we're testing the fully-packaged - * GATK jar. - * - * @return The tribble jar file, if found - * @throws FileNotFoundException If we couldn't locate a tribble jar within the dist directory - */ - private File getTribbleJarFile() throws FileNotFoundException { - File distDir = new File("dist"); - if ( ! distDir.isDirectory() ) { - throw new FileNotFoundException("The dist directory does not exist"); - } - - for ( File distDirEntry : distDir.listFiles() ) { - if ( distDirEntry.getName().startsWith("tribble") && distDirEntry.getName().endsWith(".jar") ) { - return distDirEntry; - } - } - - throw new FileNotFoundException("Could not find a tribble jar file in the dist directory."); - } - - /** - * Locates the vcf jar within the dist directory. - * - * Makes the horrible assumption that tests will always be run from the root of a Sting clone, - * but this is much less problematic than using the classpath to locate vcf.jar, since - * the classpath won't explicitly contain vcf.jar when we're testing the fully-packaged - * GATK jar. - * - * @return The vcf jar file, if found - * @throws FileNotFoundException If we couldn't locate a vcf jar within the dist directory - */ - private File getVCFJarFile() throws FileNotFoundException { - File vcfJar = new File("dist/vcf.jar"); - - if ( ! vcfJar.exists() ) { - throw new FileNotFoundException("Could not find dist/vcf.jar"); - } - - return vcfJar; - } -} diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java b/public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java similarity index 99% rename from public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java rename to public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java index 77050c069..5b8062b67 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java @@ -23,7 +23,7 @@ */ // our package -package org.broadinstitute.sting.utils.codecs.bcf2; +package org.broadinstitute.variant.bcf2; // the imports for unit testing. @@ -31,7 +31,7 @@ package org.broadinstitute.sting.utils.codecs.bcf2; import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.variantcontext.writer.BCF2Encoder; +import org.broadinstitute.variant.variantcontext.writer.BCF2Encoder; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java b/public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java similarity index 97% rename from public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java rename to public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java index ae76a374a..8a182367d 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java @@ -22,17 +22,14 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.bcf2; +package org.broadinstitute.variant.bcf2; -import org.broad.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.variant.vcf.*; -import java.io.*; import java.util.*; import org.testng.Assert; -import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java b/public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java similarity index 97% rename from public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java rename to public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java index 2f5aea951..8112f510d 100755 --- a/public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java @@ -1,5 +1,6 @@ -package org.broadinstitute.sting.utils; +package org.broadinstitute.variant.utils; +import org.broadinstitute.sting.utils.MathUtils; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java similarity index 98% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java rename to public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java index 65398c373..3ce335a00 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java @@ -24,14 +24,13 @@ */ // our package -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; // the imports for unit testing. import org.testng.Assert; import org.testng.annotations.BeforeSuite; -import org.testng.annotations.BeforeTest; import org.testng.annotations.Test; // public Allele(byte[] bases, boolean isRef) { diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java similarity index 97% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java rename to public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java index 4ce32cee7..51e600fa5 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java @@ -23,13 +23,14 @@ */ // our package -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; // the imports for unit testing. -import org.broadinstitute.sting.utils.BaseUtils; +import org.broad.tribble.TribbleException; +import org.broadinstitute.variant.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; @@ -70,7 +71,7 @@ public class GenotypeLikelihoodsUnitTest { Assert.assertEquals(gl.getAsString(), vPLString); } - @Test (expectedExceptions = UserException.MalformedVCF.class) + @Test (expectedExceptions = TribbleException.class) public void testErrorBadFormat() { GenotypeLikelihoods gl = GenotypeLikelihoods.fromPLField("adf,b,c"); gl.getAsVector(); diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java similarity index 97% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java rename to public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java index e511a7f30..7be215b2d 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java @@ -23,7 +23,7 @@ */ // our package -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; // the imports for unit testing. @@ -34,9 +34,6 @@ import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.Test; -import java.util.Arrays; -import java.util.List; - public class GenotypeUnitTest extends BaseTest { Allele A, Aref, T; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypesContextUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java similarity index 99% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypesContextUnitTest.java rename to public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java index 6ccfd87ce..04af64bd3 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypesContextUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java @@ -23,7 +23,7 @@ */ // our package -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; // the imports for unit testing. @@ -33,7 +33,6 @@ import org.broad.tribble.util.ParsingUtils; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.Utils; import org.testng.Assert; -import org.testng.annotations.BeforeMethod; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java similarity index 76% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java index 0e5522e3a..bbf6976e7 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java @@ -22,21 +22,16 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; import com.google.caliper.runner.CaliperMain; -import net.sf.picard.reference.ReferenceSequenceFile; import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; -import org.broad.tribble.readers.AsciiLineReader; -import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; -import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.variant.vcf.VCFCodec; -import java.io.*; import java.util.*; /** @@ -235,7 +230,7 @@ public class VariantContextBenchmark extends SimpleBenchmark { toMerge.add(new VariantContextBuilder(vc).genotypes(gc).make()); } - VariantContextUtils.simpleMerge(b37GenomeLocParser, toMerge, null, + VariantContextUtils.simpleMerge(toMerge, null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.UNSORTED, true, false, "set", false, true); @@ -258,54 +253,54 @@ public class VariantContextBenchmark extends SimpleBenchmark { // public void timeV13(int rep) { // for ( int i = 0; i < rep; i++ ) { -// FunctionToBenchmark func = getV13FunctionToBenchmark(); -// FeatureCodec codec = new org.broadinstitute.sting.utils.variantcontext.v13.VCFCodec(); +// FunctionToBenchmark func = getV13FunctionToBenchmark(); +// FeatureCodec codec = new org.broadinstitute.variant.variantcontext.v13.VCFCodec(); // runBenchmark(codec, func); // } // } // -// public FunctionToBenchmark getV13FunctionToBenchmark() { +// public FunctionToBenchmark getV13FunctionToBenchmark() { // switch ( operation ) { // case READ: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // ; // empty operation // } // }; // case SUBSET_TO_SAMPLES: -// return new FunctionToBenchmark() { +// return new FunctionToBenchmark() { // List samples; -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // if ( samples == null ) // samples = new ArrayList(vc.getSampleNames()).subList(0, nSamplesToTake); -// org.broadinstitute.sting.utils.variantcontext.v13.VariantContext sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values()); +// org.broadinstitute.variant.variantcontext.v13.VariantContext sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values()); // sub.getNSamples(); // } // }; // // case GET_TYPE: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // vc.getType(); // } // }; // case GET_ID: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // vc.getID(); // } // }; // case GET_GENOTYPES: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // vc.getGenotypes().size(); // } // }; // // case GET_GENOTYPES_FOR_SAMPLES: -// return new FunctionToBenchmark() { +// return new FunctionToBenchmark() { // Set samples; -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // if ( samples == null ) // samples = new HashSet(new ArrayList(vc.getSampleNames()).subList(0, nSamplesToTake)); // vc.getGenotypes(samples).size(); @@ -313,60 +308,60 @@ public class VariantContextBenchmark extends SimpleBenchmark { // }; // // case GET_ATTRIBUTE_STRING: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // vc.getExtendedAttribute("AN", null); // } // }; // // case GET_ATTRIBUTE_INT: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // vc.getAttributeAsInt("AC", 0); // } // }; // // case GET_N_SAMPLES: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // vc.getNSamples(); // } // }; // // case GET_GENOTYPES_IN_ORDER_OF_NAME: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // ; // TODO - TEST IS BROKEN // //vc.getGenotypesOrderedByName(); // } // }; // // case CALC_GENOTYPE_COUNTS: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { // vc.getHetCount(); // } // }; // // case MERGE: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) { -// List toMerge = new ArrayList(); +// return new FunctionToBenchmark() { +// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { +// List toMerge = new ArrayList(); // // for ( int i = 0; i < dupsToMerge; i++ ) { -// Map gc = new HashMap(); -// for ( final org.broadinstitute.sting.utils.variantcontext.v13.Genotype g : vc.getGenotypes().values() ) { +// Map gc = new HashMap(); +// for ( final org.broadinstitute.variant.variantcontext.v13.Genotype g : vc.getGenotypes().values() ) { // String name = g.getSampleName()+"_"+i; -// gc.put(name, new org.broadinstitute.sting.utils.variantcontext.v13.Genotype(name, +// gc.put(name, new org.broadinstitute.variant.variantcontext.v13.Genotype(name, // g.getAlleles(), g.getLog10PError(), g.getFilters(), g.getAttributes(), g.isPhased(), g.getLikelihoods().getAsVector())); -// toMerge.add(org.broadinstitute.sting.utils.variantcontext.v13.VariantContext.modifyGenotypes(vc, gc)); +// toMerge.add(org.broadinstitute.variant.variantcontext.v13.VariantContext.modifyGenotypes(vc, gc)); // } // } // -// org.broadinstitute.sting.utils.variantcontext.v13.VariantContextUtils.simpleMerge(b37GenomeLocParser, +// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.simpleMerge(b37GenomeLocParser, // toMerge, null, -// org.broadinstitute.sting.utils.variantcontext.v13.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, -// org.broadinstitute.sting.utils.variantcontext.v13.VariantContextUtils.GenotypeMergeType.UNSORTED, +// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, +// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.GenotypeMergeType.UNSORTED, // true, false, "set", false, true); // } // }; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java similarity index 99% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java index c57b2a44d..a88a76947 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import org.apache.log4j.Logger; import org.broad.tribble.FeatureCodec; @@ -30,11 +30,11 @@ import org.broad.tribble.FeatureCodecHeader; import org.broad.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec; -import org.broadinstitute.sting.utils.codecs.vcf.*; +import org.broadinstitute.variant.bcf2.BCF2Codec; +import org.broadinstitute.variant.vcf.*; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.variantcontext.writer.Options; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; +import org.broadinstitute.variant.variantcontext.writer.Options; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.testng.Assert; import java.io.File; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java similarity index 96% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java index 19620b8df..06c1bc771 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java @@ -1,21 +1,19 @@ // our package -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; // the imports for unit testing. import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.collections.Pair; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.testng.annotations.BeforeSuite; -import org.testng.annotations.BeforeTest; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import org.testng.Assert; -import java.lang.reflect.Array; import java.util.*; @@ -478,30 +476,30 @@ public class VariantContextUnitTest extends BaseTest { Pair,byte[]> result; byte[] refBytes = "TATCATCATCGGA".getBytes(); - Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "ATG".getBytes(), "ATGATGATGATG".getBytes()),4); - Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "G".getBytes(), "ATGATGATGATG".getBytes()),0); - Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "T".getBytes(), "T".getBytes()),1); - Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "AT".getBytes(), "ATGATGATCATG".getBytes()),1); - Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "CCC".getBytes(), "CCCCCCCC".getBytes()),2); + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("ATG".getBytes(), "ATGATGATGATG".getBytes()),4); + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("G".getBytes(), "ATGATGATGATG".getBytes()),0); + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("T".getBytes(), "T".getBytes()),1); + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("AT".getBytes(), "ATGATGATCATG".getBytes()),1); + Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("CCC".getBytes(), "CCCCCCCC".getBytes()),2); - Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("ATG".getBytes()),3); - Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("AAA".getBytes()),1); - Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("CACACAC".getBytes()),7); - Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("CACACA".getBytes()),2); - Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("CATGCATG".getBytes()),4); - Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("AATAATA".getBytes()),7); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("ATG".getBytes()),3); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("AAA".getBytes()),1); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CACACAC".getBytes()),7); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CACACA".getBytes()),2); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CATGCATG".getBytes()),4); + Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("AATAATA".getBytes()),7); // A*,ATC, context = ATC ATC ATC : (ATC)3 -> (ATC)4 VariantContext vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStop, Arrays.asList(nullR,atc)).make(); - result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); Assert.assertEquals(result.getFirst().toArray()[0],3); Assert.assertEquals(result.getFirst().toArray()[1],4); Assert.assertEquals(result.getSecond().length,3); // ATC*,A,ATCATC vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+3, Arrays.asList(Allele.create("AATC", true),nullA,atcatc)).make(); - result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); Assert.assertEquals(result.getFirst().toArray()[0],3); Assert.assertEquals(result.getFirst().toArray()[1],2); Assert.assertEquals(result.getFirst().toArray()[2],4); @@ -510,7 +508,7 @@ public class VariantContextUnitTest extends BaseTest { // simple non-tandem deletion: CCCC*, - refBytes = "TCCCCCCCCATG".getBytes(); vc = new VariantContextBuilder("foo", delLoc, 10, 14, Arrays.asList(ccccR,nullA)).make(); - result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); Assert.assertEquals(result.getFirst().toArray()[0],8); Assert.assertEquals(result.getFirst().toArray()[1],4); Assert.assertEquals(result.getSecond().length,1); @@ -518,7 +516,7 @@ public class VariantContextUnitTest extends BaseTest { // CCCC*,CC,-,CCCCCC, context = CCC: (C)7 -> (C)5,(C)3,(C)9 refBytes = "TCCCCCCCAGAGAGAG".getBytes(); vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(ccccR,cc, nullA,cccccc)).make(); - result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); Assert.assertEquals(result.getFirst().toArray()[0],7); Assert.assertEquals(result.getFirst().toArray()[1],5); Assert.assertEquals(result.getFirst().toArray()[2],3); @@ -528,7 +526,7 @@ public class VariantContextUnitTest extends BaseTest { // GAGA*,-,GAGAGAGA refBytes = "TGAGAGAGAGATTT".getBytes(); vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(gagaR, nullA,gagagaga)).make(); - result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes); + result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes); Assert.assertEquals(result.getFirst().toArray()[0],5); Assert.assertEquals(result.getFirst().toArray()[1],3); Assert.assertEquals(result.getFirst().toArray()[2],7); diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUtilsUnitTest.java similarity index 98% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUtilsUnitTest.java index 3ad438b26..f68d24670 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUtilsUnitTest.java @@ -21,7 +21,7 @@ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.BaseTest; @@ -29,6 +29,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; +import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; @@ -189,7 +190,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { final List priority = vcs2priority(inputs); - final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser, + final VariantContext merged = VariantContextUtils.simpleMerge( inputs, priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false); @@ -247,7 +248,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { inputs.add(new VariantContextBuilder(snpVC1).id(id).make()); } - final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser, + final VariantContext merged = VariantContextUtils.simpleMerge( inputs, null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, "set", false, false); @@ -364,7 +365,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { @Test(dataProvider = "mergeFiltered") public void testMergeFiltered(MergeFilteredTest cfg) { final List priority = vcs2priority(cfg.inputs); - final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser, + final VariantContext merged = VariantContextUtils.simpleMerge( cfg.inputs, priority, cfg.type, VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false); // test alleles are equal @@ -490,7 +491,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { @Test(dataProvider = "mergeGenotypes") public void testMergeGenotypes(MergeGenotypesTest cfg) { - final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser, + final VariantContext merged = VariantContextUtils.simpleMerge( cfg.inputs, cfg.priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false); @@ -531,7 +532,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)); final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2)); - final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser, + final VariantContext merged = VariantContextUtils.simpleMerge( Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.UNIQUIFY, false, false, "set", false, false); @@ -539,12 +540,12 @@ public class VariantContextUtilsUnitTest extends BaseTest { Assert.assertEquals(merged.getSampleNames(), new HashSet(Arrays.asList("s1.1", "s1.2"))); } - @Test(expectedExceptions = UserException.class) + @Test(expectedExceptions = IllegalStateException.class) public void testMergeGenotypesRequireUnique() { final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)); final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2)); - final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser, + final VariantContext merged = VariantContextUtils.simpleMerge( Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE, false, false, "set", false, false); } @@ -563,7 +564,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS); VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS); - final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser, + final VariantContext merged = VariantContextUtils.simpleMerge( Arrays.asList(vc1, vc2), priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, annotate, false, set, false, false); @@ -654,7 +655,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { public void testRepeatDetectorTest(RepeatDetectorTest cfg) { // test alleles are equal - Assert.assertEquals(VariantContextUtils.isTandemRepeat(cfg.vc, cfg.ref.getBytes()), cfg.isTrueRepeat); + Assert.assertEquals(GATKVariantContextUtils.isTandemRepeat(cfg.vc, cfg.ref.getBytes()), cfg.isTrueRepeat); } // -------------------------------------------------------------------------------- @@ -700,7 +701,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { @Test(dataProvider = "ReverseClippingPositionTestProvider") public void testReverseClippingPositionTestProvider(ReverseClippingPositionTestProvider cfg) { - int result = VariantContextUtils.computeReverseClipping(cfg.alleles, cfg.ref.getBytes(), 0, false); + int result = GATKVariantContextUtils.computeReverseClipping(cfg.alleles, cfg.ref.getBytes(), 0, false); Assert.assertEquals(result, cfg.expectedClip); } @@ -778,7 +779,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { @Test(dataProvider = "SplitBiallelics") public void testSplitBiallelicsNoGenotypes(final VariantContext vc, final List expectedBiallelics) { - final List biallelics = VariantContextUtils.splitVariantContextToBiallelics(vc); + final List biallelics = GATKVariantContextUtils.splitVariantContextToBiallelics(vc); Assert.assertEquals(biallelics.size(), expectedBiallelics.size()); for ( int i = 0; i < biallelics.size(); i++ ) { final VariantContext actual = biallelics.get(i); @@ -799,7 +800,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { final VariantContext vcWithGenotypes = new VariantContextBuilder(vc).genotypes(genotypes).make(); - final List biallelics = VariantContextUtils.splitVariantContextToBiallelics(vcWithGenotypes); + final List biallelics = GATKVariantContextUtils.splitVariantContextToBiallelics(vcWithGenotypes); for ( int i = 0; i < biallelics.size(); i++ ) { final VariantContext actual = biallelics.get(i); Assert.assertEquals(actual.getNSamples(), vcWithGenotypes.getNSamples()); // not dropping any samples diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java similarity index 97% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java index 8f03f1d38..c29b87aad 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java @@ -21,10 +21,9 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext; +package org.broadinstitute.variant.variantcontext; import net.sf.samtools.SAMFileHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java similarity index 95% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java rename to public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java index 5876efa12..048dee245 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broad.tribble.AbstractFeatureReader; @@ -31,14 +31,14 @@ import org.broad.tribble.Tribble; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderVersion; +import org.broadinstitute.variant.vcf.VCFCodec; +import org.broadinstitute.variant.vcf.VCFHeader; +import org.broadinstitute.variant.vcf.VCFHeaderLine; +import org.broadinstitute.variant.vcf.VCFHeaderVersion; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.variantcontext.*; +import org.broadinstitute.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java similarity index 93% rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java rename to public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java index adf3eb235..03087051a 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java @@ -23,7 +23,7 @@ */ // our package -package org.broadinstitute.sting.utils.variantcontext.writer; +package org.broadinstitute.variant.variantcontext.writer; // the imports for unit testing. @@ -33,12 +33,12 @@ import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.samtools.SAMSequenceDictionary; import org.broad.tribble.FeatureCodec; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; -import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; +import org.broadinstitute.variant.bcf2.BCF2Codec; +import org.broadinstitute.variant.vcf.VCFCodec; +import org.broadinstitute.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextTestProvider; +import org.broadinstitute.variant.variantcontext.VariantContext; +import org.broadinstitute.variant.variantcontext.VariantContextTestProvider; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java b/public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java similarity index 88% rename from public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java rename to public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java index 41ea587be..b51927e0a 100755 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import net.sf.samtools.SAMSequenceDictionary; import org.broad.tribble.AbstractFeatureReader; @@ -9,10 +9,10 @@ import org.broad.tribble.index.IndexFactory; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.writer.Options; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; +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 org.testng.annotations.BeforeTest; import org.testng.annotations.Test; diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java b/public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java similarity index 99% rename from public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java rename to public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java index 62d584ef6..2ff6ebbbf 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.PositionalBufferedStream; diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java similarity index 97% rename from public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java rename to public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java index b9ce58992..1f8e5d563 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java +++ b/public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -97,7 +97,7 @@ public class VCFIntegrationTest extends WalkerTest { @Test public void testFailingOnVCFWithoutHeaders() { - runVCFWithoutHeaders("", "", UserException.class, false); + runVCFWithoutHeaders("", "", IllegalStateException.class, false); } @Test diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLinesUnitTest.java b/public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java similarity index 99% rename from public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLinesUnitTest.java rename to public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java index b6e6c4f42..4e22603c0 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLinesUnitTest.java +++ b/public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java @@ -22,7 +22,7 @@ * OTHER DEALINGS IN THE SOFTWARE. */ -package org.broadinstitute.sting.utils.codecs.vcf; +package org.broadinstitute.variant.vcf; import org.broadinstitute.sting.BaseTest; import org.testng.annotations.DataProvider; diff --git a/public/packages/GATKEngine.xml b/public/packages/GATKEngine.xml index d0b4a52b5..27d2afa47 100644 --- a/public/packages/GATKEngine.xml +++ b/public/packages/GATKEngine.xml @@ -30,6 +30,8 @@ + + diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala index 3fe867981..b627114cf 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala @@ -4,10 +4,10 @@ import java.io.File import org.apache.commons.io.FilenameUtils import scala.io.Source._ import net.sf.samtools.SAMFileReader -import org.broadinstitute.sting.utils.codecs.vcf.{VCFHeader, VCFCodec} +import org.broadinstitute.variant.vcf.{VCFHeader, VCFCodec} import scala.collection.JavaConversions._ import org.broad.tribble.{FeatureCodec, AbstractFeatureReader} -import org.broadinstitute.sting.utils.variantcontext.VariantContext +import org.broadinstitute.variant.variantcontext.VariantContext object VCF_BAM_utilities {