VariantContext genotypes are now stored as GenotypeMap objects
-- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples -- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type. -- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous. Now everything uses GenotypeMap with a specific ordering of samples (by name) -- Integrationtests updated and all pass
This commit is contained in:
Mark DePristo
parent
4938569b3a
commit
fee9b367e4
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@ -194,7 +194,7 @@ public class VariantContextAdaptors {
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return null; // we weren't given enough reference context to create the VariantContext
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Byte refBaseForIndel = new Byte(ref.getBases()[index]);
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Map<String, Genotype> genotypes = null;
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GenotypeMap genotypes = null;
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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);
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return vc;
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} else
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@ -329,7 +329,7 @@ public class VariantContextAdaptors {
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String[] samples = hapmap.getSampleIDs();
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String[] genotypeStrings = hapmap.getGenotypes();
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>(samples.length);
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GenotypeMap genotypes = GenotypeMap.create(samples.length);
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for ( int i = 0; i < samples.length; i++ ) {
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// ignore bad genotypes
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if ( genotypeStrings[i].contains("N") )
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@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
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import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.Arrays;
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@ -54,7 +55,7 @@ public class AlleleBalance extends InfoFieldAnnotation {
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if ( !vc.isBiallelic() )
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return null;
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final Map<String, Genotype> genotypes = vc.getGenotypes();
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final GenotypeMap genotypes = vc.getGenotypes();
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if ( !vc.hasGenotypes() )
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return null;
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@ -11,6 +11,7 @@ import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.Arrays;
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@ -30,7 +31,7 @@ public class HardyWeinberg extends InfoFieldAnnotation implements WorkInProgress
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public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
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final Map<String, Genotype> genotypes = vc.getGenotypes();
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final GenotypeMap genotypes = vc.getGenotypes();
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if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
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return null;
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@ -10,6 +10,7 @@ import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.Arrays;
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@ -32,7 +33,7 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
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public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
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final Map<String, Genotype> genotypes = vc.getGenotypes();
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final GenotypeMap genotypes = vc.getGenotypes();
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if ( genotypes == null || genotypes.size() < MIN_SAMPLES )
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return null;
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@ -9,6 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
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import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.Arrays;
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@ -28,7 +29,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
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if ( stratifiedContexts.size() == 0 )
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return null;
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final Map<String, Genotype> genotypes = vc.getGenotypes();
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final GenotypeMap genotypes = vc.getGenotypes();
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if ( genotypes == null || genotypes.size() == 0 )
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return null;
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@ -13,6 +13,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.ArrayList;
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@ -32,7 +33,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
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if ( stratifiedContexts.size() == 0 )
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return null;
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final Map<String, Genotype> genotypes = vc.getGenotypes();
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final GenotypeMap genotypes = vc.getGenotypes();
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if ( genotypes == null || genotypes.size() == 0 )
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return null;
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@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.*;
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@ -216,11 +217,11 @@ public class VariantAnnotatorEngine {
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}
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}
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private Map<String, Genotype> annotateGenotypes(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
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private GenotypeMap annotateGenotypes(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
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if ( requestedGenotypeAnnotations.size() == 0 )
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return vc.getGenotypes();
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>(vc.getNSamples());
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GenotypeMap genotypes = GenotypeMap.create(vc.getNSamples());
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for ( Map.Entry<String, Genotype> g : vc.getGenotypes().entrySet() ) {
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Genotype genotype = g.getValue();
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AlignmentContext context = stratifiedContexts.get(g.getKey());
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@ -36,10 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.utils.variantcontext.*;
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import java.util.*;
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@ -190,8 +187,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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byte refByte = ref.getBase();
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// make new Genotypes based on Beagle results
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>(vc_input.getGenotypes().size());
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GenotypeMap genotypes = GenotypeMap.create(vc_input.getGenotypes().size());
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// for each genotype, create a new object with Beagle information on it
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@ -200,7 +196,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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Double alleleFrequencyH = 0.0;
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int beagleVarCounts = 0;
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Map<String,Genotype> hapmapGenotypes = null;
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GenotypeMap hapmapGenotypes = null;
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if (vc_comp != null) {
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hapmapGenotypes = vc_comp.getGenotypes();
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@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
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@ -282,11 +283,11 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
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VariantContext vc = context.getVariantContext();
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// make new Genotypes based on filters
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Map<String, Genotype> genotypes;
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GenotypeMap genotypes;
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if ( genotypeFilterExps.size() == 0 ) {
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genotypes = null;
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} else {
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genotypes = new HashMap<String, Genotype>(vc.getGenotypes().size());
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genotypes = GenotypeMap.create(vc.getGenotypes().size());
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// for each genotype, check filters then create a new object
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for ( Map.Entry<String, Genotype> genotype : vc.getGenotypes().entrySet() ) {
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@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.io.PrintStream;
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@ -85,7 +86,7 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
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*
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* @return calls
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*/
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protected abstract Map<String, Genotype> assignGenotypes(VariantContext vc,
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double[] log10AlleleFrequencyPosteriors,
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int AFofMaxLikelihood);
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protected abstract GenotypeMap assignGenotypes(VariantContext vc,
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double[] log10AlleleFrequencyPosteriors,
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int AFofMaxLikelihood);
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}
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@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.io.PrintStream;
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@ -268,14 +269,14 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
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*
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* @return calls
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*/
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public Map<String, Genotype> assignGenotypes(VariantContext vc,
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double[] log10AlleleFrequencyPosteriors,
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int AFofMaxLikelihood) {
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public GenotypeMap assignGenotypes(VariantContext vc,
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double[] log10AlleleFrequencyPosteriors,
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int AFofMaxLikelihood) {
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if ( !vc.isVariant() )
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throw new UserException("The VCF record passed in does not contain an ALT allele at " + vc.getChr() + ":" + vc.getStart());
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Map<String, Genotype> GLs = vc.getGenotypes();
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GenotypeMap GLs = vc.getGenotypes();
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double[][] pathMetricArray = new double[GLs.size()+1][AFofMaxLikelihood+1];
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int[][] tracebackArray = new int[GLs.size()+1][AFofMaxLikelihood+1];
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@ -342,7 +343,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
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}
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}
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HashMap<String, Genotype> calls = new HashMap<String, Genotype>();
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GenotypeMap calls = GenotypeMap.create();
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int startIdx = AFofMaxLikelihood;
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for (int k = sampleIdx; k > 0; k--) {
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@ -34,6 +34,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.io.PrintStream;
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@ -89,15 +90,15 @@ public class GridSearchAFEstimation extends AlleleFrequencyCalculationModel {
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*
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* @return calls
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*/
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protected Map<String, Genotype> assignGenotypes(VariantContext vc,
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double[] log10AlleleFrequencyPosteriors,
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int AFofMaxLikelihood) {
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protected GenotypeMap assignGenotypes(VariantContext vc,
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double[] log10AlleleFrequencyPosteriors,
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int AFofMaxLikelihood) {
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if ( !vc.isVariant() )
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throw new UserException("The VCF record passed in does not contain an ALT allele at " + vc.getChr() + ":" + vc.getStart());
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Allele refAllele = vc.getReference();
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Allele altAllele = vc.getAlternateAllele(0);
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HashMap<String, Genotype> calls = new HashMap<String, Genotype>();
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GenotypeMap calls = GenotypeMap.create();
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// first, the potential alt calls
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for ( String sample : AFMatrix.getSamples() ) {
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
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@ -128,7 +129,7 @@ public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
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return null;
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VariantContext variantVC = null;
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
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GenotypeMap genotypes = GenotypeMap.create();
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for ( VariantContext vc : VCs ) {
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if ( variantVC == null && vc.isVariant() )
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variantVC = vc;
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@ -265,7 +265,7 @@ public class UnifiedGenotyperEngine {
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alleles.add(refAllele);
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boolean addedAltAlleles = false;
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HashMap<String, Genotype> genotypes = new HashMap<String, Genotype>();
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GenotypeMap genotypes = GenotypeMap.create();
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for ( MultiallelicGenotypeLikelihoods GL : GLs.values() ) {
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if ( !addedAltAlleles ) {
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addedAltAlleles = true;
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@ -354,7 +354,7 @@ public class UnifiedGenotyperEngine {
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}
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// create the genotypes
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Map<String, Genotype> genotypes = afcm.get().assignGenotypes(vc, log10AlleleFrequencyPosteriors.get(), bestAFguess);
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GenotypeMap genotypes = afcm.get().assignGenotypes(vc, log10AlleleFrequencyPosteriors.get(), bestAFguess);
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// print out stats if we have a writer
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if ( verboseWriter != null )
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@ -491,7 +491,7 @@ public class UnifiedGenotyperEngine {
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}
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// create the genotypes
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Map<String, Genotype> genotypes = afcm.get().assignGenotypes(vc, log10AlleleFrequencyPosteriors.get(), bestAFguess);
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GenotypeMap genotypes = afcm.get().assignGenotypes(vc, log10AlleleFrequencyPosteriors.get(), bestAFguess);
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// *** note that calculating strand bias involves overwriting data structures, so we do that last
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HashMap<String, Object> attributes = new HashMap<String, Object>();
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@ -60,6 +60,7 @@ import org.broadinstitute.sting.utils.sam.AlignmentUtils;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypeMap;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.io.*;
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@ -1057,7 +1058,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
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stop += event_length;
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}
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Map<String,Genotype> genotypes = new HashMap<String,Genotype>();
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GenotypeMap genotypes = GenotypeMap.create();
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for ( String sample : normalSamples ) {
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@ -1147,7 +1148,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
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homRefAlleles.add( alleles.get(0));
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homRefAlleles.add( alleles.get(0));
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Map<String,Genotype> genotypes = new HashMap<String,Genotype>();
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GenotypeMap genotypes = GenotypeMap.create();
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for ( String sample : normalSamples ) {
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genotypes.put(sample,new Genotype(sample, homRefN ? homRefAlleles : alleles,Genotype.NO_NEG_LOG_10PERROR,null,attrsNormal,false));
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@ -12,10 +12,7 @@ import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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import org.broadinstitute.sting.utils.text.XReadLines;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.utils.variantcontext.*;
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import java.io.File;
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import java.io.FileNotFoundException;
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@ -296,7 +293,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
|
|||
if (tracker != null) {
|
||||
VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation());
|
||||
|
||||
Map<String, Genotype> genotypeMap = vc.getGenotypes();
|
||||
GenotypeMap genotypeMap = vc.getGenotypes();
|
||||
|
||||
for (Trio trio : trios) {
|
||||
Genotype mother = vc.getGenotype(trio.getMother());
|
||||
|
|
|
|||
|
|
@ -41,10 +41,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.*;
|
|||
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.sting.utils.variantcontext.Genotype;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
|
||||
import org.broadinstitute.sting.utils.variantcontext.*;
|
||||
|
||||
import java.io.*;
|
||||
import java.util.*;
|
||||
|
|
@ -355,7 +352,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
|
|||
UnfinishedVariantContext uvc = uvr.unfinishedVariant;
|
||||
|
||||
// Perform per-sample phasing:
|
||||
Map<String, Genotype> sampGenotypes = vc.getGenotypes();
|
||||
GenotypeMap sampGenotypes = vc.getGenotypes();
|
||||
Map<String, PhaseCounts> samplePhaseStats = new TreeMap<String, PhaseCounts>();
|
||||
for (Map.Entry<String, Genotype> sampGtEntry : sampGenotypes.entrySet()) {
|
||||
String samp = sampGtEntry.getKey();
|
||||
|
|
@ -1126,7 +1123,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
|
|||
private int start;
|
||||
private int stop;
|
||||
private Collection<Allele> alleles;
|
||||
private Map<String, Genotype> genotypes;
|
||||
private GenotypeMap genotypes;
|
||||
private double negLog10PError;
|
||||
private Set<String> filters;
|
||||
private Map<String, Object> attributes;
|
||||
|
|
@ -1137,7 +1134,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
|
|||
this.start = vc.getStart();
|
||||
this.stop = vc.getEnd();
|
||||
this.alleles = vc.getAlleles();
|
||||
this.genotypes = new HashMap<String, Genotype>(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
|
||||
this.genotypes = GenotypeMap.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());
|
||||
|
|
|
|||
|
|
@ -14,6 +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.VariantContext;
|
||||
|
||||
import java.util.HashMap;
|
||||
|
|
@ -91,13 +92,13 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
|
|||
|
||||
Set<String> allSamples = new HashSet<String>();
|
||||
|
||||
Map<String, Genotype> compSampGenotypes = null;
|
||||
GenotypeMap compSampGenotypes = null;
|
||||
if (isRelevantToPhasing(comp)) {
|
||||
allSamples.addAll(comp.getSampleNames());
|
||||
compSampGenotypes = comp.getGenotypes();
|
||||
}
|
||||
|
||||
Map<String, Genotype> evalSampGenotypes = null;
|
||||
GenotypeMap evalSampGenotypes = null;
|
||||
if (isRelevantToPhasing(eval)) {
|
||||
allSamples.addAll(eval.getSampleNames());
|
||||
evalSampGenotypes = eval.getGenotypes();
|
||||
|
|
|
|||
|
|
@ -40,6 +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.VariantContext;
|
||||
|
||||
import java.util.*;
|
||||
|
|
@ -210,7 +211,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
|
|||
}
|
||||
|
||||
// create new Genotype objects
|
||||
Map<String, Genotype> newGenotypes = new HashMap<String, Genotype>(vc.getNSamples());
|
||||
GenotypeMap newGenotypes = GenotypeMap.create(vc.getNSamples());
|
||||
for ( Map.Entry<String, Genotype> genotype : vc.getGenotypes().entrySet() ) {
|
||||
List<Allele> newAlleles = new ArrayList<Allele>();
|
||||
for ( Allele allele : genotype.getValue().getAlleles() ) {
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
|
|||
import org.broadinstitute.sting.utils.text.XReadLines;
|
||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
||||
import org.broadinstitute.sting.utils.MendelianViolation;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.utils.variantcontext.*;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
|
|
@ -41,9 +41,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
|||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.RodWalker;
|
||||
import org.broadinstitute.sting.utils.SampleUtils;
|
||||
import org.broadinstitute.sting.utils.variantcontext.Allele;
|
||||
import org.broadinstitute.sting.utils.variantcontext.Genotype;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
|
|
@ -561,7 +558,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
|
|||
return (compVCs == null || compVCs.isEmpty());
|
||||
|
||||
// check if we find it in the variant rod
|
||||
Map<String, Genotype> genotypes = vc.getGenotypes(samples);
|
||||
GenotypeMap 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.
|
||||
|
|
@ -659,7 +656,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
|
|||
if ( samples == null || samples.isEmpty() )
|
||||
return vc;
|
||||
|
||||
VariantContext sub = vc.subContextFromSamples(samples);
|
||||
VariantContext sub = vc.subContextFromSamples(samples, vc.getAlleles());
|
||||
|
||||
// if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs (because they are no longer accurate)
|
||||
if ( vc.getAlleles().size() != sub.getAlleles().size() )
|
||||
|
|
|
|||
|
|
@ -42,10 +42,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
|
|||
import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.*;
|
||||
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.VariantContext;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
|
||||
import org.broadinstitute.sting.utils.variantcontext.*;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.*;
|
||||
|
|
@ -133,7 +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);
|
||||
Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
|
||||
GenotypeMap genotypes = GenotypeMap.create(1);
|
||||
genotypes.put(sampleName, g);
|
||||
vc = VariantContext.modifyGenotypes(vc, genotypes);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -12,6 +12,7 @@ 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.VariantContext;
|
||||
|
||||
import java.io.*;
|
||||
|
|
@ -76,7 +77,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
|
|||
* @param pos position
|
||||
* @return a mapping of sample name to genotype object
|
||||
*/
|
||||
public abstract Map<String, Genotype> createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
|
||||
public abstract GenotypeMap createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
|
||||
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -5,6 +5,7 @@ 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.VariantContext;
|
||||
|
||||
import java.io.File;
|
||||
|
|
@ -118,13 +119,13 @@ public class VCF3Codec extends AbstractVCFCodec {
|
|||
* @param pos position
|
||||
* @return a mapping of sample name to genotype object
|
||||
*/
|
||||
public Map<String, Genotype> createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
|
||||
public GenotypeMap 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);
|
||||
|
||||
Map<String, Genotype> genotypes = new LinkedHashMap<String, Genotype>(nParts);
|
||||
GenotypeMap genotypes = GenotypeMap.create(nParts);
|
||||
|
||||
// get the format keys
|
||||
int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
|
||||
|
|
|
|||
|
|
@ -5,6 +5,7 @@ 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.VariantContext;
|
||||
|
||||
import java.io.File;
|
||||
|
|
@ -145,13 +146,13 @@ public class VCFCodec extends AbstractVCFCodec {
|
|||
* @param alleles the list of alleles
|
||||
* @return a mapping of sample name to genotype object
|
||||
*/
|
||||
public Map<String, Genotype> createGenotypeMap(String str, List<Allele> alleles, String chr, int pos) {
|
||||
public GenotypeMap 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);
|
||||
|
||||
Map<String, Genotype> genotypes = new LinkedHashMap<String, Genotype>(nParts);
|
||||
GenotypeMap genotypes = GenotypeMap.create(nParts);
|
||||
|
||||
// get the format keys
|
||||
int nGTKeys = ParsingUtils.split(genotypeParts[0], genotypeKeyArray, VCFConstants.GENOTYPE_FIELD_SEPARATOR_CHAR);
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@ 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 java.util.List;
|
||||
import java.util.Map;
|
||||
|
|
@ -20,6 +21,6 @@ public interface VCFParser {
|
|||
* @param pos position
|
||||
* @return a mapping of sample name to genotype object
|
||||
*/
|
||||
public Map<String, Genotype> createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
|
||||
public GenotypeMap createGenotypeMap(String str, List<Allele> alleles, String chr, int pos);
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -28,6 +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.VariantContext;
|
||||
|
||||
import java.io.*;
|
||||
|
|
@ -145,16 +146,16 @@ public class GCF {
|
|||
Map<String, Object> attributes = new HashMap<String, Object>();
|
||||
attributes.put("INFO", info);
|
||||
Byte refPadByte = refPad == 0 ? null : refPad;
|
||||
Map<String, Genotype> genotypes = decodeGenotypes(header);
|
||||
GenotypeMap genotypes = decodeGenotypes(header);
|
||||
|
||||
return new VariantContext(source, contig, start, stop, alleleMap, genotypes, negLog10PError, filters, attributes, refPadByte);
|
||||
}
|
||||
|
||||
private Map<String, Genotype> decodeGenotypes(final GCFHeader header) {
|
||||
private GenotypeMap decodeGenotypes(final GCFHeader header) {
|
||||
if ( genotypes.isEmpty() )
|
||||
return VariantContext.NO_GENOTYPES;
|
||||
else {
|
||||
Map<String, Genotype> map = new TreeMap<String, Genotype>();
|
||||
GenotypeMap map = GenotypeMap.create();
|
||||
|
||||
for ( int i = 0; i < genotypes.size(); i++ ) {
|
||||
final String sampleName = header.getSample(i);
|
||||
|
|
|
|||
|
|
@ -0,0 +1,66 @@
|
|||
/*
|
||||
* 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.Collection;
|
||||
import java.util.Map;
|
||||
import java.util.TreeMap;
|
||||
|
||||
/**
|
||||
*
|
||||
*/
|
||||
public class GenotypeMap extends TreeMap<String, Genotype> implements Map<String, Genotype> {
|
||||
public final static GenotypeMap NO_GENOTYPES = new GenotypeMap();
|
||||
|
||||
public static final GenotypeMap create() {
|
||||
return new GenotypeMap();
|
||||
}
|
||||
|
||||
public static final GenotypeMap create(int nGenotypes) {
|
||||
return new GenotypeMap();
|
||||
}
|
||||
|
||||
public static final GenotypeMap create(final GenotypeMap genotypes) {
|
||||
return create(genotypes.values());
|
||||
}
|
||||
|
||||
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();
|
||||
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;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -22,7 +22,7 @@ public class MutableVariantContext extends VariantContext {
|
|||
super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
|
||||
}
|
||||
|
||||
public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
|
||||
public MutableVariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, GenotypeMap genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
|
||||
super(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
|
||||
}
|
||||
|
||||
|
|
@ -72,7 +72,7 @@ public class MutableVariantContext extends VariantContext {
|
|||
}
|
||||
|
||||
public void clearGenotypes() {
|
||||
genotypes = new TreeMap<String, Genotype>();
|
||||
genotypes = GenotypeMap.create();
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -98,7 +98,6 @@ public class MutableVariantContext extends VariantContext {
|
|||
* @param genotypes
|
||||
*/
|
||||
public void addGenotypes(Map<String, Genotype> genotypes) {
|
||||
|
||||
for ( Map.Entry<String, Genotype> elt : genotypes.entrySet() ) {
|
||||
addGenotype(elt.getValue());
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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 Map<String, Genotype> genotypes = null;
|
||||
protected GenotypeMap genotypes = null;
|
||||
|
||||
/** Counts for each of the possible Genotype types in this context */
|
||||
protected int[] genotypeCounts = null;
|
||||
|
||||
public final static Map<String, Genotype> NO_GENOTYPES = Collections.unmodifiableMap(new HashMap<String, Genotype>());
|
||||
public final static GenotypeMap NO_GENOTYPES = GenotypeMap.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, Map<String, Genotype> 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, GenotypeMap 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, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> 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) {
|
||||
this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, null, false);
|
||||
}
|
||||
|
||||
|
|
@ -278,7 +278,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
* @param attributes attributes
|
||||
*/
|
||||
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, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes, null, false);
|
||||
this(source, contig, start, stop, alleles,
|
||||
GenotypeMap.create(genotypes),
|
||||
negLog10PError, filters, attributes, null, false);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -333,7 +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, Map<String, Genotype> genotypes,
|
||||
Collection<Allele> alleles, GenotypeMap genotypes,
|
||||
double negLog10PError, Set<String> filters, Map<String, Object> attributes,
|
||||
Byte referenceBaseForIndel, boolean genotypesAreUnparsed) {
|
||||
if ( contig == null ) { throw new IllegalArgumentException("Contig cannot be null"); }
|
||||
|
|
@ -357,9 +359,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
// we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles
|
||||
this.alleles = makeAlleles(alleles);
|
||||
|
||||
|
||||
if ( genotypes == null ) { genotypes = NO_GENOTYPES; }
|
||||
this.genotypes = Collections.unmodifiableMap(genotypes);
|
||||
this.genotypes = genotypes;
|
||||
|
||||
// cache the REF and ALT alleles
|
||||
int nAlleles = alleles.size();
|
||||
|
|
@ -382,7 +383,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
//
|
||||
// ---------------------------------------------------------------------------------------------------------
|
||||
|
||||
public static VariantContext modifyGenotypes(VariantContext vc, Map<String, Genotype> genotypes) {
|
||||
public static VariantContext modifyGenotypes(VariantContext vc, GenotypeMap 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);
|
||||
}
|
||||
|
||||
|
|
@ -447,7 +448,7 @@ 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,
|
||||
genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null,
|
||||
GenotypeMap.create(genotypes),
|
||||
getNegLog10PError(),
|
||||
filtersWereApplied() ? getFilters() : null,
|
||||
getAttributes(),
|
||||
|
|
@ -879,7 +880,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
/**
|
||||
* @return set of all Genotypes associated with this context
|
||||
*/
|
||||
public Map<String, Genotype> getGenotypes() {
|
||||
public GenotypeMap getGenotypes() {
|
||||
loadGenotypes();
|
||||
return genotypes;
|
||||
}
|
||||
|
|
@ -898,7 +899,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
* @return
|
||||
* @throws IllegalArgumentException if sampleName isn't bound to a genotype
|
||||
*/
|
||||
public Map<String, Genotype> getGenotypes(String sampleName) {
|
||||
public GenotypeMap getGenotypes(String sampleName) {
|
||||
return getGenotypes(Arrays.asList(sampleName));
|
||||
}
|
||||
|
||||
|
|
@ -910,8 +911,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
* @return
|
||||
* @throws IllegalArgumentException if sampleName isn't bound to a genotype
|
||||
*/
|
||||
public Map<String, Genotype> getGenotypes(Collection<String> sampleNames) {
|
||||
HashMap<String, Genotype> map = new HashMap<String, Genotype>();
|
||||
public GenotypeMap getGenotypes(Collection<String> sampleNames) {
|
||||
GenotypeMap map = GenotypeMap.create(sampleNames.size());
|
||||
|
||||
for ( String name : sampleNames ) {
|
||||
if ( map.containsKey(name) ) throw new IllegalArgumentException("Duplicate names detected in requested samples " + sampleNames);
|
||||
|
|
@ -1402,16 +1403,6 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
return alleleList;
|
||||
}
|
||||
|
||||
public static Map<String, Genotype> genotypeCollectionToMap(Map<String, Genotype> dest, Collection<Genotype> genotypes) {
|
||||
for ( Genotype g : genotypes ) {
|
||||
if ( dest.containsKey(g.getSampleName() ) )
|
||||
throw new IllegalArgumentException("Duplicate genotype added to VariantContext: " + g);
|
||||
dest.put(g.getSampleName(), g);
|
||||
}
|
||||
|
||||
return dest;
|
||||
}
|
||||
|
||||
// ---------------------------------------------------------------------------------------------------------
|
||||
//
|
||||
// tribble integration routines -- not for public consumption
|
||||
|
|
@ -1464,9 +1455,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
|
|||
Byte refByte = inputVC.getReferenceBaseForIndel();
|
||||
|
||||
List<Allele> alleles = new ArrayList<Allele>();
|
||||
Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();
|
||||
|
||||
Map<String, Genotype> inputGenotypes = inputVC.getGenotypes();
|
||||
GenotypeMap genotypes = GenotypeMap.create();
|
||||
GenotypeMap inputGenotypes = inputVC.getGenotypes();
|
||||
|
||||
for (Allele a : inputVC.getAlleles()) {
|
||||
// get bases for current allele and create a new one with trimmed bases
|
||||
|
|
|
|||
|
|
@ -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, genotypes != null ? VariantContext.genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes);
|
||||
return new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, GenotypeMap.create(genotypes), negLog10PError, filters, attributes);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -404,7 +404,7 @@ public class VariantContextUtils {
|
|||
*/
|
||||
public static VariantContext masterMerge(Collection<VariantContext> unsortedVCs, String masterName) {
|
||||
VariantContext master = findMaster(unsortedVCs, masterName);
|
||||
Map<String, Genotype> genotypes = master.getGenotypes();
|
||||
GenotypeMap genotypes = master.getGenotypes();
|
||||
for (Genotype g : genotypes.values()) {
|
||||
genotypes.put(g.getSampleName(), new MutableGenotype(g));
|
||||
}
|
||||
|
|
@ -526,7 +526,7 @@ public class VariantContextUtils {
|
|||
final Map<String, Object> attributesWithMaxAC = new TreeMap<String, Object>();
|
||||
double negLog10PError = -1;
|
||||
VariantContext vcWithMaxAC = null;
|
||||
Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();
|
||||
GenotypeMap genotypes = GenotypeMap.create();
|
||||
|
||||
// counting the number of filtered and variant VCs
|
||||
int nFiltered = 0;
|
||||
|
|
@ -716,7 +716,7 @@ public class VariantContextUtils {
|
|||
// nothing to do if we don't need to trim bases
|
||||
if (trimVC) {
|
||||
List<Allele> alleles = new ArrayList<Allele>();
|
||||
Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();
|
||||
GenotypeMap genotypes = GenotypeMap.create();
|
||||
|
||||
// set the reference base for indels in the attributes
|
||||
Map<String,Object> attributes = new TreeMap<String,Object>(inputVC.getAttributes());
|
||||
|
|
@ -770,8 +770,8 @@ public class VariantContextUtils {
|
|||
return inputVC;
|
||||
}
|
||||
|
||||
public static Map<String, Genotype> stripPLs(Map<String, Genotype> genotypes) {
|
||||
Map<String, Genotype> newGs = new HashMap<String, Genotype>(genotypes.size());
|
||||
public static GenotypeMap stripPLs(GenotypeMap genotypes) {
|
||||
GenotypeMap newGs = GenotypeMap.create(genotypes.size());
|
||||
|
||||
for ( Map.Entry<String, Genotype> g : genotypes.entrySet() ) {
|
||||
newGs.put(g.getKey(), g.getValue().hasLikelihoods() ? removePLs(g.getValue()) : g.getValue());
|
||||
|
|
@ -951,7 +951,7 @@ public class VariantContextUtils {
|
|||
}
|
||||
}
|
||||
|
||||
private static void mergeGenotypes(Map<String, Genotype> mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) {
|
||||
private static void mergeGenotypes(GenotypeMap 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) ) {
|
||||
|
|
@ -992,7 +992,7 @@ public class VariantContextUtils {
|
|||
}
|
||||
|
||||
// create new Genotype objects
|
||||
Map<String, Genotype> newGenotypes = new HashMap<String, Genotype>(vc.getNSamples());
|
||||
GenotypeMap newGenotypes = GenotypeMap.create(vc.getNSamples());
|
||||
for ( Map.Entry<String, Genotype> genotype : vc.getGenotypes().entrySet() ) {
|
||||
List<Allele> newAlleles = new ArrayList<Allele>();
|
||||
for ( Allele allele : genotype.getValue().getAlleles() ) {
|
||||
|
|
@ -1012,7 +1012,7 @@ public class VariantContextUtils {
|
|||
if ( allowedAttributes == null )
|
||||
return vc;
|
||||
|
||||
Map<String, Genotype> newGenotypes = new HashMap<String, Genotype>(vc.getNSamples());
|
||||
GenotypeMap newGenotypes = GenotypeMap.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() ) {
|
||||
|
|
@ -1091,7 +1091,7 @@ public class VariantContextUtils {
|
|||
}
|
||||
MergedAllelesData mergeData = new MergedAllelesData(intermediateBases, vc1, vc2); // ensures that the reference allele is added
|
||||
|
||||
Map<String, Genotype> mergedGenotypes = new HashMap<String, Genotype>();
|
||||
GenotypeMap mergedGenotypes = GenotypeMap.create();
|
||||
for (Map.Entry<String, Genotype> gt1Entry : vc1.getGenotypes().entrySet()) {
|
||||
String sample = gt1Entry.getKey();
|
||||
Genotype gt1 = gt1Entry.getValue();
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testHasAnnotsAsking1() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("8e7de435105499cd71ffc099e268a83e"));
|
||||
Arrays.asList("a6687f0d3830fa6e518b7874857f6f70"));
|
||||
executeTest("test file has annotations, asking for annotations, #1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -64,7 +64,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testNoAnnotsAsking1() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("fd1ffb669800c2e07df1e2719aa38e49"));
|
||||
Arrays.asList("b59508cf66da6b2de280a79b3b7d85b1"));
|
||||
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -80,7 +80,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testExcludeAnnotations() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("b49fe03aa4b675db80a9db38a3552c95"));
|
||||
Arrays.asList("b8e18b23568e4d2381f51d4430213040"));
|
||||
executeTest("test exclude annotations", spec);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -30,20 +30,23 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMultiSamplePilot1() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
|
||||
Arrays.asList("b27939251539439a382538e507e03507"));
|
||||
Arrays.asList("c93def488de12fb3b8199e001b7a24a8"));
|
||||
executeTest("test MultiSample Pilot1", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testWithAllelesPassedIn() {
|
||||
public void testWithAllelesPassedIn1() {
|
||||
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
|
||||
Arrays.asList("8de2602679ffc92388da0b6cb4325ef6"));
|
||||
Arrays.asList("cef4bd72cbbe72f28e9c72e2818b4708"));
|
||||
executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testWithAllelesPassedIn2() {
|
||||
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
|
||||
Arrays.asList("6458f3b8fe4954e2ffc2af972aaab19e"));
|
||||
Arrays.asList("14f5cdfc6818cbba600cbdf5fe285275"));
|
||||
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
|
||||
}
|
||||
|
||||
|
|
@ -261,7 +264,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
|
||||
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
|
||||
Arrays.asList("118918f2e9e56a3cfc5ccb2856d529c8"));
|
||||
Arrays.asList("81a1035e59cd883e413e62d34265c1a2"));
|
||||
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
|
||||
}
|
||||
|
||||
|
|
@ -271,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
|
||||
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
|
||||
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
|
||||
Arrays.asList("a20799237accd52c1b8c2ac096309c8f"));
|
||||
Arrays.asList("102b7d915f21dff0a9b6ea64c4c7d409"));
|
||||
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
|
||||
}
|
||||
|
||||
|
|
@ -281,7 +284,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation +
|
||||
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
|
||||
Arrays.asList("18ef8181157b4ac3eb8492f538467f92"));
|
||||
Arrays.asList("5900344f97bbac35d147a0a7c2bf1d0c"));
|
||||
executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
|
||||
}
|
||||
|
||||
|
|
@ -290,7 +293,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation +
|
||||
"phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
|
||||
Arrays.asList("ad884e511a751b05e64db5314314365a"));
|
||||
Arrays.asList("45e7bf21cd6358921626404e7ae76c69"));
|
||||
executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -4,6 +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.VariantContext;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.*;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
|
@ -121,7 +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>();
|
||||
Map<String, Genotype> genotypes = new HashMap<String,Genotype>();
|
||||
GenotypeMap genotypes = GenotypeMap.create();
|
||||
|
||||
alleles.add(Allele.create("-",true));
|
||||
alleles.add(Allele.create("CC",false));
|
||||
|
|
|
|||
|
|
@ -99,8 +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,
|
||||
genotypes == null ? null : VariantContext.genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes),
|
||||
1.0, filters, null, Cref.getBases()[0]);
|
||||
GenotypeMap.create(genotypes), 1.0, filters, null, Cref.getBases()[0]);
|
||||
}
|
||||
|
||||
// --------------------------------------------------------------------------------
|
||||
|
|
|
|||
Loading…
Reference in New Issue