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GenotypeMap -> GenotypeCollection

This commit is contained in:
Mark DePristo 2011-11-14 15:32:03 -05:00
parent 9b5c79b49d
commit 1fbdcb4f43
32 changed files with 424 additions and 306 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -194,7 +194,7 @@ public class VariantContextAdaptors {
return null; // we weren't given enough reference context to create the VariantContext
Byte refBaseForIndel = new Byte(ref.getBases()[index]);
GenotypeMap genotypes = null;
GenotypeCollection genotypes = null;
VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (sawNullAllele ? 1 : 0), dbsnp.getEnd() - (refAllele.isNull() ? 1 : 0), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes, refBaseForIndel);
return vc;
} else
@ -324,7 +324,7 @@ public class VariantContextAdaptors {
String[] samples = hapmap.getSampleIDs();
String[] genotypeStrings = hapmap.getGenotypes();
GenotypeMap genotypes = GenotypeMap.create(samples.length);
GenotypeCollection genotypes = GenotypeCollection.create(samples.length);
for ( int i = 0; i < samples.length; i++ ) {
// ignore bad genotypes
if ( genotypeStrings[i].contains("N") )

14
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -35,7 +35,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
@ -55,18 +55,18 @@ public class AlleleBalance extends InfoFieldAnnotation {
if ( !vc.isBiallelic() )
return null;
final GenotypeMap genotypes = vc.getGenotypes();
final GenotypeCollection genotypes = vc.getGenotypes();
if ( !vc.hasGenotypes() )
return null;
double ratio = 0.0;
double totalWeights = 0.0;
for ( Map.Entry<String, Genotype> genotype : genotypes.entrySet() ) {
for ( Genotype genotype : genotypes ) {
// we care only about het calls
if ( !genotype.getValue().isHet() )
if ( !genotype.isHet() )
continue;
AlignmentContext context = stratifiedContexts.get(genotype.getKey());
AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
if ( context == null )
continue;
@ -85,8 +85,8 @@ public class AlleleBalance extends InfoFieldAnnotation {
continue;
// weight the allele balance by genotype quality so that e.g. mis-called homs don't affect the ratio too much
ratio += genotype.getValue().getNegLog10PError() * ((double)refCount / (double)(refCount + altCount));
totalWeights += genotype.getValue().getNegLog10PError();
ratio += genotype.getNegLog10PError() * ((double)refCount / (double)(refCount + altCount));
totalWeights += genotype.getNegLog10PError();
} else if ( vc.isIndel() && context.hasExtendedEventPileup() ) {
final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
if ( indelPileup == null ) {

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

@ -11,7 +11,7 @@ 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.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
@ -31,16 +31,14 @@ public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgress
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
final GenotypeMap genotypes = vc.getGenotypes();
final GenotypeCollection genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
return null;
int refCount = 0;
int hetCount = 0;
int homCount = 0;
for ( Map.Entry<String, Genotype> genotype : genotypes.entrySet() ) {
Genotype g = genotype.getValue();
for ( final Genotype g : genotypes ) {
if ( g.isNoCall() )
continue;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
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@ -10,7 +10,7 @@ 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.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
@ -33,7 +33,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
final GenotypeMap genotypes = vc.getGenotypes();
final GenotypeCollection genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
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.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
@ -29,7 +29,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
if ( stratifiedContexts.size() == 0 )
return null;
final GenotypeMap genotypes = vc.getGenotypes();
final GenotypeCollection genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() == 0 )
return null;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -13,7 +13,7 @@ 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.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.ArrayList;
@ -33,7 +33,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
if ( stratifiedContexts.size() == 0 )
return null;
final GenotypeMap genotypes = vc.getGenotypes();
final GenotypeCollection genotypes = vc.getGenotypes();
if ( genotypes == null || genotypes.size() == 0 )
return null;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -34,7 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
@ -217,11 +217,11 @@ public class VariantAnnotatorEngine {
}
}
private GenotypeMap annotateGenotypes(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
private GenotypeCollection annotateGenotypes(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
if ( requestedGenotypeAnnotations.size() == 0 )
return vc.getGenotypes();
GenotypeMap genotypes = GenotypeMap.create(vc.getNSamples());
GenotypeCollection genotypes = GenotypeCollection.create(vc.getNSamples());
for ( Map.Entry<String, Genotype> g : vc.getGenotypes().entrySet() ) {
Genotype genotype = g.getValue();
AlignmentContext context = stratifiedContexts.get(g.getKey());

4
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -187,7 +187,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
byte refByte = ref.getBase();
// make new Genotypes based on Beagle results
GenotypeMap genotypes = GenotypeMap.create(vc_input.getGenotypes().size());
GenotypeCollection genotypes = GenotypeCollection.create(vc_input.getGenotypes().size());
// for each genotype, create a new object with Beagle information on it
@ -196,7 +196,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
Double alleleFrequencyH = 0.0;
int beagleVarCounts = 0;
GenotypeMap hapmapGenotypes = null;
GenotypeCollection hapmapGenotypes = null;
if (vc_comp != null) {
hapmapGenotypes = vc_comp.getGenotypes();

6
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@ -283,11 +283,11 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
VariantContext vc = context.getVariantContext();
// make new Genotypes based on filters
GenotypeMap genotypes;
GenotypeCollection genotypes;
if ( genotypeFilterExps.size() == 0 ) {
genotypes = null;
} else {
genotypes = GenotypeMap.create(vc.getGenotypes().size());
genotypes = GenotypeCollection.create(vc.getGenotypes().size());
// for each genotype, check filters then create a new object
for ( Map.Entry<String, Genotype> genotype : vc.getGenotypes().entrySet() ) {

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
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@ -26,17 +26,14 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.PrintStream;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
@ -86,7 +83,7 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
*
* @return calls
*/
protected abstract GenotypeMap assignGenotypes(VariantContext vc,
protected abstract GenotypeCollection assignGenotypes(VariantContext vc,
double[] log10AlleleFrequencyPosteriors,
int AFofMaxLikelihood);
}

10
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -26,14 +26,12 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.PrintStream;
@ -269,14 +267,14 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
*
* @return calls
*/
public GenotypeMap assignGenotypes(VariantContext vc,
public GenotypeCollection assignGenotypes(VariantContext vc,
double[] log10AlleleFrequencyPosteriors,
int AFofMaxLikelihood) {
if ( !vc.isVariant() )
throw new UserException("The VCF record passed in does not contain an ALT allele at " + vc.getChr() + ":" + vc.getStart());
GenotypeMap GLs = vc.getGenotypes();
GenotypeCollection GLs = vc.getGenotypes();
double[][] pathMetricArray = new double[GLs.size()+1][AFofMaxLikelihood+1];
int[][] tracebackArray = new int[GLs.size()+1][AFofMaxLikelihood+1];
@ -343,7 +341,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
}
}
GenotypeMap calls = GenotypeMap.create();
GenotypeCollection calls = GenotypeCollection.create();
int startIdx = AFofMaxLikelihood;
for (int k = sampleIdx; k > 0; k--) {

8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GridSearchAFEstimation.java
View File

@ -26,15 +26,13 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.PrintStream;
@ -90,7 +88,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
*
* @return calls
*/
protected GenotypeMap assignGenotypes(VariantContext vc,
protected GenotypeCollection assignGenotypes(VariantContext vc,
double[] log10AlleleFrequencyPosteriors,
int AFofMaxLikelihood) {
if ( !vc.isVariant() )
@ -98,7 +96,7 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
Allele refAllele = vc.getReference();
Allele altAllele = vc.getAlternateAllele(0);
GenotypeMap calls = GenotypeMap.create();
GenotypeCollection calls = GenotypeCollection.create();
// first, the potential alt calls
for ( String sample : AFMatrix.getSamples() ) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
View File

@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@ -129,7 +129,7 @@ public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
return null;
VariantContext variantVC = null;
GenotypeMap genotypes = GenotypeMap.create();
GenotypeCollection genotypes = GenotypeCollection.create();
for ( VariantContext vc : VCs ) {
if ( variantVC == null && vc.isVariant() )
variantVC = vc;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -265,7 +265,7 @@ public class UnifiedGenotyperEngine {
alleles.add(refAllele);
boolean addedAltAlleles = false;
GenotypeMap genotypes = GenotypeMap.create();
GenotypeCollection genotypes = GenotypeCollection.create();
for ( MultiallelicGenotypeLikelihoods GL : GLs.values() ) {
if ( !addedAltAlleles ) {
addedAltAlleles = true;
@ -354,7 +354,7 @@ public class UnifiedGenotyperEngine {
}
// create the genotypes
GenotypeMap genotypes = afcm.get().assignGenotypes(vc, log10AlleleFrequencyPosteriors.get(), bestAFguess);
GenotypeCollection genotypes = afcm.get().assignGenotypes(vc, log10AlleleFrequencyPosteriors.get(), bestAFguess);
// print out stats if we have a writer
if ( verboseWriter != null )
@ -491,7 +491,7 @@ public class UnifiedGenotyperEngine {
}
// create the genotypes
GenotypeMap genotypes = afcm.get().assignGenotypes(vc, log10AlleleFrequencyPosteriors.get(), bestAFguess);
GenotypeCollection genotypes = afcm.get().assignGenotypes(vc, log10AlleleFrequencyPosteriors.get(), bestAFguess);
// *** note that calculating strand bias involves overwriting data structures, so we do that last
HashMap<String, Object> attributes = new HashMap<String, Object>();

6
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
View File

@ -60,7 +60,7 @@ 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.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.*;
@ -1058,7 +1058,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
stop += event_length;
}
GenotypeMap genotypes = GenotypeMap.create();
GenotypeCollection genotypes = GenotypeCollection.create();
for ( String sample : normalSamples ) {
@ -1148,7 +1148,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
homRefAlleles.add( alleles.get(0));
homRefAlleles.add( alleles.get(0));
GenotypeMap genotypes = GenotypeMap.create();
GenotypeCollection genotypes = GenotypeCollection.create();
for ( String sample : normalSamples ) {
genotypes.put(sample,new Genotype(sample, homRefN ? homRefAlleles : alleles,Genotype.NO_NEG_LOG_10PERROR,null,attrsNormal,false));

10
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
View File

@ -293,7 +293,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
if (tracker != null) {
VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation());
GenotypeMap genotypeMap = vc.getGenotypes();
GenotypeCollection genotypeCollection = vc.getGenotypes();
for (Trio trio : trios) {
Genotype mother = vc.getGenotype(trio.getMother());
@ -306,12 +306,12 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
Genotype phasedFather = trioGenotypes.get(1);
Genotype phasedChild = trioGenotypes.get(2);
genotypeMap.put(phasedMother.getSampleName(), phasedMother);
genotypeMap.put(phasedFather.getSampleName(), phasedFather);
genotypeMap.put(phasedChild.getSampleName(), phasedChild);
genotypeCollection.put(phasedMother.getSampleName(), phasedMother);
genotypeCollection.put(phasedFather.getSampleName(), phasedFather);
genotypeCollection.put(phasedChild.getSampleName(), phasedChild);
}
VariantContext newvc = VariantContext.modifyGenotypes(vc, genotypeMap);
VariantContext newvc = VariantContext.modifyGenotypes(vc, genotypeCollection);
vcfWriter.add(newvc);
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

@ -352,7 +352,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
UnfinishedVariantContext uvc = uvr.unfinishedVariant;
// Perform per-sample phasing:
GenotypeMap sampGenotypes = vc.getGenotypes();
GenotypeCollection sampGenotypes = vc.getGenotypes();
Map<String, PhaseCounts> samplePhaseStats = new TreeMap<String, PhaseCounts>();
for (Map.Entry<String, Genotype> sampGtEntry : sampGenotypes.entrySet()) {
String samp = sampGtEntry.getKey();
@ -1123,7 +1123,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
private int start;
private int stop;
private Collection<Allele> alleles;
private GenotypeMap genotypes;
private GenotypeCollection genotypes;
private double negLog10PError;
private Set<String> filters;
private Map<String, Object> attributes;
@ -1134,7 +1134,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
this.start = vc.getStart();
this.stop = vc.getEnd();
this.alleles = vc.getAlleles();
this.genotypes = GenotypeMap.create(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
this.genotypes = GenotypeCollection.create(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
this.negLog10PError = vc.getNegLog10PError();
this.filters = vc.filtersWereApplied() ? vc.getFilters() : null;
this.attributes = new HashMap<String, Object>(vc.getAttributes());

6
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
View File

@ -14,7 +14,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.HashMap;
@ -92,13 +92,13 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
Set<String> allSamples = new HashSet<String>();
GenotypeMap compSampGenotypes = null;
GenotypeCollection compSampGenotypes = null;
if (isRelevantToPhasing(comp)) {
allSamples.addAll(comp.getSampleNames());
compSampGenotypes = comp.getGenotypes();
}
GenotypeMap evalSampGenotypes = null;
GenotypeCollection evalSampGenotypes = null;
if (isRelevantToPhasing(eval)) {
allSamples.addAll(eval.getSampleNames());
evalSampGenotypes = eval.getGenotypes();

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
View File

@ -40,7 +40,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
@ -211,7 +211,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
}
// create new Genotype objects
GenotypeMap newGenotypes = GenotypeMap.create(vc.getNSamples());
GenotypeCollection newGenotypes = GenotypeCollection.create(vc.getNSamples());
for ( Map.Entry<String, Genotype> genotype : vc.getGenotypes().entrySet() ) {
List<Allele> newAlleles = new ArrayList<Allele>();
for ( Allele allele : genotype.getValue().getAlleles() ) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -24,10 +24,8 @@
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.apache.poi.hpsf.Variant;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.text.XReadLines;
@ -558,7 +556,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
return (compVCs == null || compVCs.isEmpty());
// check if we find it in the variant rod
GenotypeMap genotypes = vc.getGenotypes(samples);
GenotypeCollection genotypes = vc.getGenotypes(samples);
for (Genotype g : genotypes.values()) {
if (sampleHasVariant(g)) {
// There is a variant called (or filtered with not exclude filtered option set) that is not HomRef for at least one of the samples.

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -130,7 +130,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
// set the appropriate sample name if necessary
if ( sampleName != null && vc.hasGenotypes() && vc.hasGenotype(variants.getName()) ) {
Genotype g = Genotype.modifyName(vc.getGenotype(variants.getName()), sampleName);
GenotypeMap genotypes = GenotypeMap.create(1);
GenotypeCollection genotypes = GenotypeCollection.create(1);
genotypes.put(sampleName, g);
vc = VariantContext.modifyGenotypes(vc, genotypes);
}

5
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -11,8 +11,7 @@ import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.*;
@ -77,7 +76,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
* @param pos position
* @return a mapping of sample name to genotype object
*/
public abstract GenotypeMap createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
public abstract GenotypeCollection createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
/**

7
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
View File

@ -5,11 +5,10 @@ import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.*;
@ -119,13 +118,13 @@ public class VCF3Codec extends AbstractVCFCodec {
* @param pos position
* @return a mapping of sample name to genotype object
*/
public GenotypeMap createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
public GenotypeCollection createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
if (genotypeParts == null)
genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
GenotypeMap genotypes = GenotypeMap.create(nParts);
GenotypeCollection genotypes = GenotypeCollection.create(nParts);
// get the format keys
int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);

7
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
View File

@ -5,11 +5,10 @@ import org.broad.tribble.readers.LineReader;
import org.broad.tribble.util.ParsingUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.*;
@ -146,13 +145,13 @@ public class VCFCodec extends AbstractVCFCodec {
* @param alleles the list of alleles
* @return a mapping of sample name to genotype object
*/
public GenotypeMap createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
public GenotypeCollection createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
if (genotypeParts == null)
genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
GenotypeMap genotypes = GenotypeMap.create(nParts);
GenotypeCollection genotypes = GenotypeCollection.create(nParts);
// get the format keys
int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);

6
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFParser.java
View File

@ -1,11 +1,9 @@
package org.broadinstitute.sting.utils.codecs.vcf;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import java.util.List;
import java.util.Map;
/**
@ -21,6 +19,6 @@ public interface VCFParser {
* @param pos position
* @return a mapping of sample name to genotype object
*/
public GenotypeMap createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
public GenotypeCollection createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
}

8
public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java
View File

@ -28,7 +28,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.*;
@ -146,16 +146,16 @@ public class GCF {
Map<String, Object> attributes = new HashMap<String, Object>();
attributes.put("INFO", info);
Byte refPadByte = refPad == 0 ? null : refPad;
GenotypeMap genotypes = decodeGenotypes(header);
GenotypeCollection genotypes = decodeGenotypes(header);
return new VariantContext(source, contig, start, stop, alleleMap, genotypes, negLog10PError, filters, attributes, refPadByte);
}
private GenotypeMap decodeGenotypes(final GCFHeader header) {
private GenotypeCollection decodeGenotypes(final GCFHeader header) {
if ( genotypes.isEmpty() )
return VariantContext.NO_GENOTYPES;
else {
GenotypeMap map = GenotypeMap.create();
GenotypeCollection map = GenotypeCollection.create();
for ( int i = 0; i < genotypes.size(); i++ ) {
final String sampleName = header.getSample(i);

325
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java 100644
View File

@ -0,0 +1,325 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.variantcontext;
import java.util.*;
/**
*
*/
public class GenotypeCollection implements List<Genotype> {
public final static GenotypeCollection NO_GENOTYPES = new GenotypeCollection();
Map<String, Integer> sampleNameToOffset = null;
boolean cacheIsInvalid = true;
final ArrayList<Genotype> genotypes;
boolean immutable = false;
// ---------------------------------------------------------------------------
//
// private constructors -- you have to use static create methods to make these classes
//
// ---------------------------------------------------------------------------
private GenotypeCollection() {
this(10, false);
}
private GenotypeCollection(final int n, final boolean immutable) {
this(new ArrayList<Genotype>(n), immutable);
}
private GenotypeCollection(final ArrayList<Genotype> genotypes, final boolean immutable) {
this.genotypes = genotypes;
this.immutable = immutable;
}
// ---------------------------------------------------------------------------
//
// public static factory methods
//
// ---------------------------------------------------------------------------
public static final GenotypeCollection create() {
return new GenotypeCollection();
}
public static final GenotypeCollection create(final int nGenotypes) {
return new GenotypeCollection(nGenotypes, true);
}
// todo -- differentiate between empty constructor and copy constructor
// todo -- create constructor (Genotype ... genotypes)
public static final GenotypeCollection create(final ArrayList<Genotype> genotypes) {
return new GenotypeCollection(genotypes, true);
}
public static final GenotypeCollection copy(final GenotypeCollection toCopy) {
return create(toCopy.genotypes);
}
// public static final GenotypeMap create(final Collection<Genotype> genotypes) {
// if ( genotypes == null )
// return null; // todo -- really should return an empty map
// else {
// GenotypeMap genotypeMap = new GenotypeMap(genotypes.size(), false);
// for ( final Genotype g : genotypes ) {
// if ( genotypeMap.containsKey(g.getSampleName() ) )
// throw new IllegalArgumentException("Duplicate genotype added to VariantContext: " + g);
// genotypeMap.put(g.getSampleName(), g);
// }
//
// //return genotypeMap.immutable(); // todo enable when we have time to dive into mutability issue
// return genotypeMap;
// }
// }
// ---------------------------------------------------------------------------
//
// Mutability methods
//
// ---------------------------------------------------------------------------
public final GenotypeCollection mutable() {
immutable = false;
return this;
}
public final GenotypeCollection immutable() {
immutable = true;
return this;
}
public boolean isMutable() {
return ! immutable;
}
public final void checkImmutability() {
if ( immutable )
throw new IllegalAccessError("GenotypeMap is currently immutable, but a mutator method was invoked on it");
}
// ---------------------------------------------------------------------------
//
// caches
//
// ---------------------------------------------------------------------------
private void invalidateCaches() {
cacheIsInvalid = true;
if ( sampleNameToOffset != null ) sampleNameToOffset.clear();
}
private void buildCache() {
cacheIsInvalid = false;
if ( sampleNameToOffset == null )
sampleNameToOffset = new HashMap<String, Integer>(genotypes.size());
for ( int i = 0; i < genotypes.size(); i++ )
sampleNameToOffset.put(genotypes.get(i).getSampleName(), i);
}
// ---------------------------------------------------------------------------
//
// Map methods
//
// ---------------------------------------------------------------------------
@Override
public void clear() {
checkImmutability();
genotypes.clear();
}
@Override
public int size() {
return genotypes.size();
}
@Override
public boolean isEmpty() {
return genotypes.isEmpty();
}
@Override
public boolean add(final Genotype genotype) {
checkImmutability();
invalidateCaches();
return genotypes.add(genotype);
}
@Override
public void add(final int i, final Genotype genotype) {
throw new UnsupportedOperationException();
}
@Override
public boolean addAll(final Collection<? extends Genotype> genotypes) {
checkImmutability();
invalidateCaches();
return this.genotypes.addAll(genotypes);
}
@Override
public boolean addAll(final int i, final Collection<? extends Genotype> genotypes) {
throw new UnsupportedOperationException();
}
@Override
public boolean contains(final Object o) {
return this.genotypes.contains(o);
}
@Override
public boolean containsAll(final Collection<?> objects) {
return this.genotypes.containsAll(objects);
}
@Override
public Genotype get(final int i) {
return genotypes.get(i);
}
public Genotype get(final String sampleName) {
buildCache();
Integer offset = sampleNameToOffset.get(sampleName);
if ( offset == null )
throw new IllegalArgumentException("Sample " + sampleName + " not found in this GenotypeCollection");
return genotypes.get(offset);
}
@Override
public int indexOf(final Object o) {
return genotypes.indexOf(o);
}
@Override
public Iterator<Genotype> iterator() {
return genotypes.iterator();
}
@Override
public int lastIndexOf(final Object o) {
return genotypes.lastIndexOf(o);
}
@Override
public ListIterator<Genotype> listIterator() {
// todo -- must be immutable
return genotypes.listIterator();
}
@Override
public ListIterator<Genotype> listIterator(final int i) {
// todo -- must be immutable
return genotypes.listIterator(i);
}
@Override
public Genotype remove(final int i) {
checkImmutability();
invalidateCaches();
return genotypes.remove(i);
}
@Override
public boolean remove(final Object o) {
checkImmutability();
invalidateCaches();
return genotypes.remove(o);
}
@Override
public boolean removeAll(final Collection<?> objects) {
checkImmutability();
invalidateCaches();
return genotypes.removeAll(objects);
}
@Override
public boolean retainAll(final Collection<?> objects) {
checkImmutability();
invalidateCaches();
return genotypes.retainAll(objects);
}
@Override
public Genotype set(final int i, final Genotype genotype) {
checkImmutability();
invalidateCaches();
return genotypes.set(i, genotype);
}
@Override
public List<Genotype> subList(final int i, final int i1) {
return genotypes.subList(i, i1);
}
@Override
public Object[] toArray() {
return genotypes.toArray();
}
@Override
public <T> T[] toArray(final T[] ts) {
return genotypes.toArray(ts);
}
public Iterable<Genotype> iterateInOrder(final Iterable<String> sampleNamesInOrder) {
return new Iterable<Genotype>() {
@Override
public Iterator<Genotype> iterator() {
return new InOrderIterator(sampleNamesInOrder.iterator());
}
};
}
private final class InOrderIterator implements Iterator<Genotype> {
final Iterator<String> sampleNamesInOrder;
private InOrderIterator(final Iterator<String> sampleNamesInOrder) {
this.sampleNamesInOrder = sampleNamesInOrder;
}
@Override
public boolean hasNext() {
return sampleNamesInOrder.hasNext();
}
@Override
public Genotype next() {
return get(sampleNamesInOrder.next());
}
@Override
public void remove() {
throw new UnsupportedOperationException();
}
}
}

191
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeMap.java
View File

@ -1,191 +0,0 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.variantcontext;
import java.util.*;
/**
*
*/
public class GenotypeMap implements Map<String, Genotype> {
final TreeMap<String, Genotype> genotypes;
boolean immutable = false;
public final static GenotypeMap NO_GENOTYPES = new GenotypeMap();
// ---------------------------------------------------------------------------
//
// private constructors -- you have to use static create methods to make these classes
//
// ---------------------------------------------------------------------------
private GenotypeMap() {
this(false);
}
private GenotypeMap(boolean immutable) {
this(new TreeMap<String, Genotype>(), immutable);
}
private GenotypeMap(final TreeMap<String, Genotype> genotypes, final boolean immutable) {
this.genotypes = genotypes;
this.immutable = immutable;
}
// ---------------------------------------------------------------------------
//
// public static factory methods
//
// ---------------------------------------------------------------------------
public static final GenotypeMap create() {
return new GenotypeMap();
}
public static final GenotypeMap create(final int nGenotypes) {
return new GenotypeMap();
}
public static final GenotypeMap create(final GenotypeMap genotypes) {
return create(genotypes.values());
}
// todo -- differentiate between empty constructor and copy constructor
// todo -- create constructor (Genotype ... genotypes)
public static final GenotypeMap create(final Map<String, Genotype> genotypes) {
return create(genotypes.values());
}
public static final GenotypeMap create(final Collection<Genotype> genotypes) {
if ( genotypes == null )
return null; // todo -- really should return an empty map
else {
GenotypeMap genotypeMap = new GenotypeMap().mutable();
for ( final Genotype g : genotypes ) {
if ( genotypeMap.containsKey(g.getSampleName() ) )
throw new IllegalArgumentException("Duplicate genotype added to VariantContext: " + g);
genotypeMap.put(g.getSampleName(), g);
}
//return genotypeMap.immutable(); // todo enable when we have time to dive into mutability issue
return genotypeMap;
}
}
// ---------------------------------------------------------------------------
//
// Mutability methods
//
// ---------------------------------------------------------------------------
public final GenotypeMap mutable() {
immutable = false;
return this;
}
public final GenotypeMap immutable() {
immutable = true;
return this;
}
public boolean isMutable() {
return ! immutable;
}
public final void checkImmutability() {
if ( immutable )
throw new IllegalAccessError("GenotypeMap is currently immutable, but a mutator method was invoked on it");
}
// ---------------------------------------------------------------------------
//
// Map methods
//
// ---------------------------------------------------------------------------
@Override
public void clear() {
checkImmutability();
genotypes.clear();
}
@Override
public int size() {
return genotypes.size();
}
@Override
public boolean isEmpty() {
return genotypes.isEmpty();
}
@Override
public boolean containsKey(final Object o) {
return genotypes.containsKey(o);
}
@Override
public boolean containsValue(final Object o) {
return genotypes.containsValue(o);
}
@Override
public Genotype get(final Object o) {
return genotypes.get(o);
}
@Override
public Genotype put(final String s, final Genotype genotype) {
checkImmutability();
return genotypes.put(s, genotype);
}
@Override
public Genotype remove(final Object o) {
checkImmutability();
return genotypes.remove(o);
}
@Override
public void putAll(final Map<? extends String, ? extends Genotype> map) {
checkImmutability();
genotypes.putAll(map);
}
@Override
public Set<String> keySet() {
return Collections.unmodifiableSet(genotypes.keySet());
}
@Override
public Collection<Genotype> values() {
return genotypes.values();
}
@Override
public Set<Entry<String, Genotype>> entrySet() {
return genotypes.entrySet();
}
}

28
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -184,12 +184,12 @@ public class VariantContext implements Feature { // to enable tribble intergrati
final protected List<Allele> alleles;
/** A mapping from sampleName -> genotype objects for all genotypes associated with this context */
protected GenotypeMap genotypes = null;
protected GenotypeCollection genotypes = null;
/** Counts for each of the possible Genotype types in this context */
protected int[] genotypeCounts = null;
public final static GenotypeMap NO_GENOTYPES = GenotypeMap.NO_GENOTYPES;
public final static GenotypeCollection NO_GENOTYPES = GenotypeCollection.NO_GENOTYPES;
// a fast cached access point to the ref / alt alleles for biallelic case
private Allele REF = null;
@ -222,7 +222,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param attributes attributes
* @param referenceBaseForIndel padded reference base
*/
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, GenotypeMap genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, GenotypeCollection genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, referenceBaseForIndel, false);
}
@ -239,7 +239,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param filters filters: use null for unfiltered and empty set for passes filters
* @param attributes attributes
*/
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, GenotypeMap genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, GenotypeCollection genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, null, false);
}
@ -279,7 +279,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
*/
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
this(source, contig, start, stop, alleles,
GenotypeMap.create(genotypes),
GenotypeCollection.create(genotypes),
negLog10PError, filters, attributes, null, false);
}
@ -335,7 +335,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param genotypesAreUnparsed true if the genotypes have not yet been parsed
*/
private VariantContext(String source, String contig, long start, long stop,
Collection<Allele> alleles, GenotypeMap genotypes,
Collection<Allele> alleles, GenotypeCollection genotypes,
double negLog10PError, Set<String> filters, Map<String, Object> attributes,
Byte referenceBaseForIndel, boolean genotypesAreUnparsed) {
if ( contig == null ) { throw new IllegalArgumentException("Contig cannot be null"); }
@ -383,7 +383,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
//
// ---------------------------------------------------------------------------------------------------------
public static VariantContext modifyGenotypes(VariantContext vc, GenotypeMap genotypes) {
public static VariantContext modifyGenotypes(VariantContext vc, GenotypeCollection genotypes) {
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap<String, Object>(vc.getAttributes()), vc.getReferenceBaseForIndel(), false);
}
@ -458,7 +458,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
*/
public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes, Collection<Allele> alleles) {
return new VariantContext(getSource(), contig, start, stop, alleles,
GenotypeMap.create(genotypes),
GenotypeCollection.create(genotypes),
getNegLog10PError(),
filtersWereApplied() ? getFilters() : null,
getAttributes(),
@ -890,7 +890,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
/**
* @return set of all Genotypes associated with this context
*/
public GenotypeMap getGenotypes() {
public GenotypeCollection getGenotypes() {
loadGenotypes();
return genotypes;
}
@ -909,7 +909,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @return
* @throws IllegalArgumentException if sampleName isn't bound to a genotype
*/
public GenotypeMap getGenotypes(String sampleName) {
public GenotypeCollection getGenotypes(String sampleName) {
return getGenotypes(Arrays.asList(sampleName));
}
@ -921,8 +921,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @return
* @throws IllegalArgumentException if sampleName isn't bound to a genotype
*/
public GenotypeMap getGenotypes(Collection<String> sampleNames) {
GenotypeMap map = GenotypeMap.create(sampleNames.size());
public GenotypeCollection getGenotypes(Collection<String> sampleNames) {
GenotypeCollection map = GenotypeCollection.create(sampleNames.size());
for ( String name : sampleNames ) {
if ( map.containsKey(name) ) throw new IllegalArgumentException("Duplicate names detected in requested samples " + sampleNames);
@ -1465,8 +1465,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
Byte refByte = inputVC.getReferenceBaseForIndel();
List<Allele> alleles = new ArrayList<Allele>();
GenotypeMap genotypes = GenotypeMap.create();
GenotypeMap inputGenotypes = inputVC.getGenotypes();
GenotypeCollection genotypes = GenotypeCollection.create();
GenotypeCollection inputGenotypes = inputVC.getGenotypes();
for (Allele a : inputVC.getAlleles()) {
// get bases for current allele and create a new one with trimmed bases

20
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -70,7 +70,7 @@ public class VariantContextUtils {
* @return VariantContext object
*/
public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
return new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, GenotypeMap.create(genotypes), negLog10PError, filters, attributes);
return new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, GenotypeCollection.create(genotypes), negLog10PError, filters, attributes);
}
/**
@ -350,7 +350,7 @@ public class VariantContextUtils {
if ( vc.hasID() ) attributes.put(VariantContext.ID_KEY, vc.getID());
// Genotypes
final GenotypeMap genotypes = GenotypeMap.create(vc.getNSamples());
final GenotypeCollection genotypes = GenotypeCollection.create(vc.getNSamples());
for ( final Genotype g : vc.getGenotypes().values() ) {
Map<String, Object> genotypeAttributes = subsetAttributes(g.commonInfo, keysToPreserve);
genotypes.put(g.getSampleName(),
@ -458,7 +458,7 @@ public class VariantContextUtils {
final Map<String, Object> attributesWithMaxAC = new TreeMap<String, Object>();
double negLog10PError = -1;
VariantContext vcWithMaxAC = null;
GenotypeMap genotypes = GenotypeMap.create();
GenotypeCollection genotypes = GenotypeCollection.create();
// counting the number of filtered and variant VCs
int nFiltered = 0;
@ -648,7 +648,7 @@ public class VariantContextUtils {
// nothing to do if we don't need to trim bases
if (trimVC) {
List<Allele> alleles = new ArrayList<Allele>();
GenotypeMap genotypes = GenotypeMap.create();
GenotypeCollection genotypes = GenotypeCollection.create();
// set the reference base for indels in the attributes
Map<String,Object> attributes = new TreeMap<String,Object>(inputVC.getAttributes());
@ -702,8 +702,8 @@ public class VariantContextUtils {
return inputVC;
}
public static GenotypeMap stripPLs(GenotypeMap genotypes) {
GenotypeMap newGs = GenotypeMap.create(genotypes.size());
public static GenotypeCollection stripPLs(GenotypeCollection genotypes) {
GenotypeCollection newGs = GenotypeCollection.create(genotypes.size());
for ( Map.Entry<String, Genotype> g : genotypes.entrySet() ) {
newGs.put(g.getKey(), g.getValue().hasLikelihoods() ? removePLs(g.getValue()) : g.getValue());
@ -883,7 +883,7 @@ public class VariantContextUtils {
}
}
private static void mergeGenotypes(GenotypeMap mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) {
private static void mergeGenotypes(GenotypeCollection mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) {
for ( Genotype g : oneVC.getGenotypes().values() ) {
String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples);
if ( ! mergedGenotypes.containsKey(name) ) {
@ -923,7 +923,7 @@ public class VariantContextUtils {
}
// create new Genotype objects
GenotypeMap newGenotypes = GenotypeMap.create(vc.getNSamples());
GenotypeCollection newGenotypes = GenotypeCollection.create(vc.getNSamples());
for ( Map.Entry<String, Genotype> genotype : vc.getGenotypes().entrySet() ) {
List<Allele> newAlleles = new ArrayList<Allele>();
for ( Allele allele : genotype.getValue().getAlleles() ) {
@ -943,7 +943,7 @@ public class VariantContextUtils {
if ( allowedAttributes == null )
return vc;
GenotypeMap newGenotypes = GenotypeMap.create(vc.getNSamples());
GenotypeCollection newGenotypes = GenotypeCollection.create(vc.getNSamples());
for ( Map.Entry<String, Genotype> genotype : vc.getGenotypes().entrySet() ) {
Map<String, Object> attrs = new HashMap<String, Object>();
for ( Map.Entry<String, Object> attr : genotype.getValue().getAttributes().entrySet() ) {
@ -1022,7 +1022,7 @@ public class VariantContextUtils {
}
MergedAllelesData mergeData = new MergedAllelesData(intermediateBases, vc1, vc2); // ensures that the reference allele is added
GenotypeMap mergedGenotypes = GenotypeMap.create();
GenotypeCollection mergedGenotypes = GenotypeCollection.create();
for (Map.Entry<String, Genotype> gt1Entry : vc1.getGenotypes().entrySet()) {
String sample = gt1Entry.getKey();
Genotype gt1 = gt1Entry.getValue();

4
public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
View File

@ -4,7 +4,7 @@ import org.broad.tribble.Tribble;
import org.broad.tribble.readers.AsciiLineReader;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
import org.broadinstitute.sting.utils.variantcontext.GenotypeCollection;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -122,7 +122,7 @@ public class VCFWriterUnitTest extends BaseTest {
List<Allele> alleles = new ArrayList<Allele>();
Set<String> filters = null;
Map<String, Object> attributes = new HashMap<String,Object>();
GenotypeMap genotypes = GenotypeMap.create();
GenotypeCollection genotypes = GenotypeCollection.create();
alleles.add(Allele.create("-",true));
alleles.add(Allele.create("CC",false));

2
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
View File

@ -99,7 +99,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
int start = 10;
int stop = start; // alleles.contains(ATC) ? start + 3 : start;
return new VariantContext(source, "1", start, stop, alleles,
GenotypeMap.create(genotypes), 1.0, filters, null, Cref.getBases()[0]);
GenotypeCollection.create(genotypes), 1.0, filters, null, Cref.getBases()[0]);
}
// --------------------------------------------------------------------------------