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Merge pull request #627 from broadinstitute/ks_picard_htsjdk_package_rename 

picard/htsjdk package rename
This commit is contained in:
kshakir 2014-05-08 13:12:22 -04:00
parent 53b2364cf8 67e44985b1
commit cca3d167db
647 changed files with 1719 additions and 1798 deletions
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2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
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@ -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.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.utils.collections.DefaultHashMap; import org.broadinstitute.sting.utils.collections.DefaultHashMap;
import org.broadinstitute.sting.utils.variant.HomoSapiensConstants; import org.broadinstitute.sting.utils.variant.HomoSapiensConstants;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.io.File; import java.io.File;
import java.lang.reflect.Field; import java.lang.reflect.Field;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
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@ -49,8 +49,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
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@ -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.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils; import htsjdk.variant.variantcontext.VariantContextUtils;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
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@ -47,8 +47,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator; package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java
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@ -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.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import htsjdk.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

14
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -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.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; import htsjdk.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import htsjdk.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

14
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
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@ -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.MostLikelyAllele;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; import htsjdk.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import htsjdk.variant.vcf.VCFStandardHeaderLines;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -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.MostLikelyAllele;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
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@ -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.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; 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.Arrays;
import java.util.HashMap; import java.util.HashMap;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GenotypeSummaries.java
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@ -55,10 +55,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import java.util.*; import java.util.*;

10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -58,16 +58,16 @@ import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.io.Serializable; import java.io.Serializable;
import java.util.*; import java.util.*;

12
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
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@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator; 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.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -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.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
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@ -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.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java
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@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele; import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
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@ -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.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MendelianViolation; import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
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@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
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@ -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.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import htsjdk.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; 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.Arrays;
import java.util.HashMap; import java.util.HashMap;

10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -57,11 +57,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -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.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines; import htsjdk.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -58,14 +58,14 @@ import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MannWhitneyU; import org.broadinstitute.sting.utils.MannWhitneyU;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; 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.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

12
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
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@ -46,14 +46,14 @@
package org.broadinstitute.sting.gatk.walkers.annotator; package org.broadinstitute.sting.gatk.walkers.annotator;
import net.sf.samtools.Cigar; import htsjdk.samtools.Cigar;
import net.sf.samtools.CigarElement; import htsjdk.samtools.CigarElement;
import net.sf.samtools.CigarOperator; import htsjdk.samtools.CigarOperator;
import net.sf.samtools.SAMRecord; import htsjdk.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
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@ -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.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFHeaderLineCount; import htsjdk.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
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@ -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.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
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@ -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.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine; import htsjdk.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasTest.java
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@ -47,8 +47,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator; package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.GenotypesContext;
import java.util.*; import java.util.*;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandOddsRatio.java
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@ -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.AnnotatorCompatible;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBasedAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
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@ -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.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.vcf.VCFHeaderLineCount; import htsjdk.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
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@ -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.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineCount; import htsjdk.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
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@ -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.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.IndelUtils; import org.broadinstitute.sting.utils.IndelUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -46,10 +46,10 @@
package org.broadinstitute.sting.gatk.walkers.bqsr; package org.broadinstitute.sting.gatk.walkers.bqsr;
import net.sf.picard.reference.IndexedFastaSequenceFile; import htsjdk.samtools.reference.IndexedFastaSequenceFile;
import net.sf.samtools.CigarElement; import htsjdk.samtools.CigarElement;
import net.sf.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileHeader;
import org.broad.tribble.Feature; import htsjdk.tribble.Feature;
import org.broadinstitute.sting.commandline.Advanced; import org.broadinstitute.sting.commandline.Advanced;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection; import org.broadinstitute.sting.commandline.ArgumentCollection;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
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@ -47,7 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.bqsr; package org.broadinstitute.sting.gatk.walkers.bqsr;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import org.broad.tribble.Feature; import htsjdk.tribble.Feature;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
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@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.diagnostics.diagnosetargets; 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.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK; 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.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.vcf.*; import htsjdk.variant.vcf.*;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
View File

@ -59,7 +59,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
View File

@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper; 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.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
View File

@ -55,8 +55,8 @@ import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
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@ -46,17 +46,17 @@
package org.broadinstitute.sting.gatk.walkers.genotyper; 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.ExactACcounts;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.sting.utils.MathUtils; 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.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; import htsjdk.variant.variantcontext.GenotypeLikelihoods;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
View File

@ -55,11 +55,11 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; 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.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
View File

@ -54,7 +54,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
View File

@ -54,7 +54,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
View File

@ -47,7 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper; 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.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils; 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.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; 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.ArrayList;
import java.util.Arrays; import java.util.Arrays;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
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@ -79,7 +79,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
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@ -56,8 +56,8 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypingEngine.java
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@ -67,8 +67,8 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils; import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import org.broadinstitute.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFConstants;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -59,7 +59,7 @@ import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -63,7 +63,7 @@ import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -49,7 +49,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
import org.broadinstitute.sting.utils.pairhmm.PairHMM; import org.broadinstitute.sting.utils.pairhmm.PairHMM;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
public class UnifiedArgumentCollection extends StandardCallerArgumentCollection { public class UnifiedArgumentCollection extends StandardCallerArgumentCollection {

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -64,12 +64,12 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; 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.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; import htsjdk.variant.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.*; import java.util.*;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotypingEngine.java
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@ -62,9 +62,9 @@ import org.broadinstitute.sting.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.io.PrintStream; import java.io.PrintStream;
import java.lang.reflect.Constructor; import java.lang.reflect.Constructor;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
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@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper; package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
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@ -50,9 +50,9 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.SimpleTimer; import org.broadinstitute.sting.utils.SimpleTimer;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.io.File; import java.io.File;
import java.util.List; import java.util.List;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
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@ -56,10 +56,10 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SimpleTimer; import org.broadinstitute.sting.utils.SimpleTimer;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.variantcontext.VariantContextBuilder;
import java.io.*; import java.io.*;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
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@ -50,7 +50,7 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
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@ -50,7 +50,7 @@ import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypingEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypingEngine;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
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@ -48,10 +48,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods; import htsjdk.variant.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.variant.variantcontext.GenotypesContext; import htsjdk.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
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@ -48,7 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
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@ -50,7 +50,7 @@ import com.google.java.contract.Requires;
import org.apache.commons.lang.ArrayUtils; import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.io.*; import java.io.*;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
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@ -49,9 +49,9 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; 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.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
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@ -49,7 +49,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
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@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
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@ -49,7 +49,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
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@ -53,7 +53,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
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@ -54,7 +54,7 @@ import org.broadinstitute.sting.utils.collections.CountSet;
import org.broadinstitute.sting.utils.haplotype.EventMap; import org.broadinstitute.sting.utils.haplotype.EventMap;
import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.haplotype.HaplotypeSizeAndBaseComparator; 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.PrintWriter;
import java.io.StringWriter; import java.io.StringWriter;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
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@ -60,7 +60,7 @@ import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM; import org.broadinstitute.sting.utils.pairhmm.FlexibleHMM;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -47,7 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller; package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import net.sf.samtools.SAMFileWriter; import htsjdk.samtools.SAMFileWriter;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection; 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.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType; import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.vcf.*; import htsjdk.variant.vcf.*;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
import java.io.PrintStream; import java.io.PrintStream;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
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@ -64,7 +64,7 @@ import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.haplotype.MergeVariantsAcrossHaplotypes; import org.broadinstitute.sting.utils.haplotype.MergeVariantsAcrossHaplotypes;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

20
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
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@ -61,18 +61,18 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment; import org.broadinstitute.sting.utils.smithwaterman.SWPairwiseAlignment;
import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType; import htsjdk.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine; import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.VariantContextUtils; import htsjdk.variant.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
View File

@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller; package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import net.sf.samtools.SAMRecord; import htsjdk.samtools.SAMRecord;
import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.haplotype.Haplotype;
import java.lang.reflect.Array; import java.lang.reflect.Array;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
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@ -48,9 +48,9 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import net.sf.samtools.Cigar; import htsjdk.samtools.Cigar;
import net.sf.samtools.CigarElement; import htsjdk.samtools.CigarElement;
import net.sf.samtools.CigarOperator; import htsjdk.samtools.CigarOperator;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*;
import org.broadinstitute.sting.utils.GenomeLoc; 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.haplotype.Haplotype;
import org.broadinstitute.sting.utils.sam.CigarUtils; import org.broadinstitute.sting.utils.sam.CigarUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; 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.File;
import java.io.PrintStream; import java.io.PrintStream;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
View File

@ -48,7 +48,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import net.sf.samtools.SAMUtils; import htsjdk.samtools.SAMUtils;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils; 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.RepeatCovariate;
import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate; import org.broadinstitute.sting.utils.recalibration.covariates.RepeatLengthCovariate;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.io.File; import java.io.File;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
View File

@ -49,7 +49,7 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.haplotype.Haplotype; import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; 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.HashMap;
import java.util.List; import java.util.List;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
View File

@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller; 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.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; 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.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import org.broadinstitute.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFSimpleHeaderLine; import htsjdk.variant.vcf.VCFSimpleHeaderLine;
import java.io.File; import java.io.File;
import java.util.*; import java.util.*;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
View File

@ -47,7 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs; package org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import net.sf.samtools.Cigar; import htsjdk.samtools.Cigar;
import org.apache.commons.lang.ArrayUtils; import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.utils.sam.CigarUtils; import org.broadinstitute.sting.utils.sam.CigarUtils;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java
View File

@ -47,9 +47,9 @@
package org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading; package org.broadinstitute.sting.gatk.walkers.haplotypecaller.readthreading;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import net.sf.samtools.Cigar; import htsjdk.samtools.Cigar;
import net.sf.samtools.CigarElement; import htsjdk.samtools.CigarElement;
import net.sf.samtools.CigarOperator; import htsjdk.samtools.CigarOperator;
import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*; import org.broadinstitute.sting.gatk.walkers.haplotypecaller.graphs.*;
import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.smithwaterman.*; import org.broadinstitute.sting.utils.smithwaterman.*;

10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
View File

@ -46,11 +46,11 @@
package org.broadinstitute.sting.gatk.walkers.indels; package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.SamPairUtil; import htsjdk.samtools.SamPairUtil;
import net.sf.samtools.SAMFileWriter; import htsjdk.samtools.SAMFileWriter;
import net.sf.samtools.SAMRecord; import htsjdk.samtools.SAMRecord;
import net.sf.samtools.SAMRecordComparator; import htsjdk.samtools.SAMRecordComparator;
import net.sf.samtools.SAMRecordCoordinateComparator; import htsjdk.samtools.SAMRecordCoordinateComparator;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
View File

@ -46,14 +46,14 @@
package org.broadinstitute.sting.gatk.walkers.indels; 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.haplotype.Haplotype;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; 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.Arrays;
import java.util.HashMap; import java.util.HashMap;

12
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -46,11 +46,11 @@
package org.broadinstitute.sting.gatk.walkers.indels; package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.*; import htsjdk.samtools.*;
import net.sf.samtools.util.RuntimeIOException; import htsjdk.samtools.util.RuntimeIOException;
import net.sf.samtools.util.SequenceUtil; import htsjdk.samtools.util.SequenceUtil;
import net.sf.samtools.util.StringUtil; import htsjdk.samtools.util.StringUtil;
import org.broad.tribble.Feature; import htsjdk.tribble.Feature;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; 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.sam.ReadUtils;
import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.text.XReadLines; 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.File;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
View File

@ -46,8 +46,8 @@
package org.broadinstitute.sting.gatk.walkers.indels; package org.broadinstitute.sting.gatk.walkers.indels;
import net.sf.samtools.Cigar; import htsjdk.samtools.Cigar;
import net.sf.samtools.SAMRecord; import htsjdk.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -61,7 +61,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils; 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.Arrays;
import java.util.LinkedHashMap; import java.util.LinkedHashMap;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
View File

@ -63,7 +63,7 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.ArrayList; import java.util.ArrayList;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
View File

@ -47,8 +47,8 @@
package org.broadinstitute.sting.gatk.walkers.phasing; package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
View File

@ -46,17 +46,17 @@
package org.broadinstitute.sting.gatk.walkers.phasing; 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.apache.log4j.Logger;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeader;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.io.File; import java.io.File;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
View File

@ -61,11 +61,11 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; 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.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.sting.utils.exceptions.UserException;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
View File

@ -46,15 +46,15 @@
package org.broadinstitute.sting.gatk.walkers.phasing; package org.broadinstitute.sting.gatk.walkers.phasing;
import net.sf.picard.reference.ReferenceSequenceFile; import htsjdk.samtools.reference.ReferenceSequenceFile;
import net.sf.samtools.util.StringUtil; import htsjdk.samtools.util.StringUtil;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; 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.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
View File

@ -64,15 +64,15 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.HasGenomeLocation; import org.broadinstitute.sting.utils.HasGenomeLocation;
import org.broadinstitute.sting.utils.SampleUtils; 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.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
import java.io.*; import java.io.*;
import java.util.*; import java.util.*;

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
View File

@ -48,8 +48,8 @@ package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype; import htsjdk.variant.variantcontext.Genotype;
class SNPallelePair extends AllelePair { class SNPallelePair extends AllelePair {

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/OverhangFixingManager.java
View File

@ -46,8 +46,8 @@
package org.broadinstitute.sting.gatk.walkers.rnaseq; package org.broadinstitute.sting.gatk.walkers.rnaseq;
import net.sf.samtools.SAMFileWriter; import htsjdk.samtools.SAMFileWriter;
import net.sf.samtools.SAMRecordCoordinateComparator; import htsjdk.samtools.SAMRecordCoordinateComparator;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java
View File

@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.rnaseq; 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.Advanced;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden; import org.broadinstitute.sting.commandline.Hidden;

10
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java
View File

@ -48,9 +48,9 @@ package org.broadinstitute.sting.gatk.walkers.simulatereads;
import cern.jet.random.Poisson; import cern.jet.random.Poisson;
import cern.jet.random.engine.MersenneTwister; import cern.jet.random.engine.MersenneTwister;
import net.sf.samtools.SAMFileHeader; import htsjdk.samtools.SAMFileHeader;
import net.sf.samtools.SAMProgramRecord; import htsjdk.samtools.SAMProgramRecord;
import net.sf.samtools.SAMReadGroupRecord; import htsjdk.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; 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.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.variant.vcf.*; import htsjdk.variant.vcf.*;
import org.broadinstitute.variant.variantcontext.*; import htsjdk.variant.variantcontext.*;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils;

12
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
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@ -57,13 +57,13 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.vcf.VCFUtils; import htsjdk.variant.vcf.VCFUtils;
import java.util.Map; import java.util.Map;
import java.util.Set; import java.util.Set;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
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@ -47,7 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.ArrayList; import java.util.ArrayList;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
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@ -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.AFCalc;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.TreeSet; import java.util.TreeSet;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
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@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.TreeSet; import java.util.TreeSet;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
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@ -49,9 +49,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.variantcontext.VariantContextBuilder;
import java.util.HashMap; import java.util.HashMap;
import java.util.List; import java.util.List;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
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@ -49,9 +49,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils; import htsjdk.variant.variantcontext.VariantContextUtils;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
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@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.TreeSet; import java.util.TreeSet;

2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
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@ -46,7 +46,7 @@
package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector; package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import java.util.TreeSet; import java.util.TreeSet;

6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
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@ -48,9 +48,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils; import htsjdk.variant.variantcontext.VariantContextUtils;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
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@ -56,12 +56,12 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import java.io.File; import java.io.File;
import java.util.*; import java.util.*;

8
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -59,12 +59,12 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants; import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils; 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.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder; import htsjdk.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import java.io.File; import java.io.File;
import java.util.*; import java.util.*;

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