diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java index 25db11101..dd61742d2 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java @@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.OutputMode; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; import org.broadinstitute.sting.utils.collections.DefaultHashMap; import org.broadinstitute.sting.utils.variant.HomoSapiensConstants; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.File; import java.lang.reflect.Field; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java index 9ba468191..2d2d57536 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java @@ -49,8 +49,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 64d45df02..2722ef67a 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -56,10 +56,10 @@ 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.variant.vcf.VCFHeaderLine; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextUtils; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java index eaa9df128..94cf7b97e 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java @@ -47,8 +47,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java index 29cee9e15..5b4edad22 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java @@ -54,10 +54,10 @@ 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.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFStandardHeaderLines; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java index 52b09d251..9adc99e02 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java @@ -54,16 +54,16 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnota import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; -import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFFormatHeaderLine; +import htsjdk.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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java index 8e5ca83e0..be3c176c6 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java @@ -54,13 +54,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnota import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -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 org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; -import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFFormatHeaderLine; +import htsjdk.variant.vcf.VCFStandardHeaderLines; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 671fd88da..22e85c8e5 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -57,12 +57,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java index 827e39c11..42f6753fa 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java @@ -56,10 +56,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummaries.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummaries.java index 1eb635420..a2e7f41fb 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummaries.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummaries.java @@ -55,10 +55,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index 0455290e3..31ec2c77a 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -58,16 +58,16 @@ import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; import java.io.Serializable; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java index 43ec537a4..fbc844fea 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.util.popgen.HardyWeinbergCalculation; +import htsjdk.tribble.util.popgen.HardyWeinbergCalculation; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -56,11 +56,11 @@ 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.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 htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java index 4039241ac..679a94f04 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java @@ -54,9 +54,9 @@ 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.GenomeLoc; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java index 3f815346d..41db36e33 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java @@ -56,11 +56,11 @@ 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.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 htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java index c7fff5a7f..69703178c 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java @@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import java.util.Arrays; import java.util.List; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java index 4e6e87797..b8ae2a17f 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java @@ -57,10 +57,10 @@ 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.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java index b2a504eb2..824085008 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java @@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java index 58f29c6a6..c940f469b 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java @@ -54,13 +54,13 @@ 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.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index 7ebbd49dd..429977344 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -57,11 +57,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -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 htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index 44e44c63b..d08dd2e14 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -56,12 +56,12 @@ 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.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFStandardHeaderLines; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index 13211c44c..06c146ed4 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -58,14 +58,14 @@ import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.MannWhitneyU; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypesContext; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java index f4528b16f..77f5a7398 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java @@ -46,14 +46,14 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java index 67cd67f3f..80beb2ccd 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java @@ -52,11 +52,11 @@ 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.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 htsjdk.variant.vcf.VCFHeaderLineCount; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java index 417f3b595..cec145e9c 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java @@ -54,9 +54,9 @@ 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.pileup.PileupElement; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java index ec1c1e729..1449dedc5 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java @@ -52,11 +52,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFFormatHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasTest.java index 2974ae746..4d1d5e015 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasTest.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasTest.java @@ -47,8 +47,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandOddsRatio.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandOddsRatio.java index 76eedeac3..e08907080 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandOddsRatio.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandOddsRatio.java @@ -52,9 +52,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java index 332d18341..16d9426f7 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java @@ -55,10 +55,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.variant.vcf.VCFHeaderLineCount; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLineCount; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java index f8efd7c3f..356b0c256 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java @@ -56,11 +56,11 @@ 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.variant.vcf.VCFHeaderLineCount; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineCount; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java index 555c75deb..cbb1d95f0 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java @@ -53,9 +53,9 @@ 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.IndelUtils; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 3da04ef86..96ebcf8e9 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -46,10 +46,10 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.CigarElement; -import net.sf.samtools.SAMFileHeader; -import org.broad.tribble.Feature; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java index b9f16132c..5bafba185 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java @@ -47,7 +47,7 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; import com.google.java.contract.Requires; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.utils.Utils; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java index fbf4b23c6..cb824f0fe 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets; -import net.sf.picard.util.PeekableIterator; +import htsjdk.samtools.util.PeekableIterator; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; @@ -62,9 +62,9 @@ import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; import java.io.PrintStream; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java index 7457acb22..e19e9aba5 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java @@ -59,7 +59,7 @@ 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.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java index 77c51f88b..66ef8e8a5 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.SAMUtils; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java index a57502bc0..fac0d64be 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java @@ -55,8 +55,8 @@ import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java index cf144a735..1c441f632 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java @@ -46,17 +46,17 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import net.sf.samtools.SAMUtils; +import htsjdk.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.variant.vcf.VCFConstants; +import htsjdk.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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.GenotypeLikelihoods; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java index 3e0437edb..1f370c07c 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java @@ -55,11 +55,11 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.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.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java index 530ba3ef8..8efea2969 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java @@ -54,7 +54,7 @@ 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.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java index 3cee8f2d8..60b406119 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java @@ -54,7 +54,7 @@ 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.haplotype.Haplotype; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java index f19057f29..3c065abdb 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java @@ -47,7 +47,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.SAMUtils; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; @@ -56,7 +56,7 @@ 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.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.ArrayList; import java.util.Arrays; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java index cadc905dc..acd5fe4a1 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java @@ -79,7 +79,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java index 2b9953782..faf8ad6c6 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java @@ -56,8 +56,8 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import java.util.List; import java.util.Map; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypingEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypingEngine.java index 6f11fe949..870b85610 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypingEngine.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypingEngine.java @@ -67,8 +67,8 @@ import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFConstants; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java index 8fe7cc10a..a34c157e4 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java @@ -59,7 +59,7 @@ import org.broadinstitute.sting.utils.haplotype.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.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 91679fe6f..85d34864c 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -63,7 +63,7 @@ import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index bdfaae22b..6b879cb47 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -49,7 +49,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; public class UnifiedArgumentCollection extends StandardCallerArgumentCollection { diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java index 91b78daaf..d76bd2c2d 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java @@ -64,12 +64,12 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.GenotypeLikelihoods; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.PrintStream; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java index 8686fb878..2cd019aaf 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java @@ -62,9 +62,9 @@ import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.GenotypesContext; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.PrintStream; import java.lang.reflect.Constructor; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java index 44c524197..7efc39e03 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; /** * Created by IntelliJ IDEA. diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java index 642a2b32f..1b94c024d 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java @@ -50,9 +50,9 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.GenotypesContext; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.File; import java.util.List; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java index cf7555bb6..dd268e19d 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java @@ -56,10 +56,10 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import java.io.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java index 9696660b1..d72877cbe 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java @@ -50,7 +50,7 @@ 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.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java index f0c7231fc..46587d90b 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java @@ -50,7 +50,7 @@ import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypingEngine; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.ArrayList; import java.util.Arrays; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java index b778195a9..5f6d15c73 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java @@ -48,10 +48,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; -import org.broadinstitute.variant.variantcontext.GenotypesContext; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.GenotypeLikelihoods; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java index 7b48b3d4d..2245ff4a7 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java @@ -48,7 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java index dfe30fa32..374177769 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java @@ -50,7 +50,7 @@ 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.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.io.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java index 2978cb8f2..74dd447f0 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java @@ -49,9 +49,9 @@ 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.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java index ea09f52e8..669094007 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java @@ -49,7 +49,7 @@ 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.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java index 325d3b722..452eeb70b 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java @@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Collections; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java index da10041dc..6f838e538 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java @@ -49,7 +49,7 @@ 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.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java index b7a646d4e..f83f69cfb 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java @@ -53,7 +53,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java index 8cadea6ec..97b922d83 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java @@ -54,7 +54,7 @@ import org.broadinstitute.sting.utils.collections.CountSet; import org.broadinstitute.sting.utils.haplotype.EventMap; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.haplotype.HaplotypeSizeAndBaseComparator; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.PrintWriter; import java.io.StringWriter; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java index a5b1716c8..beb161939 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java @@ -60,7 +60,7 @@ import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 8d86da273..3685936a8 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -47,7 +47,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; import com.google.java.contract.Ensures; -import net.sf.samtools.SAMFileWriter; +import htsjdk.samtools.SAMFileWriter; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; @@ -92,9 +92,9 @@ import org.broadinstitute.sting.utils.pairhmm.PairHMM; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.variant.GATKVCFIndexType; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; import java.io.FileNotFoundException; import java.io.PrintStream; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java index 907e8a07e..478b6888f 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java @@ -64,7 +64,7 @@ import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.haplotype.MergeVariantsAcrossHaplotypes; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java index ce074a0a8..2daf25420 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java @@ -61,18 +61,18 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; import org.broadinstitute.sting.utils.help.HelpConstants; -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 htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import 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 htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java index 102562504..78c927877 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.haplotype.Haplotype; import java.lang.reflect.Array; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java index 6291f9536..d0b53f20f 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java @@ -48,9 +48,9 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; import org.broadinstitute.sting.utils.GenomeLoc; @@ -59,7 +59,7 @@ import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.sam.CigarUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.File; import java.io.PrintStream; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java index 5891cbdd7..9d5044957 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java @@ -48,7 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.SAMUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; @@ -59,7 +59,7 @@ import org.broadinstitute.sting.utils.pairhmm.*; import org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate; import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.io.File; import java.io.FileNotFoundException; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java index f2f8a2eb6..c6dd7aa0f 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java @@ -49,7 +49,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.HashMap; import java.util.List; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java index 02b6ccaf7..07c355355 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; @@ -65,9 +65,9 @@ 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.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.VCFHeaderLine; -import org.broadinstitute.variant.vcf.VCFSimpleHeaderLine; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFSimpleHeaderLine; import java.io.File; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java index e6f460d1a..4ec950623 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java @@ -47,7 +47,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs; import com.google.java.contract.Ensures; -import net.sf.samtools.Cigar; +import htsjdk.samtools.Cigar; import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.utils.sam.CigarUtils; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java index c696c50ae..0a4264046 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java @@ -47,9 +47,9 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading; import com.google.java.contract.Ensures; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.smithwaterman.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java index 8b342dcd7..233445b18 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java @@ -46,11 +46,11 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.SamPairUtil; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMRecordComparator; -import net.sf.samtools.SAMRecordCoordinateComparator; +import htsjdk.samtools.SamPairUtil; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMRecordComparator; +import htsjdk.samtools.SAMRecordCoordinateComparator; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java index cd4ea778d..c299462ba 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java @@ -46,14 +46,14 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.haplotype.Haplotype; 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.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.Arrays; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index bd1125354..ea0f53579 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -46,11 +46,11 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.*; -import net.sf.samtools.util.RuntimeIOException; -import net.sf.samtools.util.SequenceUtil; -import net.sf.samtools.util.StringUtil; -import org.broad.tribble.Feature; +import htsjdk.samtools.*; +import htsjdk.samtools.util.RuntimeIOException; +import htsjdk.samtools.util.SequenceUtil; +import htsjdk.samtools.util.StringUtil; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; @@ -79,7 +79,7 @@ import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.File; import java.io.FileNotFoundException; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java index 532d13690..4a3e65d02 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java @@ -46,8 +46,8 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.Cigar; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index aa8b46312..27ce8c0af 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -61,7 +61,7 @@ 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.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.Arrays; import java.util.LinkedHashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index caeb1e8d7..f87823735 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -63,7 +63,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.PrintStream; import java.util.ArrayList; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java index 5453cbfd8..259734ab9 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java @@ -47,8 +47,8 @@ package org.broadinstitute.sting.gatk.walkers.phasing; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; import java.util.ArrayList; import java.util.List; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java index 98b9682d7..cc2a19131 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java @@ -46,17 +46,17 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import net.sf.picard.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFile; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.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.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.io.File; import java.io.FileNotFoundException; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index 707bf2722..ed39a2896 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -61,11 +61,11 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.io.PrintStream; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java index bb8c14ef7..b5a6a5f69 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java @@ -46,15 +46,15 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.samtools.util.StringUtil; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.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.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index 7ed77b845..79255c7f8 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -64,15 +64,15 @@ import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.HasGenomeLocation; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.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.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java index 8dca985c8..f40b24101 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java @@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.phasing; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; class SNPallelePair extends AllelePair { diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/OverhangFixingManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/OverhangFixingManager.java index 581a9e426..b6f9f083d 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/OverhangFixingManager.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/OverhangFixingManager.java @@ -46,8 +46,8 @@ package org.broadinstitute.sting.gatk.walkers.rnaseq; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMRecordCoordinateComparator; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMRecordCoordinateComparator; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java index b21a133c9..8dfa1cf7c 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.rnaseq; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java index a1f4fae49..e389292b7 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java @@ -48,9 +48,9 @@ package org.broadinstitute.sting.gatk.walkers.simulatereads; import cern.jet.random.Poisson; import cern.jet.random.engine.MersenneTwister; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMProgramRecord; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMProgramRecord; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; @@ -61,8 +61,8 @@ import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.*; -import org.broadinstitute.variant.vcf.*; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.vcf.*; +import htsjdk.variant.variantcontext.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.text.TextFormattingUtils; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java index 50687378c..288bcb6d8 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java @@ -57,13 +57,13 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.vcf.VCFUtils; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.VCFUtils; import java.util.Map; import java.util.Set; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java index ed6af3035..5fbededeb 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java @@ -47,7 +47,7 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java index 5f862862e..6a0d1a956 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java @@ -49,7 +49,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.TreeSet; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java index ff3ad26d0..7bb59e721 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.TreeSet; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java index 5fefd11cf..954398c4f 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java @@ -49,9 +49,9 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import java.util.HashMap; import java.util.List; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java index 79daef7d4..af9aa05e9 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java @@ -49,9 +49,9 @@ 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.variant.vcf.VCFConstants; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextUtils; import java.util.ArrayList; import java.util.Collections; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java index 661dcc844..c88b70c8f 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.TreeSet; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java index 36c4552d0..552f48499 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.TreeSet; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java index 946529e75..8de485ef2 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java @@ -48,9 +48,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextUtils; import java.util.ArrayList; import java.util.Collections; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java index ad723f0cf..53d367810 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java @@ -56,12 +56,12 @@ import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java index 4b5237087..95fcc6728 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java @@ -59,12 +59,12 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java index b989483cf..545b616d2 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java @@ -49,7 +49,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; /** * Created by IntelliJ IDEA. diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index f16399e62..9caef9248 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -53,15 +53,15 @@ 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.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index c5e2b8183..cb73cacb6 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -61,14 +61,14 @@ import org.broadinstitute.sting.utils.R.RScriptExecutor; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.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.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.FileNotFoundException; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java index 4d5554f4d..cf600ed4c 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java @@ -60,9 +60,9 @@ import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.HomoSapiensConstants; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFs.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFs.java index 3c53d81c9..98c8922f5 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFs.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFs.java @@ -61,9 +61,9 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java index 093bb061b..cdd6f7f5d 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java @@ -66,9 +66,9 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java index bfd8edf30..f5f3a40b0 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java @@ -50,8 +50,8 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFConstants; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java index 97bb8166a..14ced08b0 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java @@ -60,13 +60,13 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.variantcontext.Genotype; -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.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import java.util.Arrays; import java.util.Collection; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gga/GenotypingGivenAllelesUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gga/GenotypingGivenAllelesUtils.java index 72df5d35b..a3ef22cfc 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gga/GenotypingGivenAllelesUtils.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gga/GenotypingGivenAllelesUtils.java @@ -51,8 +51,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.LinkedHashSet; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java index 71d61c920..ca49751a0 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java @@ -47,12 +47,12 @@ package org.broadinstitute.sting.utils.gvcf; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.*; import java.util.Collections; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java index 9d14fca26..1307cbf21 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java @@ -47,10 +47,10 @@ package org.broadinstitute.sting.utils.gvcf; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLine; import java.util.ArrayList; import java.util.List; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java index ba58c3ae8..81c4ede80 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java @@ -50,8 +50,8 @@ import com.google.java.contract.Requires; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/LDMerger.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/LDMerger.java index bbedd1b1a..02bf2a675 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/LDMerger.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/LDMerger.java @@ -50,9 +50,9 @@ import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java index 2a435f10d..b5fe31255 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java @@ -51,7 +51,7 @@ import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java index 4d48ca82a..82bfdabe0 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java @@ -51,7 +51,7 @@ import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.Collection; import java.util.HashMap; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java index 2a7ead6c2..6625c4434 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java @@ -46,9 +46,9 @@ package org.broadinstitute.sting.utils.haplotypeBAMWriter; -import net.sf.samtools.Cigar; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMTag; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMTag; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java index 007b5402e..7c75fca12 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java @@ -46,9 +46,9 @@ package org.broadinstitute.sting.utils.haplotypeBAMWriter; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java index b80036bb2..fc615b608 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java @@ -49,7 +49,7 @@ package org.broadinstitute.sting.utils.pairhmm; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.io.File; import java.lang.reflect.Field; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java index ea93ebe4a..ff26f1095 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java @@ -53,7 +53,7 @@ import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import org.broadinstitute.sting.utils.exceptions.UserException; import static org.broadinstitute.sting.utils.pairhmm.PairHMMModel.*; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java index 15195728b..e7ce367ce 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java @@ -53,7 +53,7 @@ import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.List; import java.util.Map; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java index 419dbaca6..cb1de0fb6 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java @@ -47,8 +47,8 @@ package org.broadinstitute.sting.utils.recalibration; import com.google.java.contract.Ensures; -import net.sf.samtools.SAMTag; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.SAMTag; +import htsjdk.samtools.SAMUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index ea3781204..542f07679 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatum.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -74,7 +74,7 @@ package org.broadinstitute.sting.utils.recalibration; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; import com.google.java.contract.Requires; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.SAMUtils; import org.apache.commons.math.optimization.fitting.GaussianFunction; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummariesUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummariesUnitTest.java index 57eadfbdb..775897223 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummariesUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummariesUnitTest.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepthUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepthUnitTest.java index a118a462d..a02530c83 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepthUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepthUnitTest.java @@ -47,7 +47,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator; import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 7776e979a..60122047d 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -46,12 +46,12 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broad.tribble.readers.LineIterator; -import org.broad.tribble.readers.PositionalBufferedStream; +import htsjdk.tribble.readers.LineIterator; +import htsjdk.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java index 6d6761f1c..6bec5c6ec 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java @@ -46,15 +46,15 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.vcf.VCFConstants; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java index 39cf719dd..dce7f983e 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.bqsr; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.SAMUtils; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.recalibration.ReadCovariates; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java index 294470805..49f41d613 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java @@ -51,8 +51,8 @@ package org.broadinstitute.sting.gatk.walkers.diffengine; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java index b5c8b3f99..4fcb7698a 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java @@ -46,8 +46,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java index cc5576500..2846352ca 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.SAMUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.Walker; @@ -54,7 +54,7 @@ import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java index 445864380..7bd75353d 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java @@ -50,7 +50,7 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.*; import static org.testng.Assert.assertEquals; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java index e05cb89cc..205390c41 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java @@ -55,10 +55,10 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.GenotypeLikelihoods; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index f0d0c954a..605d4a226 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -46,14 +46,14 @@ package org.broadinstitute.sting.gatk.walkers.genotyper; -import net.sf.samtools.util.BlockCompressedInputStream; -import org.broad.tribble.readers.AsciiLineReader; +import htsjdk.samtools.util.BlockCompressedInputStream; +import htsjdk.tribble.readers.AsciiLineReader; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java index 8deddc357..fc354d875 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java @@ -50,8 +50,8 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java index c99692b1f..a79d48346 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java @@ -50,7 +50,7 @@ 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.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java index c52a36853..8cd96e7eb 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java @@ -52,7 +52,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotypingEngine; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java index 2a1128ae2..1b2dfe6e7 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java @@ -48,10 +48,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.GenotypesContext; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java index c9476f7eb..a3a70d91c 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java @@ -49,10 +49,10 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java index 664afda51..329fc54d8 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java @@ -45,7 +45,7 @@ */ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.SeqGraph; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingGraph; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java index cfdda7c4d..05de40cee 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java @@ -46,9 +46,9 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; import com.google.java.contract.Requires; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import java.util.*; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java index de6d5f8cd..f3e48209d 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngineUnitTest.java @@ -52,7 +52,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; * Date: 3/15/12 */ -import net.sf.picard.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; @@ -63,7 +63,7 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index b16aa38b7..cc32d3daf 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -46,16 +46,16 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broad.tribble.readers.LineIterator; -import org.broad.tribble.readers.PositionalBufferedStream; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.tribble.readers.LineIterator; +import htsjdk.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java index 9f13efc9c..7742c6f58 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java @@ -46,11 +46,11 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading.ReadThreadingAssembler; import org.broadinstitute.sting.utils.GenomeLoc; @@ -61,9 +61,9 @@ import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java index 16a3e9af2..e9c7ae3d8 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java @@ -58,7 +58,7 @@ import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.pairhmm.PairHMM; import org.broadinstitute.sting.utils.recalibration.covariates.RepeatCovariate; import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java index a6d2644cd..80190e837 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java @@ -57,7 +57,7 @@ import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM; import org.broadinstitute.sting.utils.pairhmm.PairHMM; import org.broadinstitute.sting.utils.sam.ClippedGATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.Reporter; import org.testng.SkipException; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java index 1cb64916c..069d1882e 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.activeregion.ActiveRegion; @@ -58,7 +58,7 @@ 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.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java index 26c511b6e..643c21188 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestHaplotypeFinderUnitTest.java @@ -46,10 +46,10 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.sam.AlignmentUtils; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java index da59b523a..876918816 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs; -import net.sf.samtools.Cigar; +import htsjdk.samtools.Cigar; import org.broadinstitute.sting.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java index a13bc4754..bbafba5de 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.KBestHaplotype; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.KBestHaplotypeFinder; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java index 0f910507e..842fa873e 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java @@ -46,8 +46,8 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerUnitTest.java index 509bf7465..22a6407c4 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerUnitTest.java @@ -46,8 +46,8 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java index 3480b6775..56c1ffb66 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java @@ -47,15 +47,15 @@ package org.broadinstitute.sting.gatk.walkers.indels; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java index 3ce0211c4..41f473cfb 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java @@ -46,10 +46,10 @@ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broad.tribble.readers.LineIterator; -import org.broad.tribble.readers.PositionalBufferedStream; +import htsjdk.tribble.readers.LineIterator; +import htsjdk.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsUnitTest.java index d0f8280af..9e70df34a 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsUnitTest.java @@ -46,9 +46,9 @@ package org.broadinstitute.sting.gatk.walkers.rnaseq; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.clipping.ReadClipperTestUtils; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java index 3e558b2dc..e759b44f8 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java @@ -58,9 +58,9 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java index 120e4bea2..81b793f4f 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java @@ -48,7 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import junit.framework.Assert; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFConstants; import org.testng.annotations.Test; /** diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index c4de50b25..7d19eafb7 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -48,9 +48,9 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFsIntegrationTest.java index 41f1cea53..cbbf612c4 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFsIntegrationTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineGVCFsIntegrationTest.java @@ -48,7 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java index f369ad210..f2771e56b 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java @@ -46,12 +46,12 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.readers.PositionalBufferedStream; +import htsjdk.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.variant.vcf.VCFCodec; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; -import org.broadinstitute.variant.vcf.VCFUtils; +import htsjdk.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFUtils; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java index 9031ea7f1..51b65425b 100755 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java @@ -46,17 +46,17 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import net.sf.picard.reference.ReferenceSequenceFile; -import org.broad.tribble.readers.PositionalBufferedStream; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.VCFCodec; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFHeader; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java index a8739dac2..f62b9c290 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java @@ -46,9 +46,9 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; @@ -59,9 +59,9 @@ import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java index 33d57d801..bb02a7990 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java @@ -55,8 +55,8 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFConstants; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java index e5df1a349..41ac6d6ca 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java @@ -46,9 +46,9 @@ package org.broadinstitute.sting.utils; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.testng.Assert; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java index 08d82281e..f7ce58b4c 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java @@ -47,7 +47,7 @@ package org.broadinstitute.sting.utils.genotyper; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java index 651beffc8..2ae037d90 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java @@ -46,9 +46,9 @@ package org.broadinstitute.sting.utils.genotyper; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -59,7 +59,7 @@ import java.util.Map; import java.util.List; import org.testng.Assert; import org.testng.annotations.Test; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java index cda022ab8..690ad8570 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java @@ -50,10 +50,10 @@ import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.ReferenceConfidenceModel; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFHeader; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java index ec4797f3d..d26ce77c1 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java @@ -47,10 +47,10 @@ package org.broadinstitute.sting.utils.gvcf; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java index a2c69e535..120e2242b 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java @@ -46,12 +46,12 @@ package org.broadinstitute.sting.utils.haplotype; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java index 1f66abe28..40d436667 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.utils.haplotypeBAMWriter; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java index 1e5417227..714d11b46 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java @@ -46,9 +46,9 @@ package org.broadinstitute.sting.utils.pairhmm; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.apache.commons.math.distribution.ExponentialDistribution; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.AssemblyResult; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.AssemblyResultSet; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java index 9706c0e9d..9160e2f66 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java @@ -48,9 +48,9 @@ package org.broadinstitute.sting.utils.pairhmm; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.sam.AlignmentUtils; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java index e6c8e1e61..9cb4583ff 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.utils.pairhmm; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.SAMUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.text.XReadLines; diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java index 711a60436..43c929bc9 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java @@ -46,7 +46,7 @@ package org.broadinstitute.sting.utils.smithwaterman; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.sam.AlignmentUtils; diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml index a26b7134b..87375c843 100644 --- a/public/external-example/pom.xml +++ b/public/external-example/pom.xml @@ -146,13 +146,7 @@ - org.broad:tribble - - ** - - - - org.broadinstitute:variant + samtools:htsjdk ** diff --git a/public/gatk-framework/src/main/java/net/sf/samtools/GATKBAMFileSpan.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java similarity index 99% rename from public/gatk-framework/src/main/java/net/sf/samtools/GATKBAMFileSpan.java rename to public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java index dc36e83c2..b68cd499e 100644 --- a/public/gatk-framework/src/main/java/net/sf/samtools/GATKBAMFileSpan.java +++ b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java @@ -23,9 +23,9 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package net.sf.samtools; +package htsjdk.samtools; -import net.sf.picard.util.PeekableIterator; +import htsjdk.samtools.util.PeekableIterator; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; diff --git a/public/gatk-framework/src/main/java/net/sf/samtools/GATKBin.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java similarity index 99% rename from public/gatk-framework/src/main/java/net/sf/samtools/GATKBin.java rename to public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java index 463707252..d1e689d63 100644 --- a/public/gatk-framework/src/main/java/net/sf/samtools/GATKBin.java +++ b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package net.sf.samtools; +package htsjdk.samtools; import java.util.ArrayList; import java.util.Collections; diff --git a/public/gatk-framework/src/main/java/net/sf/samtools/GATKChunk.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java similarity index 99% rename from public/gatk-framework/src/main/java/net/sf/samtools/GATKChunk.java rename to public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java index db52402a4..6d695f43c 100644 --- a/public/gatk-framework/src/main/java/net/sf/samtools/GATKChunk.java +++ b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package net.sf.samtools; +package htsjdk.samtools; /** * A temporary solution to work around Java access rights issues: diff --git a/public/gatk-framework/src/main/java/net/sf/samtools/PicardNamespaceUtils.java b/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java similarity index 98% rename from public/gatk-framework/src/main/java/net/sf/samtools/PicardNamespaceUtils.java rename to public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java index 131793268..00f65e54c 100644 --- a/public/gatk-framework/src/main/java/net/sf/samtools/PicardNamespaceUtils.java +++ b/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package net.sf.samtools; +package htsjdk.samtools; /** * Utils that insist on being in the same package as Picard. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Aligner.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Aligner.java index 1a9369cbb..b171b5f49 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Aligner.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Aligner.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.alignment; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; /** * Create perfect alignments from the read to the genome represented by the given BWT / suffix array. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Alignment.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Alignment.java index a4e04ab5d..1db842045 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Alignment.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/Alignment.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.alignment; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWTFiles.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWTFiles.java index 780b8b035..58ee44645 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWTFiles.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/BWTFiles.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.alignment.bwa; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; -import net.sf.samtools.util.StringUtil; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; +import htsjdk.samtools.util.StringUtil; import org.broadinstitute.sting.alignment.reference.bwt.*; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; import org.broadinstitute.sting.utils.Utils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java index 25119c3bc..d09e7f038 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.alignment.bwa.c; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.bwa.BWAAligner; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java index 169ad7aa5..5e2d6e94d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.alignment.bwa.java; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.*; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.*; import org.broadinstitute.sting.alignment.Aligner; import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.utils.BaseUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java index 39ad9072c..04022581b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.alignment.bwa.java; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayDeque; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java index a1843746a..7b9b4ea04 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.alignment.bwa.java; -import net.sf.samtools.Cigar; +import htsjdk.samtools.Cigar; import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java index f60218fe9..98c447b06 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.alignment.bwa.java; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.bwa.BWAAligner; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java index 8818cdeb1..3432c7f61 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import java.io.File; import java.io.IOException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java index 07ad0d39f..1de24410d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/ANNWriter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import java.io.File; import java.io.IOException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java index 1f51a7c6a..9f1e7933a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.picard.reference.ReferenceSequenceFileFactory; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFileFactory; +import htsjdk.samtools.SAMSequenceDictionary; import java.io.File; import java.io.IOException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java index 862ce6468..0f0d3a994 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import net.sf.picard.reference.ReferenceSequence; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.picard.reference.ReferenceSequenceFileFactory; +import htsjdk.samtools.reference.ReferenceSequence; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFileFactory; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java index c6e256a34..1d15770d3 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import net.sf.samtools.util.StringUtil; +import htsjdk.samtools.util.StringUtil; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.Comparator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java index e26f2996e..a6719c2eb 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.alignment.reference.packing; -import net.sf.picard.reference.ReferenceSequence; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.picard.reference.ReferenceSequenceFileFactory; +import htsjdk.samtools.reference.ReferenceSequence; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFileFactory; import java.io.File; import java.io.IOException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index 9ab317251..be81b491f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.commandline; import org.apache.commons.io.FileUtils; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.gatk.walkers.Multiplex; import org.broadinstitute.sting.gatk.walkers.Multiplexer; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java index d2a1735fb..34d96d979 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalSetRule; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalBinding.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalBinding.java index de57de871..7bd80d5d2 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalBinding.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/IntervalBinding.java @@ -26,10 +26,10 @@ package org.broadinstitute.sting.commandline; import com.google.java.contract.Requires; -import org.broad.tribble.AbstractFeatureReader; -import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; -import org.broad.tribble.FeatureReader; +import htsjdk.tribble.AbstractFeatureReader; +import htsjdk.tribble.Feature; +import htsjdk.tribble.FeatureCodec; +import htsjdk.tribble.FeatureReader; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBinding.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBinding.java index 87fa85858..98a06313a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBinding.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBinding.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.commandline; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBindingCollection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBindingCollection.java index d8306ea5a..a806788de 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBindingCollection.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBindingCollection.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.commandline; import com.google.java.contract.Ensures; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.utils.exceptions.UserException; import java.lang.reflect.Constructor; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineGATK.java index 728fee5c8..237366ae7 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineGATK.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineGATK.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk; -import net.sf.picard.PicardException; -import net.sf.samtools.SAMException; -import org.broad.tribble.TribbleException; +import picard.PicardException; +import htsjdk.samtools.SAMException; +import htsjdk.tribble.TribbleException; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.CommandLineProgram; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 9eee9b7e4..682dc50d5 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -26,11 +26,11 @@ package org.broadinstitute.sting.gatk; import com.google.java.contract.Ensures; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; @@ -64,7 +64,7 @@ import org.broadinstitute.sting.utils.progressmeter.ProgressMeter; import org.broadinstitute.sting.utils.recalibration.BQSRArgumentSet; import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.threading.ThreadEfficiencyMonitor; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFConstants; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadMetrics.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadMetrics.java index 29372abcd..371add094 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadMetrics.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadMetrics.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk; -import net.sf.picard.filter.SamRecordFilter; +import htsjdk.samtools.filter.SamRecordFilter; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.HashMap; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadProperties.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadProperties.java index 1ca0a8a46..b4f12b796 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadProperties.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/ReadProperties.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileReader; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileReader; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java index 9cd80d11b..7ff3622f5 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java +++ b/public/gatk-framework/src/main/java/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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; /** * @author ebanks diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 7b147ec6d..08597adc6 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.arguments; -import net.sf.samtools.SAMFileReader; +import htsjdk.samtools.SAMFileReader; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.downsampling.DownsampleType; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java index 202005e2e..10aea1537 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; /** * @author ebanks diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java index 0bd5f66c4..323006635 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.contexts; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java index 3aff745fa..ed1f25544 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.picard.util.PeekableIterator; +import htsjdk.samtools.util.PeekableIterator; import org.broadinstitute.sting.gatk.refdata.RODRecordListImpl; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java index 5e884ce53..ea195d7eb 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.picard.util.PeekableIterator; +import htsjdk.samtools.util.PeekableIterator; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.reads.ReadShard; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java index b5efbc693..b10a274a5 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.picard.reference.ReferenceSequence; +import htsjdk.samtools.reference.ReferenceSequence; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.Walker; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java index 45c9af995..46a67d05e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java index 84e27c953..1774c11b7 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java @@ -27,8 +27,8 @@ package org.broadinstitute.sting.gatk.datasources.providers; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.picard.util.PeekableIterator; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.util.PeekableIterator; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.datasources.reads.ReadShard; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java index 5fabb313f..980dc720c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; /* diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java index 5c1724378..7ef00f038 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java index 8df06b0ac..4430ed37f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import java.util.Arrays; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java index e2cf84ad7..9b3d5d40d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.picard.reference.ReferenceSequence; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.ReferenceSequence; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java index 37db2fb84..60e2b8497 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.gatk.datasources.reads.Shard; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java index 00b3351fa..368dc7622 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java @@ -25,11 +25,10 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.util.PeekableIterator; -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.GATKChunk; -import net.sf.samtools.util.BlockCompressedFilePointerUtil; -import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import htsjdk.samtools.util.PeekableIterator; +import htsjdk.samtools.GATKBAMFileSpan; +import htsjdk.samtools.GATKChunk; +import htsjdk.samtools.util.BlockCompressedFilePointerUtil; import java.util.LinkedList; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java index baa105985..44633af17 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java @@ -25,11 +25,11 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.util.PeekableIterator; -import net.sf.samtools.Bin; -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.GATKChunk; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.util.PeekableIterator; +import htsjdk.samtools.Bin; +import htsjdk.samtools.GATKBAMFileSpan; +import htsjdk.samtools.GATKChunk; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java index 2f03edb68..2cb3eafb4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.util.PeekableIterator; -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.GATKChunk; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.util.PeekableIterator; +import htsjdk.samtools.GATKBAMFileSpan; +import htsjdk.samtools.GATKChunk; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocSortedSet; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java index 1bac2fb74..a0366ac2b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.GATKChunk; -import net.sf.samtools.util.BlockCompressedInputStream; +import htsjdk.samtools.GATKBAMFileSpan; +import htsjdk.samtools.GATKChunk; +import htsjdk.samtools.util.BlockCompressedInputStream; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.IOException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java index 72b778ec9..2b3d28bab 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.util.BlockCompressedStreamConstants; +import htsjdk.samtools.util.BlockCompressedStreamConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.FileInputStream; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java index 517903da3..46842441c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java @@ -25,11 +25,11 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.util.PeekableIterator; -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.GATKChunk; -import net.sf.samtools.SAMFileSpan; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.util.PeekableIterator; +import htsjdk.samtools.GATKBAMFileSpan; +import htsjdk.samtools.GATKChunk; +import htsjdk.samtools.SAMFileSpan; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java index 6c7a6c867..7594ea28c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.Bin; -import net.sf.samtools.GATKBin; -import net.sf.samtools.GATKChunk; -import net.sf.samtools.LinearIndex; -import net.sf.samtools.seekablestream.SeekableBufferedStream; -import net.sf.samtools.seekablestream.SeekableFileStream; +import htsjdk.samtools.Bin; +import htsjdk.samtools.GATKBin; +import htsjdk.samtools.GATKChunk; +import htsjdk.samtools.LinearIndex; +import htsjdk.samtools.seekablestream.SeekableBufferedStream; +import htsjdk.samtools.seekablestream.SeekableFileStream; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java index c397b5a93..f87779572 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.*; +import htsjdk.samtools.*; import java.util.ArrayList; import java.util.Collections; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java index 2cbfa0d7a..373aa51af 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.AlignmentUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java index b476945ce..6a491e75e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.util.PeekableIterator; +import htsjdk.samtools.util.PeekableIterator; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocSortedSet; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java index 4bef8ae40..12a5d7ec6 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.SAMFileSpan; +import htsjdk.samtools.SAMFileSpan; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java index 63ac6944a..3fd0aa98f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.util.PeekableIterator; -import net.sf.samtools.*; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.util.PeekableIterator; +import htsjdk.samtools.*; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java index dc1b80efd..04f70b894 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.util.PeekableIterator; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.util.PeekableIterator; +import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index e8a2455e4..4468a6e19 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -25,11 +25,11 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.sam.MergingSamRecordIterator; -import net.sf.picard.sam.SamFileHeaderMerger; -import net.sf.samtools.*; -import net.sf.samtools.util.CloseableIterator; -import net.sf.samtools.util.RuntimeIOException; +import htsjdk.samtools.MergingSamRecordIterator; +import htsjdk.samtools.SamFileHeaderMerger; +import htsjdk.samtools.*; +import htsjdk.samtools.util.CloseableIterator; +import htsjdk.samtools.util.RuntimeIOException; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadProperties; @@ -640,7 +640,7 @@ public class SAMDataSource { final long stopCoordinate = inputStream.getFilePointer(); if(reader != null && nextRead != null) - PicardNamespaceUtils.setFileSource(nextRead,new SAMFileSource(reader,new GATKBAMFileSpan(new GATKChunk(startCoordinate,stopCoordinate)))); + PicardNamespaceUtils.setFileSource(nextRead, new SAMFileSource(reader, new GATKBAMFileSpan(new GATKChunk(startCoordinate, stopCoordinate)))); } } @@ -1130,7 +1130,7 @@ public class SAMDataSource { File indexFile; try { - Class bamFileReaderClass = Class.forName("net.sf.samtools.BAMFileReader"); + Class bamFileReaderClass = Class.forName("htsjdk.samtools.BAMFileReader"); Method indexFileLocator = bamFileReaderClass.getDeclaredMethod("findIndexFile",File.class); indexFileLocator.setAccessible(true); indexFile = (File)indexFileLocator.invoke(null,bamFile); diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/Shard.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/Shard.java index 5b4c2afda..fadeb2452 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/Shard.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/Shard.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.util.PeekableIterator; -import net.sf.samtools.SAMFileSpan; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.util.PeekableIterator; +import htsjdk.samtools.SAMFileSpan; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java index 37f1bcfac..bf00a0ff8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.util.PeekableIterator; +import htsjdk.samtools.util.PeekableIterator; import org.broadinstitute.sting.utils.GenomeLocParser; import java.util.Iterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java index cfd836f46..5f1171582 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.reads.utilities; -import net.sf.samtools.BAMIndex; -import net.sf.samtools.SAMFileReader; +import htsjdk.samtools.BAMIndex; +import htsjdk.samtools.SAMFileReader; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java index 2d86836fd..f21f1f76a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.datasources.reads.utilities; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMFileWriterFactory; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMFileWriterFactory; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.CommandLineProgram; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java index 66463e576..52298cef9 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads.utilities; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.Input; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java index f7076450b..70d775775 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.datasources.reads.utilities; -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.GATKChunk; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecordIterator; +import htsjdk.samtools.GATKBAMFileSpan; +import htsjdk.samtools.GATKChunk; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMRecordIterator; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java index d6024b9cc..9dbe3e6e4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads.utilities; -import net.sf.samtools.util.BlockGunzipper; +import htsjdk.samtools.util.BlockGunzipper; import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.Input; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java index edd3d324c..8ea4376fd 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.reference; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.gatk.datasources.reads.LocusShard; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; import org.broadinstitute.sting.gatk.datasources.reads.Shard; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java index 0b35e57b1..b2c4832e1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.rmd; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceDictionary; import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java index 3e1860517..9fd701aa5 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.rmd; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceDictionary; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java index 5b0e19ba4..a94e6fbf1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.rmd; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java index 56c370276..ecbe7376c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.text.XReadLines; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.io.File; import java.io.IOException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIterator.java index 5ec82474e..16beeaa6e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIterator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import java.util.Collection; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java index c40f8019e..5337ffe6d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerFactory.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerFactory.java index 60d37b774..000badad9 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerFactory.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerFactory.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Factory for creating FractionalDownsamplers on demand diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java index 1eabf5038..907803a1f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import java.util.LinkedList; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java index e76ce6cb3..b13c303d6 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMRecordComparator; -import net.sf.samtools.SAMRecordCoordinateComparator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMRecordComparator; +import htsjdk.samtools.SAMRecordCoordinateComparator; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsampler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsampler.java index a8df014e5..b3d709e69 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsampler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsampler.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * An extension of the basic downsampler API with reads-specific operations diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsamplerFactory.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsamplerFactory.java index c8a6b6c01..453d34e07 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsamplerFactory.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReadsDownsamplerFactory.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * A ReadsDownsamplerFactory can be used to create an arbitrary number of instances of a particular diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java index ff085d17b..0b637528e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerFactory.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerFactory.java index 7e8fe05e4..2da45826e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerFactory.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerFactory.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Factory for creating ReservoirDownsamplers on demand diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsampler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsampler.java index 897e2c05e..79bb97234 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsampler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsampler.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerFactory.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerFactory.java index 0c4003e7d..42a43c224 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerFactory.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerFactory.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Factory for creating SimplePositionalDownsamplers on demand diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index 2ea2633ee..753e396db 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.executive; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broad.tribble.TribbleException; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.tribble.TribbleException; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; import org.broadinstitute.sting.gatk.datasources.reads.Shard; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java index dc46849df..ddc8c6fe4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.executive; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index 405c07392..d6e50d748 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/MicroScheduler.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.executive; import com.google.java.contract.Ensures; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.ReadMetrics; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/WindowMaker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/WindowMaker.java index e9a2b56c2..22e91a4ab 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/WindowMaker.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/executive/WindowMaker.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.executive; -import net.sf.picard.util.PeekableIterator; +import htsjdk.samtools.util.PeekableIterator; import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.datasources.reads.Shard; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java index 85c60f02d..5b7885333 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMRecord; import java.util.Iterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadMateFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadMateFilter.java index 7bf4db1cc..cce82536e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadMateFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/BadMateFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Filter out reads whose mate maps to a different contig. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java index 37f919417..e8713c7b4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; -import net.sf.samtools.util.CloserUtil; +import htsjdk.samtools.filter.SamRecordFilter; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; +import htsjdk.samtools.util.CloserUtil; import org.broadinstitute.sting.gatk.ReadMetrics; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java index 08969eec6..bda7b6afc 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /* * Copyright (c) 2009 The Broad Institute diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java index 1b5b03c65..1a981492f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Filter out reads that fail the vendor quality check. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/LibraryReadFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/LibraryReadFilter.java index 39bcb96e1..39eef52fe 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/LibraryReadFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/LibraryReadFilter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.gatk.filters.ReadFilter; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java index 3167ba139..7082fa8a0 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.ReadProperties; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java index ebb8505c0..4c7af592d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java index 1d122ded5..27622c5f1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.QualityUtils; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java index 99d313f72..b0a0c708b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Filter out mapping quality zero reads. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java index ffae96bc2..98b665407 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Filter out reads that are not paired, have their mate unmapped, are duplicates, fail vendor quality check or both mate and read are in the same strand. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java index ea18ad368..14978916f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java index 21a832cdf..d686815c0 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Filter out reads without read groups. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformer.java index 144f3af5c..81b24a317 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformer.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformer.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.iterators.RNAReadTransformer; import org.broadinstitute.sting.gatk.iterators.ReadTransformer; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java index ade5ab079..9592fd751 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /* * Copyright (c) 2009 The Broad Institute diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java index 789ee9839..d1974368b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Filter out duplicate reads. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/Platform454Filter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/Platform454Filter.java index f30cf9d09..94dcb5cb5 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/Platform454Filter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/Platform454Filter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformFilter.java index 00bbe798b..1560b3157 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.ReadUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java index 9aa77e38e..a713b58d7 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java @@ -1,32 +1,32 @@ -/* -* Copyright (c) 2012 The Broad Institute -* -* Permission is hereby granted, free of charge, to any person -* obtaining a copy of this software and associated documentation -* files (the "Software"), to deal in the Software without -* restriction, including without limitation the rights to use, -* copy, modify, merge, publish, distribute, sublicense, and/or sell -* copies of the Software, and to permit persons to whom the -* Software is furnished to do so, subject to the following -* conditions: -* -* The above copyright notice and this permission notice shall be -* included in all copies or substantial portions of the Software. -* -* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES -* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR -* THE USE OR OTHER DEALINGS IN THE SOFTWARE. -*/ - +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.HashSet; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadFilter.java index 2387312b9..f8c49728c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadFilter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.picard.filter.SamRecordFilter; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.filter.SamRecordFilter; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java index ed06572c3..2b900a6c3 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.text.XReadLines; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadLengthFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadLengthFilter.java index 80224b786..5e17f6046 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadLengthFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadLengthFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java index 7da46690c..9e15e28dc 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java index ce1568dba..c3df813f6 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java index e576666e1..0a44915cd 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java index 232b7ed3d..e732116c6 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SampleFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SampleFilter.java index 76beed96c..b05145c6d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SampleFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SampleFilter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; import java.util.Set; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java index a71b3a853..80c993194 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.commandline.Argument; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java index d4576bb76..bd3f60905 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Filter out unmapped reads. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/OutputTracker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/OutputTracker.java index 1c3f9d991..7d3bd174f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/OutputTracker.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/OutputTracker.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.io; -import net.sf.samtools.SAMFileReader; +import htsjdk.samtools.SAMFileReader; import org.broadinstitute.sting.commandline.ArgumentSource; import org.broadinstitute.sting.gatk.io.storage.Storage; import org.broadinstitute.sting.gatk.io.storage.StorageFactory; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java index 12375c5b5..4da62850b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.io; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileWriter; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileWriter; /** * A writer that will allow unsorted BAM files to be written diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java index ebb387a8c..f5f71f265 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.io.storage; -import net.sf.samtools.*; -import net.sf.samtools.util.CloseableIterator; -import net.sf.samtools.util.ProgressLoggerInterface; -import net.sf.samtools.util.RuntimeIOException; +import htsjdk.samtools.*; +import htsjdk.samtools.util.CloseableIterator; +import htsjdk.samtools.util.ProgressLoggerInterface; +import htsjdk.samtools.util.RuntimeIOException; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java index 52a85c358..ed3a5778b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java @@ -25,21 +25,21 @@ package org.broadinstitute.sting.gatk.io.storage; -import net.sf.samtools.util.BlockCompressedOutputStream; +import htsjdk.samtools.util.BlockCompressedOutputStream; import org.apache.log4j.Logger; -import org.broad.tribble.AbstractFeatureReader; -import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; +import htsjdk.tribble.AbstractFeatureReader; +import htsjdk.tribble.Feature; +import htsjdk.tribble.FeatureCodec; import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.bcf2.BCF2Utils; -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.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.variant.bcf2.BCF2Utils; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.Options; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.vcf.VCFHeader; import java.io.*; import java.util.Arrays; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java index 4fe90f3c7..f7c478336 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.io.stubs; -import net.sf.samtools.SAMFileReader; +import htsjdk.samtools.SAMFileReader; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java index 3b89787ad..521b18e50 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.io.stubs; -import net.sf.samtools.SAMFileWriter; +import htsjdk.samtools.SAMFileWriter; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java index 3e5fe6d45..8581a0bc4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.io.stubs; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.ProgressLoggerInterface; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.ProgressLoggerInterface; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java index dbb6a3d58..c05b4ff23 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.gatk.io.stubs; -import org.broad.tribble.AbstractFeatureReader; +import htsjdk.tribble.AbstractFeatureReader; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.io.OutputStream; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java index e4210f280..7fae815f8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java @@ -25,17 +25,17 @@ package org.broadinstitute.sting.gatk.io.stubs; -import net.sf.samtools.SAMSequenceDictionary; -import org.broad.tribble.index.IndexCreator; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.tribble.index.IndexCreator; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -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.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.Options; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import java.io.File; import java.io.OutputStream; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java index c8f672e32..0464fa00d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.picard.sam.MergingSamRecordIterator; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.MergingSamRecordIterator; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import java.util.Iterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java index f5f4ec6f6..3a966f112 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.util.Iterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java index acea7391e..c5df3b711 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java index e217deac0..18988bc60 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import java.util.Iterator; import java.util.NoSuchElementException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java index 1296ce641..3344d4f51 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; /** * Iterates through a list of elements, tracking the number of elements it has seen. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java index f9d2f4802..a8f41948e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.sam.AlignmentUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java index fd5c03cc6..0b56c36a2 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; /** * * User: aaron diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java index 51c581924..cce97b30a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; import java.util.Iterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java index 2497ab4cd..1859ea1b8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java index e194a9c43..82d5a0fec 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.refdata; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java index 393581fcd..c708908ce 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.refdata; -import org.broad.tribble.FeatureCodec; +import htsjdk.tribble.FeatureCodec; import org.broadinstitute.sting.utils.GenomeLocParser; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java index fb95ba506..dbc477943 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java @@ -1,32 +1,32 @@ -/* -* Copyright (c) 2012 The Broad Institute -* -* Permission is hereby granted, free of charge, to any person -* obtaining a copy of this software and associated documentation -* files (the "Software"), to deal in the Software without -* restriction, including without limitation the rights to use, -* copy, modify, merge, publish, distribute, sublicense, and/or sell -* copies of the Software, and to permit persons to whom the -* Software is furnished to do so, subject to the following -* conditions: -* -* The above copyright notice and this permission notice shall be -* included in all copies or substantial portions of the Software. -* -* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES -* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR -* THE USE OR OTHER DEALINGS IN THE SOFTWARE. -*/ - +/* +* Copyright (c) 2012 The Broad Institute +* +* Permission is hereby granted, free of charge, to any person +* obtaining a copy of this software and associated documentation +* files (the "Software"), to deal in the Software without +* restriction, including without limitation the rights to use, +* copy, modify, merge, publish, distribute, sublicense, and/or sell +* copies of the Software, and to permit persons to whom the +* Software is furnished to do so, subject to the following +* conditions: +* +* The above copyright notice and this permission notice shall be +* included in all copies or substantial portions of the Software. +* +* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +* THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + package org.broadinstitute.sting.gatk.refdata; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index 09f053187..84465ec97 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -25,17 +25,17 @@ package org.broadinstitute.sting.gatk.refdata; -import net.sf.samtools.util.SequenceUtil; -import org.broad.tribble.Feature; -import org.broad.tribble.annotation.Strand; -import org.broad.tribble.dbsnp.OldDbSNPFeature; -import org.broad.tribble.gelitext.GeliTextFeature; +import htsjdk.samtools.util.SequenceUtil; +import htsjdk.tribble.Feature; +import htsjdk.tribble.annotation.Strand; +import htsjdk.tribble.dbsnp.OldDbSNPFeature; +import htsjdk.tribble.gelitext.GeliTextFeature; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java index 20e1d4f1c..0fce83845 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java @@ -27,14 +27,14 @@ package org.broadinstitute.sting.gatk.refdata.tracks; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; -import org.broad.tribble.NameAwareCodec; +import htsjdk.tribble.Feature; +import htsjdk.tribble.FeatureCodec; +import htsjdk.tribble.NameAwareCodec; 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.variant.vcf.AbstractVCFCodec; +import htsjdk.variant.vcf.AbstractVCFCodec; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.help.GATKDocUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java index caf45142f..b98ad4008 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java @@ -25,11 +25,11 @@ package org.broadinstitute.sting.gatk.refdata.tracks; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; -import org.broad.tribble.index.Index; -import org.broad.tribble.index.MutableIndex; +import htsjdk.tribble.index.Index; +import htsjdk.tribble.index.MutableIndex; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.utils.SequenceDictionaryUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java index 051b50d48..1b8e12c5b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.gatk.refdata.tracks; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.util.CloseableIterator; import org.apache.log4j.Logger; -import org.broad.tribble.AbstractFeatureReader; -import org.broad.tribble.CloseableTribbleIterator; -import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; +import htsjdk.tribble.AbstractFeatureReader; +import htsjdk.tribble.CloseableTribbleIterator; +import htsjdk.tribble.Feature; +import htsjdk.tribble.FeatureCodec; import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java index ea420295a..4a683e445 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java @@ -25,15 +25,15 @@ package org.broadinstitute.sting.gatk.refdata.tracks; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; -import org.broad.tribble.AbstractFeatureReader; -import org.broad.tribble.FeatureCodec; -import org.broad.tribble.Tribble; -import org.broad.tribble.TribbleException; -import org.broad.tribble.index.Index; -import org.broad.tribble.index.IndexFactory; -import org.broad.tribble.util.LittleEndianOutputStream; +import htsjdk.tribble.AbstractFeatureReader; +import htsjdk.tribble.FeatureCodec; +import htsjdk.tribble.Tribble; +import htsjdk.tribble.TribbleException; +import htsjdk.tribble.index.Index; +import htsjdk.tribble.index.IndexFactory; +import htsjdk.tribble.util.LittleEndianOutputStream; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java index 694e763dd..595bf39a4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.refdata.utils; -import net.sf.samtools.util.CloseableIterator; -import org.broad.tribble.CloseableTribbleIterator; -import org.broad.tribble.Feature; +import htsjdk.samtools.util.CloseableIterator; +import htsjdk.tribble.CloseableTribbleIterator; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java index 8cf764cae..d4a61e76a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.refdata.utils; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceDictionary; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.HasGenomeLocation; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java index cb97779e0..518c19115 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.refdata.utils; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java index 41e93c94d..ce3e5fe42 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.refdata.utils; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.utils.GenomeLoc; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDB.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDB.java index 0ca00dfdd..2530df6ab 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDB.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDB.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.samples; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.Genotype; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java index 40ef1e21c..45d5e258f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.samples; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java index 17f23de8f..b9ac812ab 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.traversals; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java index 764011a48..04adaacbc 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.traversals; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMRecordCoordinateComparator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMRecordCoordinateComparator; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider; import org.broadinstitute.sting.gatk.datasources.providers.ReadView; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java index e75747831..a7584cbd2 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.traversals; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.providers.ReadBasedReferenceOrderedView; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java index f60b7de54..e921aed05 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java @@ -26,8 +26,8 @@ package org.broadinstitute.sting.gatk.walkers; import com.google.java.contract.Ensures; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broad.tribble.Feature; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RMD.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RMD.java index cdfa24d2e..e4842008c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RMD.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RMD.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import java.lang.annotation.Documented; import java.lang.annotation.Inherited; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadFilters.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadFilters.java index 3b150e5f8..a20ca856c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadFilters.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadFilters.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers; -import net.sf.picard.filter.SamRecordFilter; +import htsjdk.samtools.filter.SamRecordFilter; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.lang.annotation.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java index 2bd255ad3..72b29e418 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import java.util.Collection; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Walker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Walker.java index 40485596d..c78b387c1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Walker.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Walker.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index 87323cf87..7c0bcb05b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/public/gatk-framework/src/main/java/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.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypesContext; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java index f5930078f..b669c9a7e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java @@ -33,12 +33,12 @@ 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.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 htsjdk.variant.vcf.VCFFormatHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.Collection; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java index da0634dd2..f9783c0ad 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java @@ -32,9 +32,9 @@ 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.BaseUtils; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java index 45e857dc0..f1c57dae1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.walkers.annotator; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFStandardHeaderLines; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java index 8ed9a9fe0..25e67a2e2 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java @@ -31,10 +31,10 @@ 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.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java index fa1a5dde5..a3596056a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java +++ b/public/gatk-framework/src/main/java/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.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFFormatHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java index 4a8c95dd1..fa656a599 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java @@ -32,10 +32,10 @@ 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.BaseUtils; -import org.broadinstitute.variant.vcf.VCFHeaderLineType; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLineType; +import htsjdk.variant.vcf.VCFInfoHeaderLine; import org.broadinstitute.sting.utils.pileup.PileupElement; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.HashMap; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java index 8c068d3e4..49a2247f1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java @@ -37,9 +37,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAn import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; import java.util.regex.Pattern; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index f2f808cad..5108c3872 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -41,10 +41,10 @@ import org.broadinstitute.sting.utils.help.HelpUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.SampleUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import it.unimi.dsi.fastutil.objects.ObjectOpenHashSet; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 25e683c2f..2f2aba983 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -36,8 +36,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.*; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java index 6b89ab4f4..7c12aefd5 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java @@ -29,10 +29,10 @@ import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.vcf.VCFConstants; import java.util.*; @@ -74,7 +74,7 @@ public final class VariantOverlapAnnotator { /** * Update rsID in vcToAnnotate with rsIDs from dbSNPBinding fetched from tracker - * @see #annotateOverlap(java.util.List, String, org.broadinstitute.variant.variantcontext.VariantContext) + * @see #annotateOverlap(java.util.List, String, htsjdk.variant.variantcontext.VariantContext) * * @param tracker non-null tracker, which we will use to update the rsID of vcToAnnotate * for VariantContexts bound to dbSNPBinding that start at vcToAnnotate @@ -122,7 +122,7 @@ public final class VariantOverlapAnnotator { /** * Add overlap attributes to vcToAnnotate against all overlapBindings in tracker * - * @see #annotateOverlap(java.util.List, String, org.broadinstitute.variant.variantcontext.VariantContext) + * @see #annotateOverlap(java.util.List, String, htsjdk.variant.variantcontext.VariantContext) * for more information * * @param tracker non-null tracker, which we will use to update the rsID of vcToAnnotate diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java index bc725815d..ec3bf25a4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java @@ -26,8 +26,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; -import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; import java.util.List; import java.util.Map; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java index 98b7cad9c..50255e5f1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; import org.broadinstitute.sting.commandline.RodBinding; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java index ec058708c..a02c5528f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java @@ -29,10 +29,10 @@ 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.variant.vcf.VCFFormatHeaderLine; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeBuilder; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFFormatHeaderLine; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeBuilder; +import htsjdk.variant.variantcontext.VariantContext; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java index ce1bb47e5..74d676268 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java @@ -29,8 +29,8 @@ 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.variant.vcf.VCFInfoHeaderLine; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFInfoHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; import java.util.List; import java.util.Map; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java index f640c99c8..0812eeaf8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index 7d5ad9b8a..d69bd59e6 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -37,10 +37,10 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java index 6e5aa250f..70a360272 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java @@ -41,13 +41,13 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; 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 htsjdk.variant.vcf.VCFFilterHeaderLine; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.PrintStream; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java index 646c57a2b..0689b49f7 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java @@ -38,15 +38,15 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.PrintStream; import java.util.Arrays; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java index 3844db38c..b8f66add3 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage; -import org.broad.tribble.bed.BEDFeature; +import htsjdk.tribble.bed.BEDFeature; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java index 0d61af305..e7635f1e8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.coverage; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java index 10a87adee..045e61b26 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java index 506ef2c72..3e5982d27 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java @@ -38,9 +38,9 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypesContext; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypesContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java index 0af1dbed5..b005bd608 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java index 796c817ff..27b10fba5 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java index 57d903f4d..411063b5e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.diffengine; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMRecordIterator; -import net.sf.samtools.util.BlockCompressedInputStream; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMRecordIterator; +import htsjdk.samtools.util.BlockCompressedInputStream; import java.io.*; import java.util.Arrays; @@ -111,7 +111,7 @@ public class BAMDiffableReader implements DiffableReader { return Arrays.equals(buffer, BAM_MAGIC); } catch ( IOException e ) { return false; - } catch ( net.sf.samtools.FileTruncatedException e ) { + } catch ( htsjdk.samtools.FileTruncatedException e ) { return false; } } diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java index 59f3d512c..fed18c657 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java @@ -26,12 +26,12 @@ package org.broadinstitute.sting.gatk.walkers.diffengine; import org.apache.log4j.Logger; -import org.broad.tribble.AbstractFeatureReader; -import org.broad.tribble.FeatureReader; +import htsjdk.tribble.AbstractFeatureReader; +import htsjdk.tribble.FeatureReader; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.variant.vcf.*; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.*; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; import java.io.*; import java.util.Iterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java index 9a02e2fac..f100dadc3 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java @@ -42,8 +42,8 @@ import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java index bce20d31a..735bcf74d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.filters; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; public class FiltrationContext { diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java index 5ef1f0cf0..564d9d7c0 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.filters; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; @@ -39,11 +39,11 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java index 21b66986a..822b73769 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java index e7b6df623..89dc7ebcb 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java index 7c2d19d30..9070f4436 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; -import org.broad.tribble.Feature; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java index 594ca239d..31842be64 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.RodBinding; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java index cfb7325a9..547eaa52f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java index 54562aa43..3746bb067 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java index 5db67a7f0..c0e2422c7 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; @@ -33,8 +33,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java index 8e99c1828..1de0f2030 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java @@ -101,9 +101,9 @@ public class ErrorThrowing extends RefWalker implements TreeRed } else if ( exceptionToThrow.equals("SamError2") ) { throw new RuntimeException(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_2); } else if ( exceptionToThrow.equals("NoSpace1") ) { - throw new net.sf.samtools.util.RuntimeIOException(new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)")); + throw new htsjdk.samtools.util.RuntimeIOException(new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)")); } else if ( exceptionToThrow.equals("NoSpace2") ) { - throw new net.sf.samtools.SAMException("Exception writing BAM index file", new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)")); + throw new htsjdk.samtools.SAMException("Exception writing BAM index file", new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)")); } else { throw new UserException.BadArgumentValue("exception", "exception isn't a recognized value " + exceptionToThrow); } diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java index 48e21fdd0..9708a8caa 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java index aada50daa..cc37414ed 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.RodBinding; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java index 48bd6feba..0c02f8cc1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.picard.reference.ReferenceSequence; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.ReferenceSequence; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java index 59b95f2ba..16b8a2d22 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.qc; -import net.sf.samtools.CigarElement; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java index 18641c18d..9174651ca 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java @@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.Reference; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.*; import java.math.BigInteger; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java index 78029eb85..4dac4cc9d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.readutils; -import net.sf.picard.reference.ReferenceSequence; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.picard.reference.ReferenceSequenceFileFactory; -import net.sf.samtools.util.StringUtil; +import htsjdk.samtools.reference.ReferenceSequence; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFileFactory; +import htsjdk.samtools.util.StringUtil; import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java index c7ed0bffd..1221820ff 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.readutils; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Output; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java index 43a1ddd74..24cc3eae3 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.readutils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMFileWriter; +import htsjdk.samtools.SAMFileWriter; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Argument; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java index c64924f09..9a518a265 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.readutils; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.gatk.CommandLineGATK; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index c75997e67..077534125 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.walkers.validation; -import net.sf.picard.reference.ReferenceSequenceFileFactory; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.reference.ReferenceSequenceFileFactory; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMSequenceDictionary; import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.bwa.BWTFiles; @@ -46,7 +46,7 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.File; import java.io.PrintStream; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java index 3aae056d9..1c5b47312 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java @@ -26,11 +26,11 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; import com.google.java.contract.Requires; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.picard.util.IntervalTree; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.util.IntervalTree; +import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; @@ -51,14 +51,14 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.VariantContextUtils; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java index c0b87b5b7..5b45434c1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java @@ -30,8 +30,8 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; /** * The Broad Institute diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java index 63c34586e..4e95d964a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java @@ -31,8 +31,8 @@ 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.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; @Analysis(description = "Counts different classes of variants in the sample") public class CountVariants extends VariantEvaluator implements StandardEval { diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java index 643948b45..ee0feb3be 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java @@ -31,8 +31,8 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java index 68fcc6aba..a496bcc78 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java @@ -33,9 +33,9 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; @Analysis(description = "Evaluation summary for indels") public class IndelSummary extends VariantEvaluator implements StandardEval { diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 3d082f23c..e6a49a4e1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -33,7 +33,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Map; import java.util.Set; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java index 2a7e29583..6478fa87f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java @@ -33,8 +33,8 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; @Analysis(description = "Evaluation summary for multi-allelic variants") public class MultiallelicSummary extends VariantEvaluator implements StandardEval { diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java index 8553ed376..fb1c33786 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java @@ -30,7 +30,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites") public class PrintMissingComp extends VariantEvaluator { diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index c5e73a875..288144b28 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -30,9 +30,9 @@ 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.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentMap; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java index 5618f607f..b0318eef7 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java @@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; @Analysis(description = "Ti/Tv Variant Evaluator") public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval { diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java index c31cf9f86..8d87fa1bc 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java @@ -30,10 +30,10 @@ 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.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Collection; import java.util.Set; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java index 13130ccb0..3905aec86 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java @@ -30,7 +30,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; public abstract class VariantEvaluator implements Comparable { private VariantEval walker; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java index 48d926115..c17394678 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; -import net.sf.picard.util.IntervalTree; +import htsjdk.samtools.util.IntervalTree; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; @@ -36,10 +36,10 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java index f18f73bac..2129a2fb6 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java @@ -29,10 +29,10 @@ 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.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java index 179161ee2..097b41c61 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java @@ -28,7 +28,7 @@ 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.MathUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Collections; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java index 202f6528a..9e196db3a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java @@ -28,7 +28,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Collections; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java index 411aed94f..b80f021a9 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java @@ -27,7 +27,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.Collections; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java index bba431ab4..dc5d10512 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java @@ -27,7 +27,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java index 120bd3cf0..6c46e8ff7 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java @@ -27,7 +27,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.HashMap; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java index afb36cdc6..7e61d6bb0 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; /** * Tag this stratification as dynamically determining the final strat based on the input data diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java index 6d00bf16a..1e8a12bb4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java @@ -28,7 +28,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java index 49c2a8808..685891143 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java @@ -27,7 +27,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java index d43db70fa..17c90ad72 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java @@ -28,7 +28,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java index 3e10d3b98..f6e51fdde 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java @@ -27,7 +27,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Collections; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java index 312e506a2..fcfcaa747 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java @@ -25,14 +25,14 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications; -import net.sf.picard.util.IntervalTree; +import htsjdk.samtools.util.IntervalTree; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java index a1a10294f..da8175170 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java @@ -28,8 +28,8 @@ 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.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextUtils; import java.util.List; import java.util.ArrayList; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java index ef077c678..1987a1ccb 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java @@ -28,7 +28,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java index 65fb2dd11..0b9aabf7e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java @@ -27,7 +27,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java index ca9a1df85..1aaa9503d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.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.evaluators.VariantEvaluator; import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/SnpEffPositionModifier.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/SnpEffPositionModifier.java index f393da6ad..f254f0e41 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/SnpEffPositionModifier.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/SnpEffPositionModifier.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff; import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff.EffectType; import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff.InfoFieldKey; import org.broadinstitute.sting.gatk.walkers.annotator.SnpEffUtil; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java index de82b18cc..9432a18ad 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java @@ -28,7 +28,7 @@ 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.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Arrays; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java index 3ca8c0bdc..53c7f2198 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java @@ -30,7 +30,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Collections; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java index 01862cf3a..cf5493511 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java @@ -27,7 +27,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.Collections; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java index 2e9512639..cf738b7a5 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java @@ -32,7 +32,7 @@ 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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Set; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java index 1cd68c610..eb8129ba7 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.util; import org.apache.commons.jexl2.Expression; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.variantcontext.VariantContextUtils; public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable { /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index 7e751e4a0..7c4168379 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -36,12 +36,12 @@ 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.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFConstants; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.VariantContextUtils; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java index d416d5d16..a04da2930 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java +++ b/public/gatk-framework/src/main/java/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.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index c3e773dcd..a49e26889 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -40,14 +40,14 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.variantcontext.VariantContextUtils; -import org.broadinstitute.variant.variantcontext.writer.Options; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.VariantContextUtils; +import htsjdk.variant.variantcontext.writer.Options; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java index c5cf997c2..db555b1d8 100755 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java @@ -29,8 +29,8 @@ import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFHeader; import java.io.PrintStream; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java index 2b18eda20..a29818458 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java @@ -35,12 +35,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java index 0cfef0b65..1bba62eb9 100755 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java @@ -37,8 +37,8 @@ import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFHeader; import java.io.PrintStream; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java index 5759abc41..be9b205c1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java @@ -27,9 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; @@ -46,14 +46,14 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.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.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java index 478a2a351..71776c432 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import net.sf.picard.liftover.LiftOver; -import net.sf.picard.util.Interval; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileReader; +import htsjdk.samtools.liftover.LiftOver; +import htsjdk.samtools.util.Interval; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileReader; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.Output; @@ -42,14 +42,14 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.writer.Options; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.variantcontext.writer.Options; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java index 29305af3f..13576a767 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java @@ -38,13 +38,13 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java index 478bba846..0fcb2b1fb 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.apache.commons.io.FilenameUtils; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; @@ -41,11 +41,11 @@ import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalSetRule; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.text.ListFileUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.File; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index e688b7f17..02b5d7cf6 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -41,12 +41,12 @@ import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.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.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.FileNotFoundException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java index a9a4cfd53..1f2d55751 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.TribbleException; +import htsjdk.tribble.TribbleException; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.gatk.CommandLineGATK; @@ -40,9 +40,9 @@ import org.broadinstitute.sting.gatk.walkers.Window; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFConstants; import java.io.File; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java index d189459c0..6bef27d0e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java @@ -37,12 +37,12 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java index e25f158f2..b7971e335 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java @@ -39,11 +39,11 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index 55b4c0029..d42dfb96e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import org.broad.tribble.TribbleException; +import htsjdk.tribble.TribbleException; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; @@ -40,12 +40,12 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.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.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import java.io.*; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 3fcabdf5b..77ac085d3 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -31,11 +31,11 @@ import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java index 5858fd8a1..8b2b4f58a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; -import net.sf.samtools.util.CloseableIterator; -import org.broad.tribble.Feature; +import htsjdk.samtools.util.CloseableIterator; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; @@ -47,12 +47,12 @@ import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.vcf.*; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java index e8ef39e3e..331dc1824 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.tools; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.picard.reference.ReferenceSequenceFileFactory; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFileFactory; import org.apache.log4j.BasicConfigurator; import org.apache.log4j.Level; -import org.broad.tribble.AbstractFeatureReader; -import org.broad.tribble.FeatureReader; -import org.broad.tribble.index.IndexCreator; +import htsjdk.tribble.AbstractFeatureReader; +import htsjdk.tribble.FeatureReader; +import htsjdk.tribble.index.IndexCreator; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Output; @@ -40,15 +40,15 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.variant.GATKVCFIndexType; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.bcf2.BCF2Codec; +import htsjdk.variant.bcf2.BCF2Codec; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.variant.vcf.VCFCodec; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.Options; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.Options; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.*; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/BaseUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/BaseUtils.java index 8edd872ee..4f744ee6a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/BaseUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/BaseUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils; -import net.sf.samtools.util.StringUtil; +import htsjdk.samtools.util.StringUtil; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/ContigComparator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/ContigComparator.java index fd6d93b44..12dda4fd2 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/ContigComparator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/ContigComparator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceDictionary; import java.util.Comparator; import java.util.Set; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLoc.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLoc.java index 4e8daa0e3..d71144f07 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLoc.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.Serializable; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocParser.java index 61478744d..b85b583ad 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -28,12 +28,12 @@ package org.broadinstitute.sting.utils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import com.google.java.contract.ThrowEnsures; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocSortedSet.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocSortedSet.java index 28cdaaf56..86817c43c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocSortedSet.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/GenomeLocSortedSet.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/IndelUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/IndelUtils.java index f674a59ba..95a6d5700 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/IndelUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/IndelUtils.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.util.ArrayList; import java.util.Arrays; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MRUCachingSAMSequenceDictionary.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MRUCachingSAMSequenceDictionary.java index c11aeb730..94bdeca27 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MRUCachingSAMSequenceDictionary.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MRUCachingSAMSequenceDictionary.java @@ -27,8 +27,8 @@ package org.broadinstitute.sting.utils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MendelianViolation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MendelianViolation.java index 7b850c61e..c82da2474 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MendelianViolation.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MendelianViolation.java @@ -26,9 +26,9 @@ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.gatk.samples.Sample; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.GenotypeType; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.GenotypeType; +import htsjdk.variant.variantcontext.VariantContext; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/QualityUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/QualityUtils.java index 543923dd6..0b5566a11 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/QualityUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/QualityUtils.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils; import com.google.java.contract.Ensures; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.SAMUtils; /** * QualityUtils is a static class (no instantiation allowed!) with some utility methods for manipulating diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SampleUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SampleUtils.java index e861af7b6..7cb5e9c77 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SampleUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SampleUtils.java @@ -25,14 +25,14 @@ package org.broadinstitute.sting.utils; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeader; import org.broadinstitute.sting.utils.text.ListFileUtils; import org.broadinstitute.sting.utils.text.XReadLines; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java index 5e834d273..775b0ecff 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/Utils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/Utils.java index 487c65483..40d76e50b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/Utils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/Utils.java @@ -27,8 +27,8 @@ package org.broadinstitute.sting.utils; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMProgramRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMProgramRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java index 0c819b4fb..3d2c24bbd 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.activeregion; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocSortedSet; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQ.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQ.java index 73e129105..b6dc23254 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQ.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQ.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.utils.baq; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.picard.reference.ReferenceSequence; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMUtils; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.ReferenceSequence; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQReadTransformer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQReadTransformer.java index d6651760a..7a87235d8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQReadTransformer.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/BAQReadTransformer.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.baq; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.WalkerManager; import org.broadinstitute.sting.gatk.iterators.ReadTransformer; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/ReadTransformingIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/ReadTransformingIterator.java index 1df41e2dd..523f71bc2 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/ReadTransformingIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/baq/ReadTransformingIterator.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.baq; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.ReadTransformer; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ClippingOp.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ClippingOp.java index fd04dbc21..09b387645 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ClippingOp.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ClippingOp.java @@ -26,9 +26,9 @@ package org.broadinstitute.sting.utils.clipping; import com.google.java.contract.Requires; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ReadClipper.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ReadClipper.java index 1b72503fa..d5be8dc11 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ReadClipper.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/clipping/ReadClipper.java @@ -26,8 +26,8 @@ package org.broadinstitute.sting.utils.clipping; import com.google.java.contract.Requires; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.sam.CigarUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java index 4a6becf6f..66a49e862 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java @@ -50,9 +50,9 @@ package org.broadinstitute.sting.utils.codecs.beagle; */ -import org.broad.tribble.AsciiFeatureCodec; -import org.broad.tribble.exception.CodecLineParsingException; -import org.broad.tribble.readers.LineIterator; +import htsjdk.tribble.AsciiFeatureCodec; +import htsjdk.tribble.exception.CodecLineParsingException; +import htsjdk.tribble.readers.LineIterator; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java index f9be12715..f4db16b31 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.codecs.beagle; -import org.broad.tribble.Feature; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.tribble.Feature; +import htsjdk.variant.variantcontext.Allele; import java.util.ArrayList; import java.util.Map; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java index b2b31b572..050a24d3d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.codecs.hapmap; -import org.broad.tribble.AsciiFeatureCodec; -import org.broad.tribble.FeatureCodecHeader; -import org.broad.tribble.annotation.Strand; -import org.broad.tribble.readers.LineIterator; +import htsjdk.tribble.AsciiFeatureCodec; +import htsjdk.tribble.FeatureCodecHeader; +import htsjdk.tribble.annotation.Strand; +import htsjdk.tribble.readers.LineIterator; import java.io.IOException; import java.util.Arrays; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java index 0f1a8b4aa..36edef068 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.utils.codecs.hapmap; -import org.broad.tribble.Feature; -import org.broad.tribble.annotation.Strand; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.tribble.Feature; +import htsjdk.tribble.annotation.Strand; +import htsjdk.variant.variantcontext.Allele; import java.util.HashMap; import java.util.Map; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java index 3c2329b8f..86f6863e6 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.codecs.refseq; -import org.broad.tribble.AsciiFeatureCodec; -import org.broad.tribble.Feature; -import org.broad.tribble.TribbleException; -import org.broad.tribble.readers.LineIterator; +import htsjdk.tribble.AsciiFeatureCodec; +import htsjdk.tribble.Feature; +import htsjdk.tribble.TribbleException; +import htsjdk.tribble.readers.LineIterator; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java index 089f7c528..0fbe03211 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.codecs.refseq; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.utils.GenomeLoc; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java index 70241a6c4..bef638e47 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.codecs.sampileup; -import org.broad.tribble.AsciiFeatureCodec; -import org.broad.tribble.exception.CodecLineParsingException; -import org.broad.tribble.readers.LineIterator; -import org.broad.tribble.util.ParsingUtils; +import htsjdk.tribble.AsciiFeatureCodec; +import htsjdk.tribble.exception.CodecLineParsingException; +import htsjdk.tribble.readers.LineIterator; +import htsjdk.tribble.util.ParsingUtils; import java.util.ArrayList; import java.util.regex.Matcher; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java index 287363601..ad39851e8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.codecs.sampileup; -import net.sf.samtools.util.StringUtil; -import org.broad.tribble.Feature; +import htsjdk.samtools.util.StringUtil; +import htsjdk.tribble.Feature; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java index cfc5d2c2d..fd2db5b83 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.utils.codecs.samread; -import net.sf.samtools.Cigar; -import net.sf.samtools.TextCigarCodec; -import net.sf.samtools.util.StringUtil; -import org.broad.tribble.AsciiFeatureCodec; -import org.broad.tribble.exception.CodecLineParsingException; -import org.broad.tribble.readers.LineIterator; -import org.broad.tribble.util.ParsingUtils; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.TextCigarCodec; +import htsjdk.samtools.util.StringUtil; +import htsjdk.tribble.AsciiFeatureCodec; +import htsjdk.tribble.exception.CodecLineParsingException; +import htsjdk.tribble.readers.LineIterator; +import htsjdk.tribble.util.ParsingUtils; /** * Decodes a simple SAM text string. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java index 1ad6ebab0..13e004625 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.codecs.samread; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; /** * Represents a SAM record read from a SAM text format file. diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java index 61ac9b5ea..56c6bdd96 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.codecs.table; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; import java.util.Arrays; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableCodec.java index f69001d9d..6f713ef8c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableCodec.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableCodec.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.codecs.table; -import org.broad.tribble.AsciiFeatureCodec; -import org.broad.tribble.readers.LineIterator; +import htsjdk.tribble.AsciiFeatureCodec; +import htsjdk.tribble.readers.LineIterator; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableFeature.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableFeature.java index 98ab9c5d8..8a564ec9e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableFeature.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/codecs/table/TableFeature.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils.codecs.table; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/UserException.java index 4db6e3d69..52f80077b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -25,16 +25,16 @@ package org.broadinstitute.sting.utils.exceptions; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMSequenceDictionary; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.variant.GATKVCFIndexType; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import java.io.File; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java index c30ac4f7f..ed4dc7437 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.utils.fasta; -import net.sf.picard.PicardException; -import net.sf.picard.reference.FastaSequenceIndex; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.picard.reference.ReferenceSequence; -import net.sf.samtools.SAMSequenceRecord; -import net.sf.samtools.util.StringUtil; +import picard.PicardException; +import htsjdk.samtools.reference.FastaSequenceIndex; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.ReferenceSequence; +import htsjdk.samtools.SAMSequenceRecord; +import htsjdk.samtools.util.StringUtil; import org.apache.log4j.Priority; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.BaseUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentUtils.java index 6068ab085..364cc3d8f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentUtils.java @@ -27,11 +27,11 @@ package org.broadinstitute.sting.utils.fragments; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.picard.util.QualityUtil; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.util.QualityUtil; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.recalibration.EventType; import org.broadinstitute.sting.utils.collections.Pair; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java index 9b12a58d5..40a70dfd8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAllele.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils.genotyper; import org.broadinstitute.sting.utils.MathUtils; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; /** * Stores the most likely and second most likely alleles, along with a threshold diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java index 49ec6f20a..859fd345b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java @@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/EventMap.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/EventMap.java index 752c880b9..da9df6594 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/EventMap.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/EventMap.java @@ -27,17 +27,17 @@ package org.broadinstitute.sting.utils.haplotype; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.AlignmentUtils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/Haplotype.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/Haplotype.java index 0c4c13840..30603df29 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/Haplotype.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/haplotype/Haplotype.java @@ -26,16 +26,16 @@ package org.broadinstitute.sting.utils.haplotype; import com.google.java.contract.Requires; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.ReadUtils; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.Arrays; import java.util.Comparator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDoclet.java index f0166bc9c..2bb49e53b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDoclet.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDoclet.java @@ -34,7 +34,7 @@ import freemarker.template.TemplateException; import org.apache.commons.io.FileUtils; import org.apache.log4j.Level; import org.apache.log4j.Logger; -import org.broad.tribble.FeatureCodec; +import htsjdk.tribble.FeatureCodec; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.walkers.qc.DocumentationTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java index 06c0e1c26..c5bcde444 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java @@ -32,7 +32,7 @@ import com.sun.javadoc.FieldDoc; import com.sun.javadoc.Tag; import org.apache.commons.lang.StringUtils; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalUtils.java index 7374dda14..18e9ad3f0 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/interval/IntervalUtils.java @@ -27,11 +27,11 @@ package org.broadinstitute.sting.utils.interval; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.picard.util.Interval; -import net.sf.picard.util.IntervalList; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.util.Interval; +import htsjdk.samtools.util.IntervalList; +import htsjdk.samtools.SAMFileHeader; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.IntervalArgumentCollection; import org.broadinstitute.sting.commandline.IntervalBinding; import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource; @@ -669,8 +669,8 @@ public class IntervalUtils { * @param locIndex The loc index for use in the file. * @return The picard interval. */ - private static net.sf.picard.util.Interval toInterval(GenomeLoc loc, int locIndex) { - return new net.sf.picard.util.Interval(loc.getContig(), loc.getStart(), loc.getStop(), false, "interval_" + locIndex); + private static htsjdk.samtools.util.Interval toInterval(GenomeLoc loc, int locIndex) { + return new htsjdk.samtools.util.Interval(loc.getContig(), loc.getStart(), loc.getStop(), false, "interval_" + locIndex); } /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java index c4b566582..c40e5fc91 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/AlignmentStateMachine.java @@ -28,9 +28,9 @@ package org.broadinstitute.sting.utils.locusiterator; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; import com.google.java.contract.Requires; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java index 17d09c844..0e018703d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LIBSPerformance.java @@ -25,11 +25,11 @@ package org.broadinstitute.sting.utils.locusiterator; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecordIterator; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecordIterator; import org.apache.log4j.Logger; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.CommandLineProgram; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java index 1243b2893..6a1451b18 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.locusiterator; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import java.util.Iterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java index 2926bdc63..942bb833b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java @@ -27,10 +27,10 @@ package org.broadinstitute.sting.utils.locusiterator; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManager.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManager.java index 669e76adc..b3676189b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManager.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManager.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.utils.locusiterator; import com.google.java.contract.Ensures; import com.google.java.contract.Invariant; import com.google.java.contract.Requires; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.CigarOperator; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.downsampling.Downsampler; import org.broadinstitute.sting.gatk.downsampling.LevelingDownsampler; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java index 9728bdb1c..40f8b53c8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.locusiterator; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.picard.util.PeekableIterator; +import htsjdk.samtools.util.PeekableIterator; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import java.util.*; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java index 9122beebb..e755835aa 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/locusiterator/SamplePartitioner.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.locusiterator; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.downsampling.Downsampler; import org.broadinstitute.sting.gatk.downsampling.PassThroughDownsampler; import org.broadinstitute.sting.gatk.downsampling.ReservoirDownsampler; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMM.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMM.java index e45cf0941..55d928fc5 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMM.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pairhmm/PairHMM.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.Allele; import java.util.Arrays; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java index 48d231199..233efd21e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/MergingPileupElementIterator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.pileup; -import net.sf.picard.util.PeekableIterator; +import htsjdk.samtools.util.PeekableIterator; import java.util.Comparator; import java.util.Iterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElement.java index 42cfc9492..a8f3f7c45 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElement.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/pileup/PileupElement.java @@ -27,8 +27,8 @@ package org.broadinstitute.sting.utils.pileup; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartComparator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartComparator.java index f05ab75bc..c249d059e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartComparator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartComparator.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import java.util.Comparator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java index fe3ce5fca..0650523fd 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentStartWithNoTiesComparator.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.sam; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import java.util.Comparator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 762ce4858..c9a1f3fda 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -27,10 +27,10 @@ package org.broadinstitute.sting.utils.sam; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java index 8d496ab96..0fd641d83 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.*; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.*; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.NGSPlatform; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialMultiSampleReadStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialMultiSampleReadStream.java index 236af6118..ef4e131d8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialMultiSampleReadStream.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialMultiSampleReadStream.java @@ -25,11 +25,11 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.picard.sam.MergingSamRecordIterator; -import net.sf.picard.sam.SamFileHeaderMerger; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.MergingSamRecordIterator; +import htsjdk.samtools.SamFileHeaderMerger; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java index 0b4d05621..3ff92f4ae 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; /* diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java index 79d31b962..fe894b61c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java index 6ec2faba5..219948b7d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java index 73990d629..91c20a4a8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import java.util.Iterator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java index 7080b69ae..88e36fd2e 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.List; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java index b8367a7df..69bddd849 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; @@ -103,7 +103,7 @@ public class ArtificialSAMUtils { */ public static SAMFileHeader createArtificialSamHeader(int numberOfChromosomes, int startingChromosome, int chromosomeSize) { SAMFileHeader header = new SAMFileHeader(); - header.setSortOrder(net.sf.samtools.SAMFileHeader.SortOrder.coordinate); + header.setSortOrder(htsjdk.samtools.SAMFileHeader.SortOrder.coordinate); SAMSequenceDictionary dict = new SAMSequenceDictionary(); // make up some sequence records for (int x = startingChromosome; x < startingChromosome + numberOfChromosomes; x++) { @@ -122,7 +122,7 @@ public class ArtificialSAMUtils { */ public static SAMFileHeader createArtificialSamHeader(final SAMSequenceDictionary dict) { SAMFileHeader header = new SAMFileHeader(); - header.setSortOrder(net.sf.samtools.SAMFileHeader.SortOrder.coordinate); + header.setSortOrder(htsjdk.samtools.SAMFileHeader.SortOrder.coordinate); header.setSequenceDictionary(dict); return header; } diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStream.java index 02381275b..4b3b718a3 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStream.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStream.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter; import org.broadinstitute.sting.utils.MathUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java index 8ca1f45d0..c4f9c1bcd 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamAnalyzer.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java index 8755cedac..b13273344 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.ProgressLoggerInterface; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.ProgressLoggerInterface; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import java.util.ArrayList; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java index a3f2e3daa..88f7e66a7 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/BySampleSAMFileWriter.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMProgramRecord; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMProgramRecord; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/CigarUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/CigarUtils.java index 70ce68a5b..31c6f6a95 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/CigarUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/CigarUtils.java @@ -26,10 +26,10 @@ package org.broadinstitute.sting.utils.sam; import com.google.java.contract.Ensures; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.smithwaterman.Parameters; import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java index ec9d7d219..951f79d45 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.utils.NGSPlatform; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java index 52e6e1c25..ad58a8f9c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils.sam; import com.google.java.contract.Ensures; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.utils.NGSPlatform; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.recalibration.EventType; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java index 55b2de42d..642e824e1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/GATKSamRecordFactory.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMRecordFactory; -import net.sf.samtools.BAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMRecordFactory; +import htsjdk.samtools.BAMRecord; import org.broadinstitute.sting.utils.exceptions.UserException; /** diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java index 728ec5597..c1e0548e1 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.*; -import net.sf.samtools.util.ProgressLoggerInterface; +import htsjdk.samtools.*; +import htsjdk.samtools.util.ProgressLoggerInterface; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.utils.Utils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUnclippedStartWithNoTiesComparator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUnclippedStartWithNoTiesComparator.java index 2281b94a7..4607f9f1b 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUnclippedStartWithNoTiesComparator.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUnclippedStartWithNoTiesComparator.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.sam; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import java.util.Comparator; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUtils.java index 2b6654bcd..704c839f8 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.sam; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.*; @@ -617,7 +617,7 @@ public class ReadUtils { } /** - * @see #readStartsWithInsertion(net.sf.samtools.Cigar, boolean) with ignoreClipOps set to true + * @see #readStartsWithInsertion(htsjdk.samtools.Cigar, boolean) with ignoreClipOps set to true */ public static CigarElement readStartsWithInsertion(final Cigar cigarForRead) { return readStartsWithInsertion(cigarForRead, true); diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java index 4ec3a2ab9..13bca872a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileReader; +import htsjdk.samtools.SAMFileReader; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java index 1a471383a..9dc739812 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.ProgressLoggerInterface; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.ProgressLoggerInterface; /** * XXX diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java index 27ead2e48..1fe8f520d 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.smithwaterman; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.sam.AlignmentUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignment.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignment.java index e730870c6..3ff0e71ac 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignment.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignment.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.utils.smithwaterman; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.sam.AlignmentUtils; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java index 4cf39d6be..88cb76a88 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/smithwaterman/SmithWaterman.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.smithwaterman; -import net.sf.samtools.Cigar; +import htsjdk.samtools.Cigar; /** * Generic interface for SmithWaterman calculations diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java index 670c6c89d..bfef5eeee 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java @@ -25,28 +25,28 @@ package org.broadinstitute.sting.utils.variant; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceDictionary; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; -import org.broad.tribble.FeatureCodecHeader; -import org.broad.tribble.index.DynamicIndexCreator; -import org.broad.tribble.index.IndexCreator; -import org.broad.tribble.index.IndexFactory; -import org.broad.tribble.index.interval.IntervalIndexCreator; -import org.broad.tribble.index.linear.LinearIndexCreator; -import org.broad.tribble.index.tabix.TabixFormat; -import org.broad.tribble.index.tabix.TabixIndexCreator; -import org.broad.tribble.readers.LineIterator; -import org.broad.tribble.readers.PositionalBufferedStream; +import htsjdk.tribble.Feature; +import htsjdk.tribble.FeatureCodec; +import htsjdk.tribble.FeatureCodecHeader; +import htsjdk.tribble.index.DynamicIndexCreator; +import htsjdk.tribble.index.IndexCreator; +import htsjdk.tribble.index.IndexFactory; +import htsjdk.tribble.index.interval.IntervalIndexCreator; +import htsjdk.tribble.index.linear.LinearIndexCreator; +import htsjdk.tribble.index.tabix.TabixFormat; +import htsjdk.tribble.index.tabix.TabixIndexCreator; +import htsjdk.tribble.readers.LineIterator; +import htsjdk.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.*; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.*; import java.io.File; import java.io.FileInputStream; diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java index 8546d3b67..be3eb1028 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java @@ -29,13 +29,13 @@ import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.apache.commons.lang.ArrayUtils; import org.apache.log4j.Logger; -import org.broad.tribble.TribbleException; -import org.broad.tribble.util.popgen.HardyWeinbergCalculation; +import htsjdk.tribble.TribbleException; +import htsjdk.tribble.util.popgen.HardyWeinbergCalculation; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.VCFConstants; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFConstants; import java.io.Serializable; import java.util.*; diff --git a/public/gatk-framework/src/test/java/net/sf/samtools/GATKBAMFileSpanUnitTest.java b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java similarity index 99% rename from public/gatk-framework/src/test/java/net/sf/samtools/GATKBAMFileSpanUnitTest.java rename to public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java index d03c6e006..aaa20c0e5 100644 --- a/public/gatk-framework/src/test/java/net/sf/samtools/GATKBAMFileSpanUnitTest.java +++ b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package net.sf.samtools; +package htsjdk.samtools; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/net/sf/samtools/GATKChunkUnitTest.java b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java similarity index 99% rename from public/gatk-framework/src/test/java/net/sf/samtools/GATKChunkUnitTest.java rename to public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java index 09a87d311..2b08fc4d4 100644 --- a/public/gatk-framework/src/test/java/net/sf/samtools/GATKChunkUnitTest.java +++ b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java @@ -23,7 +23,7 @@ * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ -package net.sf.samtools; +package htsjdk.samtools; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java index 08eb0f5df..c2c28e0f1 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java @@ -30,21 +30,21 @@ import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.apache.log4j.PatternLayout; import org.apache.log4j.spi.LoggingEvent; -import org.broad.tribble.readers.LineIterator; -import org.broad.tribble.readers.PositionalBufferedStream; +import htsjdk.tribble.readers.LineIterator; +import htsjdk.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.commandline.CommandLineUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.crypt.CryptUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.io.IOUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.bcf2.BCF2Codec; -import org.broadinstitute.variant.variantcontext.Genotype; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFCodec; -import org.broadinstitute.variant.vcf.VCFConstants; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.bcf2.BCF2Codec; +import htsjdk.variant.variantcontext.Genotype; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import org.testng.Assert; import org.testng.Reporter; import org.testng.SkipException; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/ExampleToCopyUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/ExampleToCopyUnitTest.java index 06bab8fc0..409c5d97f 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/ExampleToCopyUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/ExampleToCopyUnitTest.java @@ -29,10 +29,10 @@ package org.broadinstitute.sting; // the imports for unit testing. -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; @@ -46,10 +46,10 @@ import org.broadinstitute.sting.utils.sam.ArtificialBAMBuilder; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/WalkerTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/WalkerTest.java index c6bfebace..f40504fc4 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/WalkerTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/WalkerTest.java @@ -26,20 +26,20 @@ package org.broadinstitute.sting; import org.apache.commons.lang.StringUtils; -import org.broad.tribble.Tribble; -import org.broad.tribble.index.Index; -import org.broad.tribble.index.IndexFactory; -import org.broad.tribble.index.tabix.TabixFormat; -import org.broad.tribble.util.TabixUtils; +import htsjdk.tribble.Tribble; +import htsjdk.tribble.index.Index; +import htsjdk.tribble.index.IndexFactory; +import htsjdk.tribble.index.tabix.TabixFormat; +import htsjdk.tribble.util.TabixUtils; import org.broadinstitute.sting.gatk.CommandLineExecutable; 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.classloader.JVMUtils; -import org.broadinstitute.variant.bcf2.BCF2Utils; +import htsjdk.variant.bcf2.BCF2Utils; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.StingException; import org.testng.Assert; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptorUnitTest.java index 85ad5d575..47ffb16ce 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptorUnitTest.java @@ -26,12 +26,12 @@ package org.broadinstitute.sting.commandline; import it.unimi.dsi.fastutil.objects.ObjectArrayList; -import net.sf.samtools.SAMFileWriter; +import htsjdk.samtools.SAMFileWriter; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.io.stubs.*; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java index 29ba95963..daa0651e7 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java @@ -26,9 +26,9 @@ package org.broadinstitute.sting.commandline; import org.apache.commons.io.FileUtils; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingCollectionUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingCollectionUnitTest.java index 853c51543..a5217cf73 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingCollectionUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingCollectionUnitTest.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.UserException; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingUnitTest.java index 2e18c972f..9ca0bde78 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/RodBindingUnitTest.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.Test; import org.testng.annotations.BeforeMethod; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/CommandLineGATKUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/CommandLineGATKUnitTest.java index 0532cbf3f..ca7333779 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/CommandLineGATKUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/CommandLineGATKUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk; -import net.sf.samtools.SAMFileReader; +import htsjdk.samtools.SAMFileReader; import org.broadinstitute.sting.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java index 4012a07a9..850bafc0c 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.gatk; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.util.CloseableIterator; -import org.broad.tribble.readers.LineIterator; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.util.CloseableIterator; +import htsjdk.tribble.readers.LineIterator; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; @@ -53,11 +53,11 @@ import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSamRecordFactory; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; -import org.broadinstitute.variant.vcf.VCFCodec; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/ReadMetricsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/ReadMetricsUnitTest.java index 02d0c66b9..8393d2ca6 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/ReadMetricsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/ReadMetricsUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.*; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.*; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedViewUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedViewUnitTest.java index 784bd727e..bd32eb511 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedViewUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedViewUnitTest.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.picard.util.PeekableIterator; -import net.sf.samtools.SAMFileHeader; -import org.broad.tribble.BasicFeature; -import org.broad.tribble.Feature; +import htsjdk.samtools.util.PeekableIterator; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.tribble.BasicFeature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.gatk.refdata.RODRecordListImpl; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java index 414135acb..6ff28f982 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java @@ -34,8 +34,8 @@ import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard; import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import net.sf.picard.reference.ReferenceSequence; -import net.sf.samtools.util.StringUtil; +import htsjdk.samtools.reference.ReferenceSequence; +import htsjdk.samtools.util.StringUtil; import java.util.Collections; /* diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java index 7540f319f..ff609142d 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.picard.reference.ReferenceSequence; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.samtools.*; +import htsjdk.samtools.reference.ReferenceSequence; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.*; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; @@ -44,6 +44,7 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; import java.io.FileNotFoundException; +import java.io.IOException; import java.util.*; /** * User: hanna @@ -336,6 +337,9 @@ public abstract class LocusViewTemplate extends BaseTest { public void reset() { return; } + + public void close() throws IOException { + } }; } diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java index 9ebb7f858..04d30172f 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java @@ -30,8 +30,8 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.testng.annotations.Test; -import net.sf.samtools.*; -import net.sf.picard.reference.ReferenceSequence; +import htsjdk.samtools.*; +import htsjdk.samtools.reference.ReferenceSequence; /* * Copyright (c) 2009 The Broad Institute diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java index 4d9283beb..804786d7b 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.datasources.reads.MockLocusShard; @@ -49,7 +49,7 @@ import java.io.FileNotFoundException; import java.util.Arrays; import java.util.Collections; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; /** * User: hanna * Date: May 27, 2009 diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java index 5de9c153b..310424024 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import net.sf.samtools.SAMSequenceRecord; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMSequenceRecord; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancerUnitTest.java index e768faba4..698fd534f 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancerUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileSpan; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileSpan; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java index 36fe20940..498a8ddb6 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.GATKBAMFileSpan; -import net.sf.samtools.GATKChunk; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.GATKBAMFileSpan; +import htsjdk.samtools.GATKChunk; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java index 7940c24d0..e4405bd20 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMSequenceDictionary; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java index 052e05718..3db6b0ac9 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java index 1339a4dfe..04a1f9fc1 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java @@ -27,10 +27,10 @@ package org.broadinstitute.sting.gatk.datasources.reads; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; -import net.sf.picard.util.SamLocusIterator; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.util.SamLocusIterator; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; import java.io.File; import java.util.Iterator; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java index 283898dd0..4200b7b1e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java @@ -27,10 +27,10 @@ package org.broadinstitute.sting.gatk.datasources.reads; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMFileWriterFactory; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.samtools.SAMFileWriterFactory; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java index 40ec42ef1..f48459c1e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java index 280e48679..c4c1aa0c7 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.*; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.*; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SeekableBufferedStreamUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SeekableBufferedStreamUnitTest.java index 4cb19d154..89989d834 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SeekableBufferedStreamUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SeekableBufferedStreamUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.reads; -import net.sf.samtools.seekablestream.SeekableBufferedStream; -import net.sf.samtools.seekablestream.SeekableFileStream; +import htsjdk.samtools.seekablestream.SeekableBufferedStream; +import htsjdk.samtools.seekablestream.SeekableFileStream; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.StingException; import org.testng.Assert; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java index 27cc08471..4a9f9e587 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java @@ -26,11 +26,11 @@ package org.broadinstitute.sting.gatk.datasources.reads; import com.google.caliper.Param; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; import java.io.File; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java index 2e72d1679..6ef702a3b 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java @@ -45,7 +45,7 @@ import org.testng.annotations.Test; import java.io.File; import java.io.FileNotFoundException; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; /** * User: hanna * Date: May 21, 2009 diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java index edcc36a16..0a71486b2 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.datasources.rmd; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broad.tribble.Feature; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.refdata.utils.*; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java index c587d5e08..bdfd0f4dc 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMFileHeader; import org.apache.log4j.Logger; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIteratorUnitTest.java index a39e8ee90..bdd2cdcc4 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIteratorUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerUnitTest.java index 4fd9e491c..2f90e3aef 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java index e66d2a15d..c6103e7a1 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerUnitTest.java index 66abfd29b..ff1cfc63b 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerUnitTest.java index afe8729c2..26839af4b 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.downsampling; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/AllowNCigarMalformedReadFilterUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/AllowNCigarMalformedReadFilterUnitTest.java index d169bf7e9..728061b48 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/AllowNCigarMalformedReadFilterUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/AllowNCigarMalformedReadFilterUnitTest.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java index 310d9dadb..403aa85a7 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.Cigar; +import htsjdk.samtools.Cigar; import org.broadinstitute.sting.utils.clipping.ReadClipperTestUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.testng.Assert; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilterUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilterUnitTest.java index 0d8515dde..43f51dcf0 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilterUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/MalformedReadFilterUnitTest.java @@ -26,10 +26,10 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.Cigar; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformerUnitTest.java index 90bc3870c..667082eb2 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/NDNCigarReadTransformerUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.Cigar; +import htsjdk.samtools.Cigar; import org.broadinstitute.sting.utils.sam.CigarUtils; import org.testng.Assert; import org.testng.annotations.BeforeClass; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadFilterTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadFilterTest.java index 5b6f67c42..0511b06dd 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadFilterTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadFilterTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.filters; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java index 1be31b293..5c7c5b5ed 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java @@ -30,8 +30,8 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.testng.annotations.Test; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMReadGroupRecord; import java.util.List; import java.util.ArrayList; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java index b001e6805..436101934 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java @@ -27,10 +27,10 @@ package org.broadinstitute.sting.gatk.iterators; import static org.testng.Assert.fail; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.BaseTest; import org.testng.Assert; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIteratorUnitTest.java index 5d037bc4b..686142575 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIteratorUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.testng.Assert; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java index f5358a8ce..0c109ba15 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.BaseTest; import static org.testng.Assert.assertEquals; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIteratorUnitTest.java index 86f80c55d..1c684403a 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIteratorUnitTest.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.iterators; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.testng.Assert; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java index 0e23d3dc4..112f869de 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.refdata; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.apache.log4j.Logger; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.commandline.Tags; @@ -38,9 +38,9 @@ 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.sam.ArtificialSAMUtils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.*; import java.util.*; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java index 579ecd681..ac17ec8ed 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java @@ -26,18 +26,18 @@ package org.broadinstitute.sting.gatk.refdata.tracks; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.tribble.Feature; +import htsjdk.tribble.FeatureCodec; 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.variant.vcf.VCF3Codec; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCF3Codec; +import htsjdk.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.BeforeMethod; import org.testng.annotations.DataProvider; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java index dc31d55e1..5f399c9a6 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java @@ -26,11 +26,11 @@ package org.broadinstitute.sting.gatk.refdata.tracks; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broad.tribble.Tribble; -import org.broad.tribble.index.Index; -import org.broad.tribble.util.LittleEndianOutputStream; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.tribble.Tribble; +import htsjdk.tribble.index.Index; +import htsjdk.tribble.util.LittleEndianOutputStream; +import htsjdk.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/CheckableCloseableTribbleIterator.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/CheckableCloseableTribbleIterator.java index 3dbac4e12..80978171e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/CheckableCloseableTribbleIterator.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/CheckableCloseableTribbleIterator.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.refdata.utils; -import org.broad.tribble.CloseableTribbleIterator; -import org.broad.tribble.Feature; +import htsjdk.tribble.CloseableTribbleIterator; +import htsjdk.tribble.Feature; import java.util.ArrayList; import java.util.Iterator; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java index 3412d2ed6..ef5e66640 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.gatk.refdata.utils; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broad.tribble.Feature; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFCodec; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java index 741764f81..a7d30e8cc 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.refdata.utils; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMSequenceDictionary; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java index 988355813..f8c1ccb00 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.refdata.utils; -import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; -import org.broad.tribble.TribbleIndexedFeatureReader; +import htsjdk.tribble.Feature; +import htsjdk.tribble.FeatureCodec; +import htsjdk.tribble.TribbleIndexedFeatureReader; import java.io.IOException; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestRMDTrackBuilder.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestRMDTrackBuilder.java index 02b1fa2f7..d6cdc144f 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestRMDTrackBuilder.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/refdata/utils/TestRMDTrackBuilder.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.gatk.refdata.utils; -import net.sf.samtools.SAMSequenceDictionary; -import org.broad.tribble.FeatureCodec; -import org.broad.tribble.Tribble; -import org.broad.tribble.index.Index; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.tribble.FeatureCodec; +import htsjdk.tribble.Tribble; +import htsjdk.tribble.index.Index; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.gatk.refdata.tracks.IndexDictionaryUtils; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java index 23f8bc1f7..a632be407 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.samples; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TAROrderedReadCacheUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TAROrderedReadCacheUnitTest.java index 62f4bdc88..e7adc4bea 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TAROrderedReadCacheUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TAROrderedReadCacheUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.traversals; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.sam.ArtificialBAMBuilder; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java index 30c0c83b5..74c54755c 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.traversals; import com.google.java.contract.PreconditionError; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.datasources.reads.*; @@ -40,7 +40,7 @@ import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; import org.broadinstitute.sting.utils.sam.*; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java index fd9e46a06..9cb14275a 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.traversals; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java index 5b52d4e33..1b73ddd02 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.traversals; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.picard.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.Tags; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java index c9c126295..bbf365769 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.gatk.walkers.readutils; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.sam.ArtificialReadsTraversal; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariantsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariantsUnitTest.java index 83d571748..eae6d31b3 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariantsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariantsUnitTest.java @@ -26,9 +26,9 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsUnitTest.java index ca60c6cfe..2a8104b61 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsUnitTest.java @@ -27,9 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.variantutils; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.Utils; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/tools/CatVariantsIntegrationTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/tools/CatVariantsIntegrationTest.java index d99b194b8..cfa3da8c8 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/tools/CatVariantsIntegrationTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/tools/CatVariantsIntegrationTest.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.tools; import org.apache.commons.lang.StringUtils; -import org.broad.tribble.AbstractFeatureReader; +import htsjdk.tribble.AbstractFeatureReader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.MD5DB; import org.broadinstitute.sting.MD5Mismatch; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserBenchmark.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserBenchmark.java index 478f02530..bd6adb7c7 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserBenchmark.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserBenchmark.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; -import net.sf.picard.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import java.io.File; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java index b94b6cda1..21a4f09e6 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java @@ -26,20 +26,20 @@ package org.broadinstitute.sting.utils; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; -import org.broad.tribble.BasicFeature; -import org.broad.tribble.Feature; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; +import htsjdk.tribble.BasicFeature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; @@ -119,7 +119,7 @@ public class GenomeLocParserUnitTest extends BaseTest { @Test public void testContigHasColon() { SAMFileHeader header = new SAMFileHeader(); - header.setSortOrder(net.sf.samtools.SAMFileHeader.SortOrder.coordinate); + header.setSortOrder(htsjdk.samtools.SAMFileHeader.SortOrder.coordinate); SAMSequenceDictionary dict = new SAMSequenceDictionary(); SAMSequenceRecord rec = new SAMSequenceRecord("c:h:r1", 10); rec.setSequenceLength(10); diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java index 443cf2771..2801ac7ba 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocUnitTest.java index c3ab22b4c..42def9fb7 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/GenomeLocUnitTest.java @@ -29,8 +29,8 @@ package org.broadinstitute.sting.utils; // the imports for unit testing. -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java index 7a5fcf0c2..f94f5178b 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java @@ -26,10 +26,10 @@ package org.broadinstitute.sting.utils; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/NGSPlatformUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/NGSPlatformUnitTest.java index ea4d0cc66..f07d38f72 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/NGSPlatformUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/NGSPlatformUnitTest.java @@ -29,9 +29,9 @@ package org.broadinstitute.sting.utils; // the imports for unit testing. -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SequenceDictionaryUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SequenceDictionaryUtilsUnitTest.java index a95b5b6ce..36c95fd0d 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SequenceDictionaryUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/SequenceDictionaryUtilsUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils; -import net.sf.samtools.SAMSequenceDictionary; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.SAMSequenceDictionary; +import htsjdk.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActiveRegionUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActiveRegionUnitTest.java index 0f9b8531a..bf94f85ae 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActiveRegionUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActiveRegionUnitTest.java @@ -29,8 +29,8 @@ package org.broadinstitute.sting.utils.activeregion; // the imports for unit testing. -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileStateUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileStateUnitTest.java index f199a0d82..76e04b1f6 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileStateUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileStateUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.activeregion; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java index f208815f7..0c6d7a199 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/ActivityProfileUnitTest.java @@ -29,7 +29,7 @@ package org.broadinstitute.sting.utils.activeregion; // the imports for unit testing. -import net.sf.picard.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java index fb238ef54..615b5552e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/activeregion/BandPassActivityProfileUnitTest.java @@ -29,9 +29,9 @@ package org.broadinstitute.sting.utils.activeregion; // the imports for unit testing. -import net.sf.picard.reference.ReferenceSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFile; import org.apache.commons.lang.ArrayUtils; -import org.broad.tribble.readers.LineIterator; +import htsjdk.tribble.readers.LineIterator; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; @@ -39,9 +39,9 @@ import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.variant.GATKVCFUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.vcf.VCFCodec; -import org.broadinstitute.variant.vcf.VCFHeader; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFHeader; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/baq/BAQUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/baq/BAQUnitTest.java index da82e9de5..054d0d5e7 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/baq/BAQUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/baq/BAQUnitTest.java @@ -41,8 +41,8 @@ import java.io.PrintStream; import java.util.List; import java.util.ArrayList; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.*; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.*; /** * Basic unit test for BAQ calculation diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java index 6dd4d8104..295d0137c 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperTestUtils.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.clipping; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.CigarUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java index cd12c3b9b..7e9ba843e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/clipping/ReadClipperUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.utils.clipping; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.sam.CigarUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java index 1ac79dcf3..9f5eb5fb8 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java @@ -25,11 +25,11 @@ package org.broadinstitute.sting.utils.codecs.hapmap; -import org.broad.tribble.annotation.Strand; -import org.broad.tribble.readers.LineIterator; -import org.broad.tribble.readers.LineIteratorImpl; -import org.broad.tribble.readers.LineReaderUtil; -import org.broad.tribble.readers.PositionalBufferedStream; +import htsjdk.tribble.annotation.Strand; +import htsjdk.tribble.readers.LineIterator; +import htsjdk.tribble.readers.LineIteratorImpl; +import htsjdk.tribble.readers.LineReaderUtil; +import htsjdk.tribble.readers.PositionalBufferedStream; import org.broadinstitute.sting.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java index 0c1b5b069..89f5733c2 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java @@ -29,9 +29,9 @@ package org.broadinstitute.sting.utils.fasta; // the imports for unit testing. -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.picard.reference.ReferenceSequence; -import net.sf.samtools.SAMSequenceRecord; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.ReferenceSequence; +import htsjdk.samtools.SAMSequenceRecord; import org.apache.commons.lang.StringUtils; import org.apache.log4j.Priority; import org.broadinstitute.sting.BaseTest; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsBenchmark.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsBenchmark.java index e06149f67..563ff5a66 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsBenchmark.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsBenchmark.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.fragments; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java index 93de7c9cf..01205a48e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/fragments/FragmentUtilsUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.fragments; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/EventMapUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/EventMapUnitTest.java index d0b418b96..cf6c4515b 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/EventMapUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/EventMapUnitTest.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.utils.haplotype; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; -import org.broadinstitute.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContext; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeUnitTest.java index cfbc4a3e0..5e057e77a 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeUnitTest.java @@ -26,17 +26,17 @@ package org.broadinstitute.sting.utils.haplotype; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.TextCigarCodec; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.TextCigarCodec; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc; import org.broadinstitute.sting.utils.haplotype.Haplotype; -import org.broadinstitute.variant.variantcontext.Allele; -import org.broadinstitute.variant.variantcontext.VariantContext; -import org.broadinstitute.variant.variantcontext.VariantContextBuilder; +import htsjdk.variant.variantcontext.Allele; +import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.variantcontext.VariantContextBuilder; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java index 2be2745de..4f8c15b5e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java @@ -25,13 +25,13 @@ package org.broadinstitute.sting.utils.interval; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.picard.reference.ReferenceSequenceFile; -import net.sf.picard.util.Interval; -import net.sf.picard.util.IntervalList; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.reference.ReferenceSequenceFile; +import htsjdk.samtools.util.Interval; +import htsjdk.samtools.util.IntervalList; +import htsjdk.samtools.SAMFileHeader; import org.apache.commons.io.FileUtils; -import org.broad.tribble.Feature; +import htsjdk.tribble.Feature; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.commandline.IntervalBinding; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java index d856805f8..ed5178a3e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LIBS_position.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.locusiterator; -import net.sf.samtools.Cigar; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.Cigar; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMRecord; /** * Created with IntelliJ IDEA. diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java index 9c3472752..54ed88ebb 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorBenchmark.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.locusiterator; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.QualityUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java index ee65109ca..5875c1f22 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateBaseTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.locusiterator; -import net.sf.samtools.*; -import net.sf.samtools.util.CloseableIterator; +import htsjdk.samtools.*; +import htsjdk.samtools.util.CloseableIterator; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java index 54554ee64..02ffb921e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByStateUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.utils.locusiterator; -import net.sf.samtools.CigarOperator; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.CigarOperator; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.downsampling.DownsampleType; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java index eb759fc1c..e39a751c4 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/locusiterator/PerSampleReadStateManagerUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.locusiterator; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java index 39058233e..a7ccda392 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/PileupElementUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.pileup; -import net.sf.samtools.CigarElement; -import net.sf.samtools.CigarOperator; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.CigarOperator; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.locusiterator.AlignmentStateMachine; import org.broadinstitute.sting.utils.locusiterator.LIBS_position; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java index 02b11b970..c83f7ba9f 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/pileup/ReadBackedPileupUnitTest.java @@ -25,9 +25,9 @@ package org.broadinstitute.sting.utils.pileup; -import net.sf.samtools.CigarElement; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.CigarElement; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java index fbf0242a3..fca18e62c 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.*; +import htsjdk.samtools.*; import org.apache.commons.lang.ArrayUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.pileup.PileupElement; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java index 68ba0b624..b45394f7c 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMRecord; import org.broadinstitute.sting.BaseTest; import org.testng.Assert; import org.testng.annotations.DataProvider; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java index ced60606e..409ba3553 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorUnitTest.java @@ -30,8 +30,8 @@ import static org.testng.Assert.assertTrue; import static org.testng.Assert.fail; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; /* diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java index 6f8fed8e0..3df3d027f 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterUnitTest.java @@ -30,8 +30,8 @@ import static org.testng.Assert.assertTrue; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; import org.broadinstitute.sting.BaseTest; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMRecord; +import htsjdk.samtools.SAMFileHeader; import java.util.ArrayList; import java.util.List; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorUnitTest.java index da2784a03..643e7e760 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorUnitTest.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.utils.sam; import org.broadinstitute.sting.BaseTest; import static org.testng.Assert.assertEquals; import org.testng.annotations.Test; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /* diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsUnitTest.java index ec6782cc0..8a45890cf 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsUnitTest.java @@ -31,7 +31,7 @@ import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; import static org.testng.Assert.fail; import org.testng.annotations.Test; -import net.sf.samtools.SAMRecord; +import htsjdk.samtools.SAMRecord; /** * Created by IntelliJ IDEA. diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java index 5f474efc4..8dbcb496c 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ArtificialSingleSampleReadStreamUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMReadGroupRecord; +import htsjdk.samtools.SAMFileHeader; +import htsjdk.samtools.SAMReadGroupRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java index 837f3fa45..efdda7f68 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.testng.Assert; import org.testng.annotations.BeforeClass; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java index eca27fcb2..8dd72ace1 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/MisencodedBaseQualityUnitTest.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java index 5732e5746..01fe15e6a 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/sam/ReadUtilsUnitTest.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.sam; -import net.sf.picard.reference.IndexedFastaSequenceFile; -import net.sf.samtools.SAMFileHeader; +import htsjdk.samtools.reference.IndexedFastaSequenceFile; +import htsjdk.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.BaseUtils; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java index e5b49dc65..377817a16 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java @@ -25,10 +25,10 @@ package org.broadinstitute.sting.utils.variant; -import org.broad.tribble.index.DynamicIndexCreator; -import org.broad.tribble.index.IndexCreator; -import org.broad.tribble.index.interval.IntervalIndexCreator; -import org.broad.tribble.index.linear.LinearIndexCreator; +import htsjdk.tribble.index.DynamicIndexCreator; +import htsjdk.tribble.index.IndexCreator; +import htsjdk.tribble.index.interval.IntervalIndexCreator; +import htsjdk.tribble.index.linear.LinearIndexCreator; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; @@ -36,8 +36,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.variant.vcf.VCFHeader; -import org.broadinstitute.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java index 0e0e52dba..f3dd98044 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java @@ -31,7 +31,7 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; -import org.broadinstitute.variant.variantcontext.*; +import htsjdk.variant.variantcontext.*; import org.testng.Assert; import org.testng.annotations.BeforeSuite; import org.testng.annotations.DataProvider; diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java index 7bd266151..688663abf 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java @@ -25,19 +25,19 @@ package org.broadinstitute.sting.utils.variant; -import org.broad.tribble.AbstractFeatureReader; -import org.broad.tribble.Tribble; -import org.broad.tribble.index.AbstractIndex; -import org.broad.tribble.index.ChrIndex; -import org.broad.tribble.index.Index; -import org.broad.tribble.index.IndexFactory; -import org.broad.tribble.index.interval.IntervalTreeIndex; -import org.broad.tribble.index.linear.LinearIndex; -import org.broad.tribble.index.tabix.TabixIndex; -import org.broad.tribble.util.TabixUtils; +import htsjdk.tribble.AbstractFeatureReader; +import htsjdk.tribble.Tribble; +import htsjdk.tribble.index.AbstractIndex; +import htsjdk.tribble.index.ChrIndex; +import htsjdk.tribble.index.Index; +import htsjdk.tribble.index.IndexFactory; +import htsjdk.tribble.index.interval.IntervalTreeIndex; +import htsjdk.tribble.index.linear.LinearIndex; +import htsjdk.tribble.index.tabix.TabixIndex; +import htsjdk.tribble.util.TabixUtils; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.WalkerTest; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.variant.vcf.VCFCodec; import org.testng.Assert; import org.testng.TestException; import org.testng.annotations.DataProvider; @@ -253,8 +253,8 @@ public class VCFIntegrationTest extends WalkerTest { } private static boolean equivalentLinearIndices(LinearIndex thisIndex, LinearIndex otherIndex, String chr) throws NoSuchFieldException, IllegalAccessException { - org.broad.tribble.index.linear.LinearIndex.ChrIndex thisChr = (org.broad.tribble.index.linear.LinearIndex.ChrIndex)getChrIndex(thisIndex, chr); - org.broad.tribble.index.linear.LinearIndex.ChrIndex otherChr = (org.broad.tribble.index.linear.LinearIndex.ChrIndex)getChrIndex(otherIndex, chr); + htsjdk.tribble.index.linear.LinearIndex.ChrIndex thisChr = (htsjdk.tribble.index.linear.LinearIndex.ChrIndex)getChrIndex(thisIndex, chr); + htsjdk.tribble.index.linear.LinearIndex.ChrIndex otherChr = (htsjdk.tribble.index.linear.LinearIndex.ChrIndex)getChrIndex(otherIndex, chr); return thisChr.getName().equals(otherChr.getName()) && //thisChr.getTotalSize() == otherChr.getTotalSize() && TODO: why does this differ? @@ -263,8 +263,8 @@ public class VCFIntegrationTest extends WalkerTest { } private static boolean equivalentIntervalIndices(IntervalTreeIndex thisIndex, IntervalTreeIndex otherIndex, String chr) throws NoSuchFieldException, IllegalAccessException { - org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex thisChr = (org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex)getChrIndex(thisIndex, chr); - org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex otherChr = (org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex)getChrIndex(otherIndex, chr); + htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex thisChr = (htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex)getChrIndex(thisIndex, chr); + htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex otherChr = (htsjdk.tribble.index.interval.IntervalTreeIndex.ChrIndex)getChrIndex(otherIndex, chr); // TODO: compare trees? return thisChr.getName().equals(otherChr.getName()); diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java index bb794dca4..dcb7a3862 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VariantContextBenchmark.java @@ -27,10 +27,10 @@ package org.broadinstitute.sting.utils.variant; import com.google.caliper.Param; import com.google.caliper.SimpleBenchmark; -import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; -import org.broadinstitute.variant.variantcontext.*; -import org.broadinstitute.variant.vcf.VCFCodec; +import htsjdk.tribble.Feature; +import htsjdk.tribble.FeatureCodec; +import htsjdk.variant.variantcontext.*; +import htsjdk.variant.vcf.VCFCodec; import java.util.ArrayList; import java.util.HashSet; @@ -254,54 +254,54 @@ 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.variant.variantcontext.v13.VCFCodec(); +// FunctionToBenchmark func = getV13FunctionToBenchmark(); +// FeatureCodec codec = new htsjdk.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.variant.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final htsjdk.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.variant.variantcontext.v13.VariantContext vc) { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { // if ( samples == null ) // samples = new ArrayList(vc.getSampleNames()).subList(0, nSamplesToTake); -// org.broadinstitute.variant.variantcontext.v13.VariantContext sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values()); +// htsjdk.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.variant.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { // vc.getType(); // } // }; // case GET_ID: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { // vc.getID(); // } // }; // case GET_GENOTYPES: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final htsjdk.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.variant.variantcontext.v13.VariantContext vc) { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { // if ( samples == null ) // samples = new HashSet(new ArrayList(vc.getSampleNames()).subList(0, nSamplesToTake)); // vc.getGenotypes(samples).size(); @@ -309,60 +309,60 @@ public class VariantContextBenchmark extends SimpleBenchmark { // }; // // case GET_ATTRIBUTE_STRING: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { // vc.getExtendedAttribute("AN", null); // } // }; // // case GET_ATTRIBUTE_INT: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { // vc.getAttributeAsInt("AC", 0); // } // }; // // case GET_N_SAMPLES: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { // vc.getNSamples(); // } // }; // // case GET_GENOTYPES_IN_ORDER_OF_NAME: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { // ; // TODO - TEST IS BROKEN // //vc.getGenotypesOrderedByName(); // } // }; // // case CALC_GENOTYPE_COUNTS: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { +// return new FunctionToBenchmark() { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { // vc.getHetCount(); // } // }; // // case MERGE: -// return new FunctionToBenchmark() { -// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) { -// List toMerge = new ArrayList(); +// return new FunctionToBenchmark() { +// public void run(final htsjdk.variant.variantcontext.v13.VariantContext vc) { +// List toMerge = new ArrayList(); // // for ( int i = 0; i < dupsToMerge; i++ ) { -// Map gc = new HashMap(); -// for ( final org.broadinstitute.variant.variantcontext.v13.Genotype g : vc.getGenotypes().values() ) { +// Map gc = new HashMap(); +// for ( final htsjdk.variant.variantcontext.v13.Genotype g : vc.getGenotypes().values() ) { // String name = g.getSampleName()+"_"+i; -// gc.put(name, new org.broadinstitute.variant.variantcontext.v13.Genotype(name, +// gc.put(name, new htsjdk.variant.variantcontext.v13.Genotype(name, // g.getAlleles(), g.getLog10PError(), g.getFilters(), g.getAttributes(), g.isPhased(), g.getLikelihoods().getAsVector())); -// toMerge.add(org.broadinstitute.variant.variantcontext.v13.VariantContext.modifyGenotypes(vc, gc)); +// toMerge.add(htsjdk.variant.variantcontext.v13.VariantContext.modifyGenotypes(vc, gc)); // } // } // -// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.simpleMerge(b37GenomeLocParser, +// htsjdk.variant.variantcontext.v13.VariantContextUtils.simpleMerge(b37GenomeLocParser, // toMerge, null, -// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, -// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.GenotypeMergeType.UNSORTED, +// htsjdk.variant.variantcontext.v13.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, +// htsjdk.variant.variantcontext.v13.VariantContextUtils.GenotypeMergeType.UNSORTED, // true, false, "set", false, true, false); // } // }; diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml index 9e06dce73..a8500815c 100644 --- a/public/gatk-package/pom.xml +++ b/public/gatk-package/pom.xml @@ -28,15 +28,10 @@ gatk-framework ${project.version} - + - org.broad - tribble - - - - org.broadinstitute - variant + samtools + htsjdk diff --git a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java index 51cc576aa..a1ad05e24 100644 --- a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java +++ b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java @@ -24,12 +24,12 @@ */ package org.broadinstitute.sting.queue.extensions.gatk; -import net.sf.samtools.BAMIndex; -import net.sf.samtools.SAMFileWriter; -import org.broad.tribble.Tribble; +import htsjdk.samtools.BAMIndex; +import htsjdk.samtools.SAMFileWriter; +import htsjdk.tribble.Tribble; import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.lang.annotation.Annotation; diff --git a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java index a036a8923..45b4e529c 100644 --- a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java +++ b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java @@ -25,12 +25,12 @@ package org.broadinstitute.sting.queue.extensions.gatk; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMFileWriter; +import htsjdk.samtools.SAMFileReader; +import htsjdk.samtools.SAMFileWriter; import org.apache.commons.lang.StringEscapeUtils; import org.apache.commons.lang.StringUtils; import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper; -import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; +import htsjdk.variant.variantcontext.writer.VariantContextWriter; import java.io.File; import java.io.InputStream; diff --git a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java index e97eff262..51b08f324 100644 --- a/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java +++ b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.queue.extensions.gatk; -import net.sf.picard.filter.SamRecordFilter; +import htsjdk.samtools.filter.SamRecordFilter; import org.broadinstitute.sting.commandline.ParsingEngine; import org.broadinstitute.sting.gatk.WalkerManager; import org.broadinstitute.sting.gatk.walkers.Walker; diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala index f580ba116..899551d0f 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala @@ -33,7 +33,7 @@ import org.broadinstitute.sting.queue.util.ClassFieldCache import java.io.File /** - * Merges BAM files using net.sf.picard.sam.MergeSamFiles. + * Merges BAM files using htsjdk.samtools.MergeSamFiles. */ class BamGatherFunction extends MergeSamFiles with GatherFunction with RetryMemoryLimit { this.assumeSorted = Some(true) diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala index 34e59e00c..c4c193110 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala @@ -29,10 +29,10 @@ import java.io.File import collection.JavaConversions._ import org.broadinstitute.sting.utils.interval.{IntervalSetRule, IntervalMergingRule, IntervalUtils} import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource -import net.sf.samtools.SAMFileHeader +import htsjdk.samtools.SAMFileHeader import org.broadinstitute.sting.utils.GenomeLoc import org.broadinstitute.sting.commandline._ -import org.broad.tribble.Feature +import htsjdk.tribble.Feature case class GATKIntervals(reference: File, intervals: Seq[File], intervalsString: Seq[String], intervalSetRule: IntervalSetRule, intervalMergingRule: IntervalMergingRule, intervalPadding: Option[Int], diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala index c33908f4a..0ca404f28 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala @@ -37,7 +37,7 @@ import java.io.File */ class AddOrReplaceReadGroups extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "AddOrReplaceReadGroups" - javaMainClass = "net.sf.picard.sam.AddOrReplaceReadGroups" + javaMainClass = "picard.sam.AddOrReplaceReadGroups" @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala index 3fd9a3c6d..cbad1206b 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala @@ -27,7 +27,7 @@ package org.broadinstitute.sting.queue.extensions.picard import org.broadinstitute.sting.commandline.{Argument, Output, Input} import java.io.File -import net.sf.picard.analysis.MetricAccumulationLevel +import picard.analysis.MetricAccumulationLevel /** * Created with IntelliJ IDEA. @@ -38,7 +38,7 @@ import net.sf.picard.analysis.MetricAccumulationLevel */ class CalculateHsMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction { analysisName = "CalculateHsMetrics" - javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics" + javaMainClass = "picard.analysis.directed.CalculateHsMetrics" @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala index 14c10c581..620be56a7 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala @@ -37,7 +37,7 @@ import java.io.File */ class CollectGcBiasMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction { analysisName = "CollectGcBiasMetrics" - javaMainClass = "net.sf.picard.analysis.CollectGcBiasMetrics" + javaMainClass = "picard.analysis.CollectGcBiasMetrics" @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala index 3c122ee60..18079808c 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala @@ -37,7 +37,7 @@ import java.io.File */ class CollectMultipleMetrics extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardMetricsFunction{ analysisName = "CollectMultipleMetrics" - javaMainClass = "net.sf.picard.analysis.CollectMultipleMetrics" + javaMainClass = "picard.analysis.CollectMultipleMetrics" @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala index 7b9e657bf..11e2aa349 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala @@ -56,7 +56,7 @@ import java.io.File class FastqToSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction /*with PicardBamFunction*/ { analysisName = "FastqToSam" - javaMainClass = "net.sf.picard.sam.FastqToSam" + javaMainClass = "picard.sam.FastqToSam" @Input(shortName = "fq1", fullName = "input_fq_file1", required = true, doc = "Input Fastq file to extract reads from (single-end fastq or, if paired, first end of the pair fastq)") var fastq: File = _ diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala index 7567434e2..68d0c9ef3 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala @@ -37,7 +37,7 @@ import java.io.File */ class MarkDuplicates extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "MarkDuplicates" - javaMainClass = "net.sf.picard.sam.MarkDuplicates" + javaMainClass = "picard.sam.MarkDuplicates" @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala index c4df6776c..1333d4a19 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala @@ -37,7 +37,7 @@ import java.io.File */ class MergeSamFiles extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "MergeSamFiles" - javaMainClass = "net.sf.picard.sam.MergeSamFiles" + javaMainClass = "picard.sam.MergeSamFiles" @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala index 8fb21477c..08ac5352e 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala @@ -27,8 +27,8 @@ package org.broadinstitute.sting.queue.extensions.picard import java.io.File import org.broadinstitute.sting.queue.function.JavaCommandLineFunction -import net.sf.samtools.SAMFileReader.ValidationStringency -import net.sf.samtools.SAMFileHeader.SortOrder +import htsjdk.samtools.SAMFileReader.ValidationStringency +import htsjdk.samtools.SAMFileHeader.SortOrder /** * Wraps a Picard function that operates on BAM files. diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala index 137098292..b48715292 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala @@ -27,8 +27,8 @@ package org.broadinstitute.sting.queue.extensions.picard import java.io.File import org.broadinstitute.sting.queue.function.JavaCommandLineFunction -import net.sf.samtools.SAMFileReader.ValidationStringency -import net.sf.samtools.SAMFileHeader.SortOrder +import htsjdk.samtools.SAMFileReader.ValidationStringency +import htsjdk.samtools.SAMFileHeader.SortOrder /** * Wraps a Picard function that operates on BAM files but doesn't output a new BAM file (i.e. QC metric files). diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala index 837340cca..ff17cfda6 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala @@ -36,7 +36,7 @@ import java.io.File */ class ReorderSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "ReorderSam" - javaMainClass = "net.sf.picard.sam.ReorderSam" + javaMainClass = "picard.sam.ReorderSam" @Input(doc="Input file (bam or sam) to extract reads from.", shortName = "input", fullName = "input_bam_files", required = true) var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala index 666e0b70d..c099faf4c 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala @@ -37,7 +37,7 @@ import java.io.File */ class RevertSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "RevertSam" - javaMainClass = "net.sf.picard.sam.RevertSam" + javaMainClass = "picard.sam.RevertSam" @Input(shortName = "input", fullName = "input_bam_files", required = true, doc = "The input SAM or BAM files to revert.") var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala index e09e0c100..adc0afb2f 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala @@ -37,7 +37,7 @@ import java.io.File */ class SamToFastq extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "SamToFastq" - javaMainClass = "net.sf.picard.sam.SamToFastq" + javaMainClass = "picard.sam.SamToFastq" @Input(shortName = "input", fullName = "input_bam_files", required = true, doc = "Input SAM/BAM file to extract reads from.") var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala index 6acc216bb..d34b421f4 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala @@ -37,7 +37,7 @@ import java.io.File */ class SortSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "SortSam" - javaMainClass = "net.sf.picard.sam.SortSam" + javaMainClass = "picard.sam.SortSam" @Input(doc="The input SAM or BAM files to sort.", shortName = "input", fullName = "input_bam_files", required = true) var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala index 4d6a110b6..5690b488d 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala @@ -27,7 +27,7 @@ package org.broadinstitute.sting.queue.extensions.picard import org.broadinstitute.sting.commandline._ -import net.sf.picard.sam.ValidateSamFile.Mode +import picard.sam.ValidateSamFile.Mode import java.io.File @@ -39,7 +39,7 @@ import java.io.File */ class ValidateSamFile extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction { analysisName = "ValidateSamFile" - javaMainClass = "net.sf.picard.sam.ValidateSamFile" + javaMainClass = "picard.sam.ValidateSamFile" @Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", shortName = "input", fullName = "input_bam_files", required = true) var input: Seq[File] = Nil diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala index 56e7cd32f..6c17ff47e 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala @@ -30,7 +30,7 @@ import org.broadinstitute.sting.queue.function.InProcessFunction import org.broadinstitute.sting.commandline._ import org.broadinstitute.sting.utils.text.XReadLines import java.io.{PrintStream, PrintWriter, File} -import net.sf.samtools.{SAMSequenceRecord, SAMSequenceDictionary} +import htsjdk.samtools.{SAMSequenceRecord, SAMSequenceDictionary} import org.broadinstitute.sting.utils.{GenomeLocParser, GenomeLoc} class VCFSimpleMerge extends InProcessFunction { diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala index b078bcd4f..cad16a6df 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala @@ -27,7 +27,7 @@ package org.broadinstitute.sting.queue.util import java.io.File import io.Source._ -import net.sf.samtools.{SAMReadGroupRecord, SAMFileReader} +import htsjdk.samtools.{SAMReadGroupRecord, SAMFileReader} import collection.JavaConversions._ diff --git a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala index 5802faff2..f500be0fb 100644 --- a/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala +++ b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala @@ -28,10 +28,10 @@ package org.broadinstitute.sting.queue.util import java.io.File import org.apache.commons.io.FilenameUtils import scala.io.Source._ -import net.sf.samtools.SAMFileReader -import org.broadinstitute.variant.vcf.{VCFHeader, VCFCodec} +import htsjdk.samtools.SAMFileReader +import htsjdk.variant.vcf.{VCFHeader, VCFCodec} import scala.collection.JavaConversions._ -import org.broad.tribble.AbstractFeatureReader +import htsjdk.tribble.AbstractFeatureReader object VCF_BAM_utilities { diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml index cb75a6891..3a266236c 100644 --- a/public/queue-package/pom.xml +++ b/public/queue-package/pom.xml @@ -44,7 +44,7 @@ - net.sf + picard picard diff --git a/public/repo/net/sf/picard/1.111.1920/picard-1.111.1920.jar b/public/repo/net/sf/picard/1.111.1920/picard-1.111.1920.jar deleted file mode 100644 index 4933ed477..000000000 Binary files a/public/repo/net/sf/picard/1.111.1920/picard-1.111.1920.jar and /dev/null differ diff --git a/public/repo/net/sf/sam/1.111.1920/sam-1.111.1920.jar b/public/repo/net/sf/sam/1.111.1920/sam-1.111.1920.jar deleted file mode 100644 index 7f6839e1b..000000000 Binary files a/public/repo/net/sf/sam/1.111.1920/sam-1.111.1920.jar and /dev/null differ diff --git a/public/repo/org/broad/tribble/1.111.1920/tribble-1.111.1920.jar b/public/repo/org/broad/tribble/1.111.1920/tribble-1.111.1920.jar deleted file mode 100644 index 804db912a..000000000 Binary files a/public/repo/org/broad/tribble/1.111.1920/tribble-1.111.1920.jar and /dev/null differ diff --git a/public/repo/org/broad/tribble/1.111.1920/tribble-1.111.1920.pom b/public/repo/org/broad/tribble/1.111.1920/tribble-1.111.1920.pom deleted file mode 100644 index af3cf6095..000000000 --- a/public/repo/org/broad/tribble/1.111.1920/tribble-1.111.1920.pom +++ /dev/null @@ -1,15 +0,0 @@ - - - 4.0.0 - org.broad - tribble - 1.111.1920 - tribble - - - net.sf - sam - 1.111.1920 - - - diff --git a/public/repo/org/broadinstitute/variant/1.111.1920/variant-1.111.1920.jar b/public/repo/org/broadinstitute/variant/1.111.1920/variant-1.111.1920.jar deleted file mode 100644 index b0447f3df..000000000 Binary files a/public/repo/org/broadinstitute/variant/1.111.1920/variant-1.111.1920.jar and /dev/null differ diff --git a/public/repo/org/broadinstitute/variant/1.111.1920/variant-1.111.1920.pom b/public/repo/org/broadinstitute/variant/1.111.1920/variant-1.111.1920.pom deleted file mode 100644 index ca20e97d9..000000000 --- a/public/repo/org/broadinstitute/variant/1.111.1920/variant-1.111.1920.pom +++ /dev/null @@ -1,31 +0,0 @@ - - - 4.0.0 - org.broadinstitute - variant - 1.111.1920 - variant - - - org.broad - tribble - 1.111.1920 - - - net.sf - sam - 1.111.1920 - - - org.apache.commons - commons-jexl - 2.1.1 - - - - com.google.code.cofoja - cofoja - 1.0-r139 - - - diff --git a/public/repo/picard/picard/1.112.1452/picard-1.112.1452.jar b/public/repo/picard/picard/1.112.1452/picard-1.112.1452.jar new file mode 100644 index 000000000..c56a3a92d Binary files /dev/null and b/public/repo/picard/picard/1.112.1452/picard-1.112.1452.jar differ diff --git a/public/repo/net/sf/picard/1.111.1920/picard-1.111.1920.pom b/public/repo/picard/picard/1.112.1452/picard-1.112.1452.pom similarity index 69% rename from public/repo/net/sf/picard/1.111.1920/picard-1.111.1920.pom rename to public/repo/picard/picard/1.112.1452/picard-1.112.1452.pom index 14e5c9c88..bd617dde1 100644 --- a/public/repo/net/sf/picard/1.111.1920/picard-1.111.1920.pom +++ b/public/repo/picard/picard/1.112.1452/picard-1.112.1452.pom @@ -1,25 +1,15 @@ 4.0.0 - net.sf + picard picard - 1.111.1920 + 1.112.1452 picard - net.sf - sam - 1.111.1920 - - - org.broadinstitute - variant - 1.111.1920 - - - org.broad - tribble - 1.111.1920 + samtools + htsjdk + 1.112.1452 diff --git a/public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.jar b/public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.jar new file mode 100644 index 000000000..80b759ec7 Binary files /dev/null and b/public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.jar differ diff --git a/public/repo/net/sf/sam/1.111.1920/sam-1.111.1920.pom b/public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.pom similarity index 64% rename from public/repo/net/sf/sam/1.111.1920/sam-1.111.1920.pom rename to public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.pom index 266aa93dd..0b8c2db4d 100644 --- a/public/repo/net/sf/sam/1.111.1920/sam-1.111.1920.pom +++ b/public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.pom @@ -1,10 +1,10 @@ 4.0.0 - net.sf - sam - 1.111.1920 - sam-jdk + samtools + htsjdk + 1.112.1452 + htsjdk org.testng @@ -17,5 +17,11 @@ snappy-java 1.0.3-rc3 + + + com.google.code.cofoja + cofoja + 1.0-r139 + diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml index fe807da50..38078312f 100644 --- a/public/sting-root/pom.xml +++ b/public/sting-root/pom.xml @@ -42,12 +42,9 @@ 10 -Xmx${test.maxmemory} -XX:+UseParallelOldGC -XX:ParallelGCThreads=${java.gc.threads} -XX:GCTimeLimit=${java.gc.timeLimit} -XX:GCHeapFreeLimit=${java.gc.heapFreeLimit} - - 1.111.1920 - ${picard.public.version} - ${picard.public.version} - ${picard.public.version} - ${picard.public.version} + + 1.112.1452 + 1.112.1452 @@ -69,9 +66,9 @@ 1.0-r139 - net.sf - sam - ${sam.version} + samtools + htsjdk + ${htsjdk.version} org.testng @@ -80,20 +77,10 @@ - net.sf + picard picard ${picard.version} - - org.broad - tribble - ${tribble.version} - - - org.broadinstitute - variant - ${variant.version} - log4j log4j diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml index fddd43946..ab4b7e1b7 100644 --- a/public/sting-utils/pom.xml +++ b/public/sting-utils/pom.xml @@ -21,21 +21,13 @@ - net.sf - sam + samtools + htsjdk - net.sf + picard picard - - org.broad - tribble - - - org.broadinstitute - variant - log4j log4j