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Merge branch 'master' of github.com:broadinstitute/gsa-unstable

This commit is contained in:
Ryan Poplin 2012-12-19 11:31:40 -05:00
parent aa39037be8 e6797d2869
commit 54e5c84018
314 changed files with 1852 additions and 1864 deletions
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34
build.xml
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@ -644,12 +644,8 @@
<target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
<jar jarfile="${dist.dir}/StingUtils.jar">
<fileset dir="${java.classes}">
<include name="**/utils/**/*.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/utils/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
@ -659,7 +655,7 @@
<include name="**/${R.package.path}/**/*.tar.gz"/>
</fileset>
<fileset dir="${R.script.staging.dir}">
<include name="**/utils/**/*.R"/>
<include name="**/sting/utils/**/*.R"/>
</fileset>
<manifest>
<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
@ -667,14 +663,10 @@
</jar>
</target>
<target name="vcf.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/vcf.jar">
<target name="variant.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/variant.jar">
<fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
<include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/>
<include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**"/>
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
<include name="org/broadinstitute/variant/**/*.class"/>
</fileset>
</jar>
</target>
@ -685,7 +677,7 @@
<include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
<include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
<include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
<include name="org/broadinstitute/sting/utils/BaseUtils.class"/>
<include name="org/broadinstitute/variant/utils/BaseUtils.class"/>
<include name="org/broadinstitute/sting/utils/Utils.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
<include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
@ -703,12 +695,12 @@
<fileset dir="${java.contracts.dir}" />
<fileset dir="${java.classes}">
<include name="${resource.file}" />
<include name="**/gatk/**/*.class" />
<include name="**/alignment/**/*.class"/>
<include name="**/sting/gatk/**/*.class" />
<include name="**/sting/alignment/**/*.class"/>
</fileset>
<fileset dir="${R.script.staging.dir}">
<include name="**/gatk/**/*.R"/>
<include name="**/alignment/**/*.R"/>
<include name="**/sting/gatk/**/*.R"/>
<include name="**/sting/alignment/**/*.R"/>
</fileset>
<fileset dir="${key.dir}">
<include name="**/*.key"/>
@ -719,7 +711,7 @@
</jar>
<jar jarfile="${dist.dir}/Aligner.jar">
<fileset dir="${java.classes}" includes="**/alignment/**/*.class" />
<fileset dir="${java.classes}" includes="**/sting/alignment/**/*.class" />
</jar>
<subant target="dist" genericantfile="build.xml">
@ -755,7 +747,7 @@
</jar>
</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">
<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.pileup.*;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;
import java.util.*;

21
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java
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@ -39,16 +39,27 @@ public class HeaderElement {
*
* @param location the reference location for the new element
*/
public HeaderElement(int location) {
public HeaderElement(final int location) {
this(new BaseAndQualsCounts(), new BaseAndQualsCounts(), 0, 0, location, new LinkedList<Integer>());
}
/**
* Creates a new HeaderElement with the following default values: - empty consensusBaseCounts - empty
* filteredBaseCounts - empty mappingQuality list
*
* @param location the reference location for the new element
*/
public HeaderElement(final int location, final int insertionsToTheRight) {
this(new BaseAndQualsCounts(), new BaseAndQualsCounts(), insertionsToTheRight, 0, location, new LinkedList<Integer>());
}
/**
* Creates a new HeaderElement with all given parameters
*
* @param consensusBaseCounts the BaseCounts object for the running consensus synthetic read
* @param filteredBaseCounts the BaseCounts object for the filtered data synthetic read
* @param insertionsToTheRight number of insertions to the right of this HeaderElement
* @param nSoftClippedBases number of softclipped bases of this HeaderElement
* @param location the reference location of this reference element
* @param mappingQuality the list of mapping quality values of all reads that contributed to this
* HeaderElement
@ -151,6 +162,14 @@ public class HeaderElement {
throw new ReviewedStingException("Removed too many insertions, header is now negative!");
}
public boolean hasInsertionToTheRight() {
return insertionsToTheRight > 0;
}
public int numInsertionsToTheRight() {
return insertionsToTheRight;
}
/**
* Whether or not the HeaderElement is variant due to excess insertions
*

11
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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@ -645,8 +645,15 @@ public class SlidingWindow {
}
}
for (int i = 0; i <= lastStop; i++) // clean up the window header elements up until the end of the variant region. (we keep the last element in case the following element had a read that started with insertion)
windowHeader.remove();
// clean up the window header elements up until the end of the variant region.
// note that we keep the last element of the region in the event that the following element has a read that starts with insertion.
if ( lastStop >= 0 ) {
for (int i = 0; i < lastStop; i++)
windowHeader.remove();
final HeaderElement lastOfRegion = windowHeader.remove();
if ( lastOfRegion.hasInsertionToTheRight() )
windowHeader.addFirst(new HeaderElement(lastOfRegion.getLocation(), lastOfRegion.numInsertionsToTheRight()));
}
}
return allReads;
}

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.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

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.ExactACset;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods;
import java.util.*;

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.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;

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.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

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.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
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 org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.ArrayList;
import java.util.Arrays;

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.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.variantcontext.*;
import java.util.*;

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.Utils;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import java.io.*;
import java.util.*;

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.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import java.util.ArrayList;
import java.util.Arrays;

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

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

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.ActivityProfileResult;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.fragments.FragmentCollection;
@ -61,8 +61,8 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.io.FileNotFoundException;
import java.io.PrintStream;
@ -242,7 +242,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
samplesList.addAll( samples );
// initialize the UnifiedGenotyper Engine which is used to call into the exact model
final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection( SCAC ); // this adapter is used so that the full set of unused UG arguments aren't exposed to the HC user
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
// create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested
UnifiedArgumentCollection simpleUAC = new UnifiedArgumentCollection(UAC);
@ -252,7 +252,7 @@ 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.CONTAMINATION_FRACTION = 0.0;
simpleUAC.exactCallsLog = null;
UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
// initialize the output VCF header
final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());

20
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
View File

@ -39,18 +39,18 @@ import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.SWPairwiseAlignment;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import java.util.*;

5
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
View File

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

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
View File

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

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
View File

@ -11,8 +11,8 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.jgrapht.graph.DefaultDirectedGraph;
import java.io.PrintStream;

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.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;
import java.util.*;

7
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
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@ -18,6 +18,7 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
final String COREDUCTION_BAM_B = validationDataLocation + "coreduction.test.B.bam";
final String COREDUCTION_L = " -L 1:1,853,860-1,854,354 -L 1:1,884,131-1,892,057";
final String OFFCONTIG_BAM = privateTestDir + "readOffb37contigMT.bam";
final String INSERTIONS_AT_EDGE_OF_CONSENSUS_BAM = privateTestDir + "rr-too-many-insertions.bam";
private void RRTest(String testName, String args, String md5) {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, BAM) + " -o %s ";
@ -30,6 +31,12 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
RRTest("testDefaultCompression ", L, "98080d3c53f441564796fc143cf510da");
}
@Test(enabled = true)
public void testInsertionsAtEdgeOfConsensus() {
String base = String.format("-T ReduceReads -npt -R %s -I %s ", REF, INSERTIONS_AT_EDGE_OF_CONSENSUS_BAM) + " -o %s ";
executeTest("testInsertionsAtEdgeOfConsensus", new WalkerTestSpec(base, Arrays.asList("2a6e08a0206bd8ec7671224c4a55dae0")));
}
@Test(enabled = true)
public void testMultipleIntervals() {
String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110";

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.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import org.testng.Assert;
import org.testng.annotations.Test;

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.Utils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

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.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

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.QualityUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.variant.variantcontext.*;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider;

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.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider;

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java
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@ -3,10 +3,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
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@ -10,9 +10,9 @@ import net.sf.picard.reference.ReferenceSequenceFile;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;

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.walkers.genotyper.ArtificialReadPileupTestProvider;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.jgrapht.graph.DefaultDirectedGraph;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.util.*;

2
protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
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@ -29,7 +29,7 @@ package org.broadinstitute.sting.utils.pairhmm;
// the imports for unit testing.
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.testng.Assert;
import org.testng.annotations.DataProvider;

2
public/java/src/org/broadinstitute/sting/alignment/Alignment.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.alignment;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

2
public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
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@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

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 org.broadinstitute.sting.alignment.Aligner;
import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;

2
public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
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@ -6,7 +6,7 @@ import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.alignment.bwa.BWAAligner;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.reference.bwt.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import java.io.File;

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.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
/**
* @author ebanks

2
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
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@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.File;
import java.io.PrintStream;

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.RodBinding;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
/**
* @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.Requires;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;

12
public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
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@ -30,14 +30,14 @@ import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureCodec;
import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.variant.bcf2.BCF2Utils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.writer.Options;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.Options;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import java.io.*;
import java.util.Arrays;

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.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;

16
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
View File

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

2
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

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

4
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
View File

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

1
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
View File

@ -39,7 +39,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;

2
public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
View File

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

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.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ClippingOp;
import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;

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.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

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.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.Collection;

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

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

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.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

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.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
import java.util.*;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
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@ -1,12 +1,12 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

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.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

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.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -34,13 +34,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

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.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -33,20 +33,20 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.Serializable;
import java.util.*;

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.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

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

@ -7,9 +7,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

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.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

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

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

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

@ -11,10 +11,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

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

@ -2,12 +2,12 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

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

@ -8,13 +8,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

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.GenotypeAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.List;

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

@ -7,11 +7,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

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

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

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

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

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

@ -10,12 +10,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

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

@ -10,14 +10,14 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.MannWhitneyU;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypesContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

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

@ -7,14 +7,14 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Allele;
import java.util.*;

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.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

7
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
View File

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

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

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

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

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

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

@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.HashMap;

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

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

13
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

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

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

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

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

@ -8,9 +8,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAn
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.IndelUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFHeaderLineType;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.*;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
View File

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

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
View File

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

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

@ -4,10 +4,10 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
View File

@ -4,8 +4,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
View File

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

9
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
View File

@ -35,10 +35,11 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.util.*;
@ -132,7 +133,7 @@ public class BeagleOutputToVCF extends RodWalker<Integer, Integer> {
// setup the header fields
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 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"));

17
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
View File

@ -38,14 +38,15 @@ import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibratio
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFilterHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFFilterHeaderLine;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.io.File;
import java.io.PrintStream;
@ -231,7 +232,7 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
private final static double[] DIPLOID_FLAT_LOG10_LIKELIHOODS = MathUtils.toLog10(new double[]{ 0.33, 0.33, 0.33 });
public void writeBeagleOutput(VariantContext preferredVC, VariantContext otherVC, boolean isValidationSite, double prior) {
GenomeLoc currentLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),preferredVC);
GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), preferredVC);
StringBuffer beagleOut = new StringBuffer();
String marker = String.format("%s:%d ",currentLoc.getContig(),currentLoc.getStart());
@ -344,7 +345,7 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
// setup the header fields
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"));
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.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import java.io.PrintStream;
import java.util.Arrays;
@ -90,7 +90,7 @@ public class VariantsToBeagleUnphased extends RodWalker<Integer, Integer> {
throw new UserException.BadArgumentValue("bootstrap", "Bootstrap value must be fraction between 0 and 1");
if ( bootstrapVCFOutput != null ) {
Set<VCFHeaderLine> hInfo = VCFUtils.getHeaderFields(getToolkit());
Set<VCFHeaderLine> hInfo = GATKVCFUtils.getHeaderFields(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) {
GenomeLoc currentLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),vc);
GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc);
StringBuffer beagleOut = new StringBuffer();
String marker = String.format("%s:%d ",currentLoc.getContig(), currentLoc.getStart());

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.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
import org.broadinstitute.sting.utils.clipping.ReadClipper;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
View File

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

2
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
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.UserException;
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.RODRecordList;
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.SampleUtils;
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;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
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.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.variant.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
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.GATKReportTable;
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.help.DocumentedGATKFeature;
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.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.variant.variantcontext.*;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
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;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import java.util.HashSet;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
View File

@ -28,9 +28,9 @@ import org.apache.log4j.Logger;
import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureReader;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.*;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import java.io.*;
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.collections.Pair;
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.List;

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