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Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 

This is an intermediate commit so that there is a record of these changes in our
commit history. Next step is to isolate the test classes as well, and then move
the entire package to the Picard repository and replace it with a jar in our repo.

-Removed all dependencies on org.broadinstitute.sting (still need to do the test classes,
though)

-Had to split some of the utility classes into "GATK-specific" vs generic methods
(eg., GATKVCFUtils vs. VCFUtils)

-Placement of some methods and choice of exception classes to replace the StingExceptions
and UserExceptions may need to be tweaked until everyone is happy, but this can be
done after the move.
This commit is contained in:
David Roazen 2012-12-18 14:56:48 -05:00
parent 46c7ea834d
commit 07b369ca7e
311 changed files with 1816 additions and 1861 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

34
build.xml
View File

@ -644,12 +644,8 @@
<target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage"> <target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
<jar jarfile="${dist.dir}/StingUtils.jar"> <jar jarfile="${dist.dir}/StingUtils.jar">
<fileset dir="${java.classes}"> <fileset dir="${java.classes}" includes="**/sting/utils/**/*.class"/>
<include name="**/utils/**/*.class"/> <fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
<exclude name="**/utils/codecs/vcf/**/*.class"/>
<exclude name="**/utils/variantcontext/**/*.class"/>
</fileset>
<fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/> <fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/> <fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/> <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
@ -659,7 +655,7 @@
<include name="**/${R.package.path}/**/*.tar.gz"/> <include name="**/${R.package.path}/**/*.tar.gz"/>
</fileset> </fileset>
<fileset dir="${R.script.staging.dir}"> <fileset dir="${R.script.staging.dir}">
<include name="**/utils/**/*.R"/> <include name="**/sting/utils/**/*.R"/>
</fileset> </fileset>
<manifest> <manifest>
<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" /> <attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
@ -667,14 +663,10 @@
</jar> </jar>
</target> </target>
<target name="vcf.jar" depends="gatk.compile,init.jar"> <target name="variant.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/vcf.jar"> <jar jarfile="${dist.dir}/variant.jar">
<fileset dir="${java.classes}"> <fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/> <include name="org/broadinstitute/variant/**/*.class"/>
<include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/>
<include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**"/>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
</fileset> </fileset>
</jar> </jar>
</target> </target>
@ -685,7 +677,7 @@
<include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/> <include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
<include name="org/broadinstitute/sting/utils/GenomeLoc.class"/> <include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
<include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/> <include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
<include name="org/broadinstitute/sting/utils/BaseUtils.class"/> <include name="org/broadinstitute/variant/utils/BaseUtils.class"/>
<include name="org/broadinstitute/sting/utils/Utils.class"/> <include name="org/broadinstitute/sting/utils/Utils.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/> <include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
<include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/> <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
@ -703,12 +695,12 @@
<fileset dir="${java.contracts.dir}" /> <fileset dir="${java.contracts.dir}" />
<fileset dir="${java.classes}"> <fileset dir="${java.classes}">
<include name="${resource.file}" /> <include name="${resource.file}" />
<include name="**/gatk/**/*.class" /> <include name="**/sting/gatk/**/*.class" />
<include name="**/alignment/**/*.class"/> <include name="**/sting/alignment/**/*.class"/>
</fileset> </fileset>
<fileset dir="${R.script.staging.dir}"> <fileset dir="${R.script.staging.dir}">
<include name="**/gatk/**/*.R"/> <include name="**/sting/gatk/**/*.R"/>
<include name="**/alignment/**/*.R"/> <include name="**/sting/alignment/**/*.R"/>
</fileset> </fileset>
<fileset dir="${key.dir}"> <fileset dir="${key.dir}">
<include name="**/*.key"/> <include name="**/*.key"/>
@ -719,7 +711,7 @@
</jar> </jar>
<jar jarfile="${dist.dir}/Aligner.jar"> <jar jarfile="${dist.dir}/Aligner.jar">
<fileset dir="${java.classes}" includes="**/alignment/**/*.class" /> <fileset dir="${java.classes}" includes="**/sting/alignment/**/*.class" />
</jar> </jar>
<subant target="dist" genericantfile="build.xml"> <subant target="dist" genericantfile="build.xml">
@ -755,7 +747,7 @@
</jar> </jar>
</target> </target>
<target name="sting.jar" depends="sting-utils.jar, vcf.jar, gatk.jar, queue.jar" /> <target name="sting.jar" depends="sting-utils.jar, variant.jar, gatk.jar, queue.jar" />
<target name="init.manifests" depends="sting.jar"> <target name="init.manifests" depends="sting.jar">
<pathconvert property="jar.classpath" pathsep=" "> <pathconvert property="jar.classpath" pathsep=" ">

3
protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
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@ -30,7 +30,8 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.*; import java.util.*;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
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@ -8,8 +8,8 @@ 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.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.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

6
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
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@ -29,13 +29,13 @@ import net.sf.samtools.SAMUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACcounts; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.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.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods;
import java.util.*; import java.util.*;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
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@ -31,11 +31,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.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.sting.utils.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import java.util.*; import java.util.*;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
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@ -8,7 +8,7 @@ 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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*; import java.util.*;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
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@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import java.util.*; import java.util.*;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import net.sf.samtools.SAMUtils; import net.sf.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.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
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@ -31,7 +31,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
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;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*; import java.util.*;

8
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
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@ -10,10 +10,10 @@ 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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import java.io.*; import java.io.*;
import java.util.*; import java.util.*;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
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@ -4,7 +4,7 @@ import org.apache.commons.lang.ArrayUtils;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
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.sting.utils.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;

9
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
View File

@ -27,9 +27,10 @@ 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.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import java.util.*; import java.util.*;
@ -532,7 +533,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
} }
// if there is no mass on the (new) likelihoods, then just no-call the sample // if there is no mass on the (new) likelihoods, then just no-call the sample
if ( MathUtils.sum(newLikelihoods) > VariantContextUtils.SUM_GL_THRESH_NOCALL ) { if ( MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) {
newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES)); newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES));
} }
else { else {
@ -544,7 +545,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
gb.PL(newLikelihoods); gb.PL(newLikelihoods);
// if we weren't asked to assign a genotype, then just no-call the sample // if we weren't asked to assign a genotype, then just no-call the sample
if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > VariantContextUtils.SUM_GL_THRESH_NOCALL ) if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL )
gb.alleles(NO_CALL_ALLELES); gb.alleles(NO_CALL_ALLELES);
else else
assignGenotype(gb, newLikelihoods, allelesToUse, ploidy); assignGenotype(gb, newLikelihoods, allelesToUse, ploidy);

8
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
View File

@ -36,7 +36,9 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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.sting.utils.variantcontext.*; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.*;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.*; import java.util.*;
@ -158,7 +160,7 @@ public class GenotypingEngine {
} }
// Merge the event to find a common reference representation // Merge the event to find a common reference representation
final VariantContext mergedVC = VariantContextUtils.simpleMerge(genomeLocParser, eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false); final VariantContext mergedVC = VariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
if( mergedVC == null ) { continue; } if( mergedVC == null ) { continue; }
// let's update the Allele keys in the mapper because they can change after merging when there are complex events // let's update the Allele keys in the mapper because they can change after merging when there are complex events
@ -200,7 +202,7 @@ public class GenotypingEngine {
VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, call); VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, call);
if( annotatedCall.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary! if( annotatedCall.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary!
annotatedCall = VariantContextUtils.reverseTrimAlleles(annotatedCall); annotatedCall = GATKVariantContextUtils.reverseTrimAlleles(annotatedCall);
} }
returnCalls.add( annotatedCall ); returnCalls.add( annotatedCall );

12
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -48,8 +48,8 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState; import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult; import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.variant.vcf.*;
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.sting.utils.fragments.FragmentCollection; import org.broadinstitute.sting.utils.fragments.FragmentCollection;
@ -61,8 +61,8 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.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.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
import java.io.PrintStream; import java.io.PrintStream;
@ -238,7 +238,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
samplesList.addAll( samples ); samplesList.addAll( samples );
// initialize the UnifiedGenotyper Engine which is used to call into the exact model // initialize the UnifiedGenotyper Engine which is used to call into the exact model
final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection( SCAC ); // this adapter is used so that the full set of unused UG arguments aren't exposed to the HC user final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection( SCAC ); // this adapter is used so that the full set of unused UG arguments aren't exposed to the HC user
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY); UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
// create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested // create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested
UnifiedArgumentCollection simpleUAC = new UnifiedArgumentCollection(UAC); UnifiedArgumentCollection simpleUAC = new UnifiedArgumentCollection(UAC);
@ -248,7 +248,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
simpleUAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling simpleUAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling
simpleUAC.CONTAMINATION_FRACTION = 0.0; simpleUAC.CONTAMINATION_FRACTION = 0.0;
simpleUAC.exactCallsLog = null; simpleUAC.exactCallsLog = null;
UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY); UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
// initialize the output VCF header // initialize the output VCF header
final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit()); final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());

20
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
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@ -39,18 +39,18 @@ import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.SWPairwiseAlignment; import org.broadinstitute.sting.utils.SWPairwiseAlignment;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import java.util.*; import java.util.*;

5
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -29,16 +29,13 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pairhmm.*; import org.broadinstitute.sting.utils.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.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.PrintStream;
import java.util.*; import java.util.*;
public class LikelihoodCalculationEngine { public class LikelihoodCalculationEngine {

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.activeregion.ActiveRegion; import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.ArrayList; import java.util.ArrayList;

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
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@ -11,8 +11,8 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.jgrapht.graph.DefaultDirectedGraph; import org.jgrapht.graph.DefaultDirectedGraph;
import java.io.PrintStream; import java.io.PrintStream;

2
protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource; import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
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.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.*; import java.util.*;

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
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@ -28,11 +28,11 @@ import net.sf.samtools.SAMUtils;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.Test; import org.testng.annotations.Test;

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java
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@ -4,8 +4,8 @@ import org.broadinstitute.sting.BaseTest;
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.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;
import org.testng.annotations.Test; import org.testng.annotations.Test;

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java
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@ -4,7 +4,7 @@ import org.broadinstitute.sting.BaseTest;
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.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;
import org.testng.annotations.Test; import org.testng.annotations.Test;

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java
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@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
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.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.BeforeSuite; import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
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@ -2,10 +2,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods; import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.BeforeSuite; import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java
View File

@ -3,10 +3,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;
import org.testng.annotations.Test; import org.testng.annotations.Test;

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
View File

@ -10,9 +10,9 @@ import net.sf.picard.reference.ReferenceSequenceFile;
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;

5
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java
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@ -10,16 +10,11 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.genotyper.ArtificialReadPileupTestProvider; import org.broadinstitute.sting.gatk.walkers.genotyper.ArtificialReadPileupTestProvider;
import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.jgrapht.graph.DefaultDirectedGraph; import org.jgrapht.graph.DefaultDirectedGraph;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.*; import java.util.*;

2
protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
View File

@ -29,7 +29,7 @@ package org.broadinstitute.sting.utils.pairhmm;
// the imports for unit testing. // the imports for unit testing.
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.DataProvider; import org.testng.annotations.DataProvider;

2
public/java/src/org/broadinstitute/sting/alignment/Alignment.java
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.alignment; package org.broadinstitute.sting.alignment;
import net.sf.samtools.*; import net.sf.samtools.*;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

2
public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
View File

@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
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;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

2
public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
View File

@ -4,7 +4,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.*; import net.sf.samtools.*;
import org.broadinstitute.sting.alignment.Aligner; import org.broadinstitute.sting.alignment.Aligner;
import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File; import java.io.File;

2
public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.alignment.bwa.BWAAligner; import org.broadinstitute.sting.alignment.bwa.BWAAligner;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.reference.bwt.*; import org.broadinstitute.sting.alignment.reference.bwt.*;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import java.io.File; import java.io.File;

2
public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
View File

@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.arguments;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
/** /**
* @author ebanks * @author ebanks

2
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
View File

@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.File; import java.io.File;
import java.io.PrintStream; import java.io.PrintStream;

2
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.arguments;
import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
/** /**
* @author ebanks * @author ebanks

2
public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.contexts;
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.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;

12
public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
View File

@ -30,14 +30,14 @@ import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodec;
import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub; import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils; import org.broadinstitute.variant.bcf2.BCF2Utils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.variant.vcf.VCFHeader;
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.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.writer.Options; import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import java.io.*; import java.io.*;
import java.util.Arrays; import java.util.Arrays;

2
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
View File

@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File; import java.io.File;

16
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
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@ -29,13 +29,13 @@ import org.broadinstitute.sting.gatk.CommandLineExecutable;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.io.OutputTracker; import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.writer.Options; import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import java.io.File; import java.io.File;
import java.io.OutputStream; import java.io.OutputStream;
@ -232,7 +232,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
} }
if ( UPDATE_CONTIG_HEADERS ) if ( UPDATE_CONTIG_HEADERS )
vcfHeader = VCFUtils.withUpdatedContigs(vcfHeader, engine); vcfHeader = GATKVCFUtils.withUpdatedContigs(vcfHeader, engine);
} }
outputTracker.getStorage(this).writeHeader(vcfHeader); outputTracker.getStorage(this).writeHeader(vcfHeader);

2
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature; import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import java.util.*; import java.util.*;

4
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
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@ -33,9 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec; import org.broadinstitute.variant.vcf.AbstractVCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.GATKDocUtils; import org.broadinstitute.sting.utils.help.GATKDocUtils;

1
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
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@ -39,7 +39,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.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;

2
public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.samples;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import java.util.*; import java.util.*;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
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@ -37,7 +37,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; 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.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ClippingOp; import org.broadinstitute.sting.utils.clipping.ClippingOp;
import org.broadinstitute.sting.utils.clipping.ClippingRepresentation; import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -32,12 +32,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
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.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAn
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
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.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.Collection; import java.util.Collection;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
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@ -37,10 +37,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
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@ -2,11 +2,11 @@ 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.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
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.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*; import java.util.*;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
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@ -35,12 +35,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import java.util.*; import java.util.*;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
View File

@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.annotator; package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*; import java.util.*;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
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@ -8,13 +8,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
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.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

14
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -7,17 +7,17 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
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.codecs.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.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.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
View File

@ -34,13 +34,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
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.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.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.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
View File

@ -8,11 +8,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
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.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -33,20 +33,20 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Haplotype; import org.broadinstitute.sting.utils.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.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.Serializable; import java.io.Serializable;
import java.util.*; import java.util.*;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
View File

@ -9,11 +9,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation; import org.broadinstitute.sting.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.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
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@ -7,9 +7,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.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.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
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@ -10,11 +10,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; import org.broadinstitute.sting.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.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
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@ -6,10 +6,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
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@ -11,10 +11,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.sting.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.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
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@ -2,12 +2,12 @@ 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.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*; import java.util.*;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
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@ -8,13 +8,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.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.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
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@ -31,14 +31,14 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
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.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
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@ -7,11 +7,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
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.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
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.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
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@ -6,11 +6,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -8,11 +8,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
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@ -10,12 +10,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.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.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines; import org.broadinstitute.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.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -10,14 +10,14 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.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.codecs.vcf.VCFHeaderLine; import org.broadinstitute.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.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext; import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
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@ -7,14 +7,14 @@ import net.sf.samtools.SAMRecord;
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.gatk.walkers.indels.PairHMMIndelErrorModel; import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
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.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*; import java.util.*;

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
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@ -31,11 +31,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
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@ -35,9 +35,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;
@ -212,7 +213,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
// Make sure that the SnpEff version number and command-line header lines are present in the VCF header of // Make sure that the SnpEff version number and command-line header lines are present in the VCF header of
// the SnpEff rod, and that the file was generated by a supported version of SnpEff: // the SnpEff rod, and that the file was generated by a supported version of SnpEff:
VCFHeader snpEffVCFHeader = VCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName()); VCFHeader snpEffVCFHeader = GATKVCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName());
VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY); VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY);
VCFHeaderLine snpEffCommandLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_COMMAND_LINE_KEY); VCFHeaderLine snpEffCommandLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_COMMAND_LINE_KEY);

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
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@ -7,10 +7,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
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@ -31,12 +31,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.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.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;
@ -57,7 +57,7 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa
if ( !vc.isIndel()) if ( !vc.isIndel())
return null; return null;
Pair<List<Integer>,byte[]> result = VariantContextUtils.getNumTandemRepeatUnits(vc, ref.getForwardBases()); Pair<List<Integer>,byte[]> result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, ref.getForwardBases());
if (result == null) if (result == null)
return null; return null;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
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@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
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.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
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.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashMap; import java.util.HashMap;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
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@ -10,11 +10,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation; import org.broadinstitute.sting.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.sting.utils.codecs.vcf.VCFHeaderLineCount; import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

13
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -35,13 +35,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.util.*; import java.util.*;
@ -225,7 +226,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
// note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>(); Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(engine.getVCFAnnotationDescriptions()); hInfo.addAll(engine.getVCFAnnotationDescriptions());
for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) { for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) {
if ( isUniqueHeaderLine(line, hInfo) ) if ( isUniqueHeaderLine(line, hInfo) )
hInfo.add(line); hInfo.add(line);
} }
@ -237,7 +238,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
continue; continue;
} }
VCFInfoHeaderLine targetHeaderLine = null; VCFInfoHeaderLine targetHeaderLine = null;
for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) { for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) {
if ( line instanceof VCFInfoHeaderLine ) { if ( line instanceof VCFInfoHeaderLine ) {
VCFInfoHeaderLine infoline = (VCFInfoHeaderLine)line; VCFInfoHeaderLine infoline = (VCFInfoHeaderLine)line;
if ( infoline.getID().equals(expression.fieldName) ) { if ( infoline.getID().equals(expression.fieldName) ) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -32,9 +32,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import java.util.*; import java.util.*;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
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@ -8,9 +8,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAn
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.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.sting.utils.codecs.vcf.VCFHeaderLineType; import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*; import java.util.*;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
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@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.commandline.RodBinding; import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List; import java.util.List;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
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@ -4,10 +4,10 @@ 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;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine; import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder; import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List; import java.util.List;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
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@ -4,8 +4,8 @@ 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;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap; import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine; import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
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@ -25,7 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces; package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.util.List; import java.util.List;

9
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
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@ -35,10 +35,11 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature; import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.util.*; import java.util.*;
@ -132,7 +133,7 @@ public class BeagleOutputToVCF extends RodWalker<Integer, Integer> {
// setup the header fields // setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>(); final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit())); hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit()));
hInfo.add(new VCFFormatHeaderLine("OG",1, VCFHeaderLineType.String, "Original Genotype input to Beagle")); hInfo.add(new VCFFormatHeaderLine("OG",1, VCFHeaderLineType.String, "Original Genotype input to Beagle"));
hInfo.add(new VCFInfoHeaderLine("R2", 1, VCFHeaderLineType.Float, "r2 Value reported by Beagle on each site")); hInfo.add(new VCFInfoHeaderLine("R2", 1, VCFHeaderLineType.Float, "r2 Value reported by Beagle on each site"));
hInfo.add(new VCFInfoHeaderLine("NumGenotypesChanged", 1, VCFHeaderLineType.Integer, "The number of genotypes changed by Beagle")); hInfo.add(new VCFInfoHeaderLine("NumGenotypesChanged", 1, VCFHeaderLineType.Integer, "The number of genotypes changed by Beagle"));

17
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
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@ -38,14 +38,15 @@ import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibratio
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFilterHeaderLine; import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.variant.vcf.VCFFilterHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.io.File; import java.io.File;
import java.io.PrintStream; import java.io.PrintStream;
@ -231,7 +232,7 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
private final static double[] DIPLOID_FLAT_LOG10_LIKELIHOODS = MathUtils.toLog10(new double[]{ 0.33, 0.33, 0.33 }); private final static double[] DIPLOID_FLAT_LOG10_LIKELIHOODS = MathUtils.toLog10(new double[]{ 0.33, 0.33, 0.33 });
public void writeBeagleOutput(VariantContext preferredVC, VariantContext otherVC, boolean isValidationSite, double prior) { public void writeBeagleOutput(VariantContext preferredVC, VariantContext otherVC, boolean isValidationSite, double prior) {
GenomeLoc currentLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),preferredVC); GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), preferredVC);
StringBuffer beagleOut = new StringBuffer(); StringBuffer beagleOut = new StringBuffer();
String marker = String.format("%s:%d ",currentLoc.getContig(),currentLoc.getStart()); String marker = String.format("%s:%d ",currentLoc.getContig(),currentLoc.getStart());
@ -344,7 +345,7 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
// setup the header fields // setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>(); Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames)); hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
hInfo.add(new VCFFilterHeaderLine("bootstrap","This site used for genotype bootstrapping with ProduceBeagleInputWalker")); hInfo.add(new VCFFilterHeaderLine("bootstrap","This site used for genotype bootstrapping with ProduceBeagleInputWalker"));
bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames))); bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));

20
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
View File

@ -36,16 +36,16 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine; import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.Arrays; import java.util.Arrays;
@ -90,7 +90,7 @@ public class VariantsToBeagleUnphased extends RodWalker<Integer, Integer> {
throw new UserException.BadArgumentValue("bootstrap", "Bootstrap value must be fraction between 0 and 1"); throw new UserException.BadArgumentValue("bootstrap", "Bootstrap value must be fraction between 0 and 1");
if ( bootstrapVCFOutput != null ) { if ( bootstrapVCFOutput != null ) {
Set<VCFHeaderLine> hInfo = VCFUtils.getHeaderFields(getToolkit()); Set<VCFHeaderLine> hInfo = GATKVCFUtils.getHeaderFields(getToolkit());
bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit()))); bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit())));
} }
} }
@ -141,7 +141,7 @@ public class VariantsToBeagleUnphased extends RodWalker<Integer, Integer> {
} }
public void writeUnphasedBeagleOutput(VariantContext vc, boolean makeMissing) { public void writeUnphasedBeagleOutput(VariantContext vc, boolean makeMissing) {
GenomeLoc currentLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),vc); GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc);
StringBuffer beagleOut = new StringBuffer(); StringBuffer beagleOut = new StringBuffer();
String marker = String.format("%s:%d ",currentLoc.getContig(), currentLoc.getStart()); String marker = String.format("%s:%d ",currentLoc.getContig(), currentLoc.getStart());

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
View File

@ -38,7 +38,7 @@ import org.broadinstitute.sting.gatk.filters.*;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer; import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
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.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.GATKLiteUtils; import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
import org.broadinstitute.sting.utils.clipping.ReadClipper; import org.broadinstitute.sting.utils.clipping.ReadClipper;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
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@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.*;
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.variant.utils.BaseUtils;
import java.io.File; import java.io.File;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
@ -305,7 +306,7 @@ public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, Ca
public CallableBaseState map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public CallableBaseState map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
CalledState state; CalledState state;
if (BaseUtils.isNBase(ref.getBase())) { if ( BaseUtils.isNBase(ref.getBase())) {
state = CalledState.REF_N; state = CalledState.REF_N;
} else { } else {
// count up the depths of all and QC+ bases // count up the depths of all and QC+ bases

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
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.fragments.FragmentCollection; import org.broadinstitute.sting.utils.fragments.FragmentCollection;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
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@ -41,7 +41,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec; import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
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@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.coverage; package org.broadinstitute.sting.gatk.walkers.coverage;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import java.util.HashMap; import java.util.HashMap;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
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@ -30,7 +30,7 @@ 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;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
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@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.report.GATKReport; import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable; import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.QualityUtils;
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;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
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@ -34,12 +34,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.variant.vcf.VCFHeader;
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.variantcontext.*; import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.util.*; import java.util.*;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
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@ -24,7 +24,7 @@
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets; package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.HashSet; import java.util.HashSet;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
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@ -28,9 +28,9 @@ import org.apache.log4j.Logger;
import org.broad.tribble.AbstractFeatureReader; import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureReader; import org.broad.tribble.FeatureReader;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.*; import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.*; import java.io.*;
import java.util.Iterator; import java.util.Iterator;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
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@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Collections; import java.util.Collections;
import java.util.List; import java.util.List;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
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@ -31,7 +31,7 @@ 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;
import org.broadinstitute.sting.gatk.walkers.RefWalker; import org.broadinstitute.sting.gatk.walkers.RefWalker;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import java.io.PrintStream; import java.io.PrintStream;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
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@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.filters;
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.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
public class ClusteredSnps { public class ClusteredSnps {
private GenomeLocParser genomeLocParser; private GenomeLocParser genomeLocParser;
@ -32,7 +32,7 @@ public class ClusteredSnps {
throw new UserException.BadInput("The clustered SNPs filter does not work in the presence of non-variant records; see the documentation for more details"); throw new UserException.BadInput("The clustered SNPs filter does not work in the presence of non-variant records; see the documentation for more details");
// find the nth variant // find the nth variant
GenomeLoc left = VariantContextUtils.getLocation(genomeLocParser,variants[i].getVariantContext()); GenomeLoc left = GATKVariantContextUtils.getLocation(genomeLocParser, variants[i].getVariantContext());
GenomeLoc right = null; GenomeLoc right = null;
int snpsSeen = 1; int snpsSeen = 1;
@ -40,7 +40,7 @@ public class ClusteredSnps {
while ( ++currentIndex < variants.length ) { while ( ++currentIndex < variants.length ) {
if ( variants[currentIndex] != null && variants[currentIndex].getVariantContext() != null && variants[currentIndex].getVariantContext().isVariant() ) { if ( variants[currentIndex] != null && variants[currentIndex].getVariantContext() != null && variants[currentIndex].getVariantContext().isVariant() ) {
if ( ++snpsSeen == snpThreshold ) { if ( ++snpsSeen == snpThreshold ) {
right = VariantContextUtils.getLocation(genomeLocParser,variants[currentIndex].getVariantContext()); right = GATKVariantContextUtils.getLocation(genomeLocParser, variants[currentIndex].getVariantContext());
break; break;
} }
} }

2
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
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@ -26,7 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.filters; package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.variant.variantcontext.VariantContext;
public class FiltrationContext { public class FiltrationContext {

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