GenotypingEngines and walkers now use AFCalc(ulator) providers rathern than instanciate their own (fixed) calculators directly.
Changes: ------- * GenotypingEngine uses now a AFCalc provider instead of its own thread-local with one-time initialized and fixed AF calculator. * All walkers that use a GenotypingEngine now are passing the appropiate AF calculator provider. For now most just use a fix calculator (FixedAFCalculatorProvider) except GenotypeGVCFs as this one now can cope with mixture of ploidies failing-over to a general-ploidy calculator when the preferred implementation is not capable to handle a site's analysis.
This commit is contained in:
Valentin Ruano-Rubio
parent
935bd1394b
commit
3cdeab6e9e
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@ -60,6 +60,7 @@ import org.broadinstitute.gatk.utils.collections.Pair;
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import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
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import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
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import htsjdk.variant.variantcontext.*;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import java.util.*;
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@ -286,8 +287,8 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
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builder.attributes(attributes);
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// create the genotypes; no-call everyone for now
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final GenotypesContext genotypes = GenotypesContext.create();
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final List<Allele> noCall = new ArrayList<Allele>();
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noCall.add(Allele.NO_CALL);
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final int ploidy = UAC.genotypeArgs.samplePloidy;
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final List<Allele> noCall = GATKVariantContextUtils.noCallAlleles(ploidy);
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for ( PoolGenotypeData sampleData : GLs ) {
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// extract from multidimensional array
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@ -60,8 +60,8 @@ import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
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import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
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import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalc;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcResult;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider;
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import org.broadinstitute.gatk.utils.GenomeLoc;
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import org.broadinstitute.gatk.utils.GenomeLocParser;
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import org.broadinstitute.gatk.utils.MathUtils;
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@ -81,8 +81,11 @@ import java.util.*;
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public abstract class GenotypingEngine<Config extends StandardCallerArgumentCollection> {
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public static final String NUMBER_OF_DISCOVERED_ALLELES_KEY = "NDA";
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public static final String LOW_QUAL_FILTER_NAME = "LowQual";
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protected final AFCalculatorProvider afCalculatorProvider ;
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protected Logger logger;
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protected final Config configuration;
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@ -100,20 +103,6 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
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protected final GenomeLocParser genomeLocParser;
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// the model used for calculating p(non-ref)
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protected ThreadLocal<AFCalc> afcm = getAlleleFrequencyCalculatorThreadLocal();
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protected ThreadLocal<AFCalc> getAlleleFrequencyCalculatorThreadLocal() {
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return new ThreadLocal<AFCalc>() {
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@Override
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public AFCalc initialValue() {
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return AFCalcFactory.createAFCalc(configuration, numberOfGenomes, false, logger);
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}
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};
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}
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/**
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* Construct a new genotyper engine, on a specific subset of samples.
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*
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@ -124,10 +113,17 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
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*
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* @throws IllegalArgumentException if any of {@code samples}, {@code configuration} or {@code genomeLocParser} is {@code null}.
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*/
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protected GenotypingEngine(final Config configuration,final SampleList samples, final GenomeLocParser genomeLocParser) {
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protected GenotypingEngine(final Config configuration, final SampleList samples,
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final GenomeLocParser genomeLocParser, final AFCalculatorProvider afCalculatorProvider) {
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if (configuration == null)
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throw new IllegalArgumentException("the configuration cannot be null");
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if (samples == null)
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throw new IllegalArgumentException("the sample list provided cannot be null");
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if (afCalculatorProvider == null)
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throw new IllegalArgumentException("the AF calculator provider cannot be null");
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this.afCalculatorProvider = afCalculatorProvider;
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this.configuration = configuration;
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logger = Logger.getLogger(getClass());
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this.samples = samples;
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@ -220,7 +216,10 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
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if (hasTooManyAlternativeAlleles(vc) || vc.getNSamples() == 0)
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return emptyCallContext(tracker,refContext,rawContext);
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final AFCalcResult AFresult = afcm.get().getLog10PNonRef(vc, getAlleleFrequencyPriors(model));
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final int defaultPloidy = configuration.genotypeArgs.samplePloidy;
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final int maxAltAlleles = configuration.genotypeArgs.MAX_ALTERNATE_ALLELES;
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final AFCalc afCalculator = afCalculatorProvider.getInstance(vc,defaultPloidy,maxAltAlleles);
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final AFCalcResult AFresult = afCalculator.getLog10PNonRef(vc, defaultPloidy,maxAltAlleles, getAlleleFrequencyPriors(vc,defaultPloidy,model));
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final OutputAlleleSubset outputAlternativeAlleles = calculateOutputAlleleSubset(AFresult);
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@ -260,7 +259,8 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
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builder.filter(LOW_QUAL_FILTER_NAME);
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// create the genotypes
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final GenotypesContext genotypes = afcm.get().subsetAlleles(vc, outputAlleles, true,configuration.genotypeArgs.samplePloidy);
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final GenotypesContext genotypes = afCalculator.subsetAlleles(vc, defaultPloidy, outputAlleles, true);
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builder.genotypes(genotypes);
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// *** note that calculating strand bias involves overwriting data structures, so we do that last
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@ -60,6 +60,7 @@ import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.gatk.utils.pileup.PileupElement;
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import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
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import htsjdk.variant.variantcontext.*;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import java.util.*;
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@ -130,8 +131,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
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// create the genotypes; no-call everyone for now
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GenotypesContext genotypes = GenotypesContext.create();
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final List<Allele> noCall = new ArrayList<Allele>();
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noCall.add(Allele.NO_CALL);
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final int ploidy = UAC.genotypeArgs.samplePloidy;
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final List<Allele> noCall = GATKVariantContextUtils.noCallAlleles(ploidy);
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// For each sample, get genotype likelihoods based on pileup
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// compute prior likelihoods on haplotypes, and initialize haplotype likelihood matrix with them.
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@ -148,6 +149,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
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final GenotypeBuilder b = new GenotypeBuilder(sample.getKey());
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final double[] genotypeLikelihoods = pairModel.computeDiploidReadHaplotypeLikelihoods(pileup, haplotypeMap, ref, eventLength, perReadAlleleLikelihoodMap.get(sample.getKey()), UAC.getSampleContamination().get(sample.getKey()));
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b.PL(genotypeLikelihoods);
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b.alleles(noCall);
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b.DP(getFilteredDepth(pileup));
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genotypes.add(b.make());
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@ -64,6 +64,7 @@ import org.broadinstitute.gatk.utils.pileup.PileupElement;
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import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.gatk.utils.pileup.ReadBackedPileupImpl;
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import htsjdk.variant.variantcontext.*;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import java.util.*;
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@ -180,7 +181,8 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
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// create the genotypes; no-call everyone for now
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final GenotypesContext genotypes = GenotypesContext.create();
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final int ploidy = UAC.genotypeArgs.samplePloidy;
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final List<Allele> noCall = GATKVariantContextUtils.noCallAlleles(ploidy);
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for ( SampleGenotypeData sampleData : GLs ) {
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final double[] allLikelihoods = sampleData.GL.getLikelihoods();
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final double[] myLikelihoods = new double[numLikelihoods];
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@ -193,6 +195,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
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final double[] genotypeLikelihoods = MathUtils.normalizeFromLog10(myLikelihoods, false, true);
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gb.PL(genotypeLikelihoods);
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gb.DP(sampleData.depth);
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gb.alleles(noCall);
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if (UAC.annotateAllSitesWithPLs)
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gb.attribute(UnifiedGenotypingEngine.PL_FOR_ALL_SNP_ALLELES_KEY,GenotypeLikelihoods.fromLog10Likelihoods(MathUtils.normalizeFromLog10(allLikelihoods, false, true)));
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genotypes.add(gb.make());
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@ -46,10 +46,12 @@
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package org.broadinstitute.gatk.tools.walkers.genotyper;
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import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
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import org.broadinstitute.gatk.engine.walkers.*;
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import org.broadinstitute.gatk.utils.commandline.*;
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import htsjdk.variant.variantcontext.GenotypeLikelihoods;
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import htsjdk.variant.variantcontext.VariantContext;
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import htsjdk.variant.variantcontext.writer.VariantContextWriter;
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import htsjdk.variant.vcf.*;
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import org.broadinstitute.gatk.engine.CommandLineGATK;
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import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
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import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
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import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
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import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
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@ -59,18 +61,18 @@ import org.broadinstitute.gatk.engine.filters.BadMateFilter;
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import org.broadinstitute.gatk.engine.filters.MappingQualityUnavailableFilter;
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import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
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import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
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import org.broadinstitute.gatk.engine.walkers.*;
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import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
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import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider;
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import org.broadinstitute.gatk.utils.SampleUtils;
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import org.broadinstitute.gatk.utils.baq.BAQ;
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import org.broadinstitute.gatk.utils.help.HelpConstants;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import htsjdk.variant.vcf.*;
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import org.broadinstitute.gatk.utils.commandline.*;
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import org.broadinstitute.gatk.utils.exceptions.UserException;
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import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
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import htsjdk.variant.variantcontext.GenotypeLikelihoods;
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import htsjdk.variant.variantcontext.VariantContext;
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import htsjdk.variant.variantcontext.writer.VariantContextWriter;
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import org.broadinstitute.gatk.utils.help.HelpConstants;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import java.io.PrintStream;
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import java.util.*;
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@ -284,7 +286,9 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
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verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tMLE\tMAP");
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final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
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genotypingEngine = new UnifiedGenotypingEngine(UAC, samples, toolkit.getGenomeLocParser(), toolkit.getArguments().BAQMode);
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final AFCalculatorProvider afCalcAFCalculatorProvider = FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),UAC,logger);
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genotypingEngine = new UnifiedGenotypingEngine(UAC, samples, toolkit.getGenomeLocParser(), afCalcAFCalculatorProvider, toolkit.getArguments().BAQMode);
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genotypingEngine.setVerboseWriter(verboseWriter);
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genotypingEngine.setAnnotationEngine(annotationEngine);
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@ -308,6 +312,8 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
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writer.writeHeader(new VCFHeader(headerInfo, samplesForHeader));
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}
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public static Set<VCFHeaderLine> getHeaderInfo(final UnifiedArgumentCollection UAC,
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final VariantAnnotatorEngine annotationEngine,
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final DbsnpArgumentCollection dbsnp) {
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@ -55,6 +55,7 @@ import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
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import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
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import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcResult;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider;
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import org.broadinstitute.gatk.utils.BaseUtils;
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import org.broadinstitute.gatk.utils.GenomeLocParser;
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import org.broadinstitute.gatk.utils.baq.BAQ;
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@ -104,9 +105,9 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
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*
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* @throws NullPointerException if either {@code configuration} or {@code toolkit} is {@code null}.
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*/
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public UnifiedGenotypingEngine(final UnifiedArgumentCollection configuration,
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public UnifiedGenotypingEngine(final UnifiedArgumentCollection configuration, final AFCalculatorProvider afCalculatorProvider,
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final GenomeAnalysisEngine toolkit) {
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this(configuration,toolkit.getSampleList(),toolkit.getGenomeLocParser(),toolkit.getArguments().BAQMode);
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this(configuration,toolkit.getSampleList(),toolkit.getGenomeLocParser(),afCalculatorProvider,toolkit.getArguments().BAQMode);
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}
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@ -123,10 +124,10 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
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* @throws IllegalArgumentException if {@code baqCalculationMode} is {@code null}.
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*/
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public UnifiedGenotypingEngine(final UnifiedArgumentCollection configuration,
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final SampleList samples, final GenomeLocParser genomeLocParser,
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final SampleList samples, final GenomeLocParser genomeLocParser, final AFCalculatorProvider afCalculatorProvider,
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final BAQ.CalculationMode baqCalculationMode) {
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super(configuration,samples,genomeLocParser);
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super(configuration,samples,genomeLocParser,afCalculatorProvider);
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if (baqCalculationMode == null)
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throw new IllegalArgumentException("the BAQ calculation mode cannot be null");
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@ -416,7 +417,9 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
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final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap) {
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final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts,orientation,
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allAllelesToUse, false, model, perReadAlleleLikelihoodMap);
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return afcm.get().getLog10PNonRef(vc, getAlleleFrequencyPriors(model));
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final int defaultPloidy = configuration.genotypeArgs.samplePloidy;
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final int maxAltAlleles = configuration.genotypeArgs.MAX_ALTERNATE_ALLELES;
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return afCalculatorProvider.getInstance(vc, defaultPloidy, maxAltAlleles).getLog10PNonRef(vc, defaultPloidy, maxAltAlleles, getAlleleFrequencyPriors(vc,defaultPloidy,model));
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}
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private Map<String, AlignmentContext> getFilteredAndStratifiedContexts(final ReferenceContext refContext,
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@ -480,7 +483,7 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
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AFline.append('\t');
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AFline.append(i).append('/').append(numberOfGenomes).append('\t');
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AFline.append(String.format("%.2f\t", ((float) i) / numberOfGenomes));
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AFline.append(String.format("%.8f\t", getAlleleFrequencyPriors(model)[i]));
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AFline.append(String.format("%.8f\t", getAlleleFrequencyPriors(vc,configuration.genotypeArgs.samplePloidy,model)[i]));
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verboseWriter.println(AFline.toString());
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}
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@ -51,6 +51,7 @@ import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine;
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import org.broadinstitute.gatk.utils.MathUtils;
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import org.broadinstitute.gatk.utils.Utils;
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import htsjdk.variant.variantcontext.*;
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import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
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import java.util.ArrayList;
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import java.util.Arrays;
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@ -70,11 +71,11 @@ public class AFCalcTestBuilder {
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final int nSamples;
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final int numAltAlleles;
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final AFCalcFactory.Calculation modelType;
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final AFCalculatorImplementation modelType;
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final PriorType priorType;
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public AFCalcTestBuilder(final int nSamples, final int numAltAlleles,
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final AFCalcFactory.Calculation modelType, final PriorType priorType) {
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final AFCalculatorImplementation modelType, final PriorType priorType) {
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this.nSamples = nSamples;
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this.numAltAlleles = numAltAlleles;
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this.modelType = modelType;
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@ -100,7 +101,7 @@ public class AFCalcTestBuilder {
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}
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public AFCalc makeModel() {
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return AFCalcFactory.createAFCalc(modelType, nSamples, getNumAltAlleles(), 2);
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return AFCalcFactory.createCalculator(modelType, nSamples, getNumAltAlleles(), HomoSapiensConstants.DEFAULT_PLOIDY);
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}
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public double[] makePriors() {
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@ -68,6 +68,7 @@ import org.broadinstitute.gatk.engine.walkers.*;
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import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
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import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
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import org.broadinstitute.gatk.tools.walkers.genotyper.*;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider;
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import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
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import org.broadinstitute.gatk.utils.GenomeLoc;
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import org.broadinstitute.gatk.utils.GenomeLocParser;
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@ -96,6 +97,7 @@ import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
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import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
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import org.broadinstitute.gatk.utils.sam.ReadUtils;
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import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
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import java.io.FileNotFoundException;
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@ -697,7 +699,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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// Seems that at least with some test data we can lose genuine haploid variation if we use
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// UGs engine with ploidy == 1
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simpleUAC.genotypeArgs.samplePloidy = Math.max(2,SCAC.genotypeArgs.samplePloidy);
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activeRegionEvaluationGenotyperEngine = new UnifiedGenotypingEngine(simpleUAC, toolkit);
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||||
activeRegionEvaluationGenotyperEngine = new UnifiedGenotypingEngine(simpleUAC,
|
||||
FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),simpleUAC,logger), toolkit);
|
||||
activeRegionEvaluationGenotyperEngine.setLogger(logger);
|
||||
|
||||
if( SCAC.CONTAMINATION_FRACTION_FILE != null )
|
||||
|
|
@ -707,7 +711,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
|
|||
throw new UserException("HaplotypeCaller cannot be run in both GENOTYPE_GIVEN_ALLELES mode and in consensus mode. Please choose one or the other.");
|
||||
|
||||
final GenomeLocParser genomeLocParser = toolkit.getGenomeLocParser();
|
||||
genotypingEngine = new HaplotypeCallerGenotypingEngine( SCAC, samplesList, genomeLocParser, !doNotRunPhysicalPhasing);
|
||||
|
||||
genotypingEngine = new HaplotypeCallerGenotypingEngine( SCAC, samplesList, genomeLocParser, FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),SCAC,logger), !doNotRunPhysicalPhasing);
|
||||
// initialize the output VCF header
|
||||
final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
|
||||
|
||||
|
|
@ -880,7 +885,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
|
|||
// if we don't have any data, just abort early
|
||||
return new ActivityProfileState(ref.getLocus(), 0.0);
|
||||
|
||||
final List<Allele> noCall = Collections.singletonList(Allele.NO_CALL); // used to noCall all genotypes until the exact model is applied
|
||||
final int ploidy = activeRegionEvaluationGenotyperEngine.getConfiguration().genotypeArgs.samplePloidy;
|
||||
final List<Allele> noCall = GATKVariantContextUtils.noCallAlleles(ploidy); // used to noCall all genotypes until the exact model is applied
|
||||
final Map<String, AlignmentContext> splitContexts = AlignmentContextUtils.splitContextBySampleName(context);
|
||||
final GenotypesContext genotypes = GenotypesContext.create(splitContexts.keySet().size());
|
||||
final MathUtils.RunningAverage averageHQSoftClips = new MathUtils.RunningAverage();
|
||||
|
|
|
|||
|
|
@ -51,8 +51,7 @@ import com.google.java.contract.Requires;
|
|||
import htsjdk.variant.variantcontext.*;
|
||||
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.*;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalc;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorProvider;
|
||||
import org.broadinstitute.gatk.utils.GenomeLoc;
|
||||
import org.broadinstitute.gatk.utils.GenomeLocParser;
|
||||
import org.broadinstitute.gatk.utils.Utils;
|
||||
|
|
@ -71,7 +70,6 @@ import java.util.*;
|
|||
*/
|
||||
public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeCallerArgumentCollection> {
|
||||
|
||||
private final static List<Allele> NO_CALL = Collections.singletonList(Allele.NO_CALL);
|
||||
private static final int ALLELE_EXTENSION = 2;
|
||||
private static final String phase01 = "0|1";
|
||||
private static final String phase10 = "1|0";
|
||||
|
|
@ -91,8 +89,8 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
|
|||
* @param genomeLocParser {@inheritDoc}
|
||||
* @param doPhysicalPhasing whether to try physical phasing.
|
||||
*/
|
||||
public HaplotypeCallerGenotypingEngine(final HaplotypeCallerArgumentCollection configuration, final SampleList samples, final GenomeLocParser genomeLocParser, final boolean doPhysicalPhasing) {
|
||||
super(configuration,samples,genomeLocParser);
|
||||
public HaplotypeCallerGenotypingEngine(final HaplotypeCallerArgumentCollection configuration, final SampleList samples, final GenomeLocParser genomeLocParser, final AFCalculatorProvider afCalculatorProvider, final boolean doPhysicalPhasing) {
|
||||
super(configuration,samples,genomeLocParser,afCalculatorProvider);
|
||||
if (genomeLocParser == null)
|
||||
throw new IllegalArgumentException("the genome location parser provided cannot be null");
|
||||
this.doPhysicalPhasing= doPhysicalPhasing;
|
||||
|
|
@ -100,25 +98,6 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
|
|||
genotypingModel = new InfiniteRandomMatingPopulationModel();
|
||||
}
|
||||
|
||||
/**
|
||||
* {@inheritDoc}
|
||||
*/
|
||||
public HaplotypeCallerGenotypingEngine(final HaplotypeCallerArgumentCollection configuration, final SampleList samples, final GenomeLocParser genomeLocParser) {
|
||||
this(configuration,samples,genomeLocParser,false);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected ThreadLocal<AFCalc> getAlleleFrequencyCalculatorThreadLocal() {
|
||||
return new ThreadLocal<AFCalc>() {
|
||||
|
||||
@Override
|
||||
public AFCalc initialValue() {
|
||||
return AFCalcFactory.createAFCalc(configuration, numberOfGenomes,
|
||||
configuration.emitReferenceConfidence != ReferenceConfidenceMode.NONE , logger);
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Change the merge variant across haplotypes for this engine.
|
||||
*
|
||||
|
|
@ -226,6 +205,8 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
|
|||
// Walk along each position in the key set and create each event to be outputted
|
||||
final Set<Haplotype> calledHaplotypes = new HashSet<>();
|
||||
final List<VariantContext> returnCalls = new ArrayList<>();
|
||||
final int ploidy = configuration.genotypeArgs.samplePloidy;
|
||||
final List<Allele> noCallAlleles = GATKVariantContextUtils.noCallAlleles(ploidy);
|
||||
|
||||
for( final int loc : startPosKeySet ) {
|
||||
if( loc >= activeRegionWindow.getStart() && loc <= activeRegionWindow.getStop() ) { // genotyping an event inside this active region
|
||||
|
|
@ -276,7 +257,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
|
|||
if (emitReferenceConfidence)
|
||||
readAlleleLikelihoods.addNonReferenceAllele(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
|
||||
|
||||
final GenotypesContext genotypes = calculateGLsForThisEvent( readAlleleLikelihoods, mergedVC );
|
||||
final GenotypesContext genotypes = calculateGLsForThisEvent( readAlleleLikelihoods, mergedVC, noCallAlleles );
|
||||
final VariantContext call = calculateGenotypes(new VariantContextBuilder(mergedVC).genotypes(genotypes).make(), calculationModel);
|
||||
if( call != null ) {
|
||||
|
||||
|
|
@ -698,14 +679,14 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
|
|||
*/
|
||||
@Requires({"readLikelihoods!= null", "mergedVC != null"})
|
||||
@Ensures("result != null")
|
||||
private GenotypesContext calculateGLsForThisEvent( final ReadLikelihoods<Allele> readLikelihoods, final VariantContext mergedVC ) {
|
||||
private GenotypesContext calculateGLsForThisEvent( final ReadLikelihoods<Allele> readLikelihoods, final VariantContext mergedVC, final List<Allele> noCallAlleles ) {
|
||||
final List<Allele> vcAlleles = mergedVC.getAlleles();
|
||||
final AlleleList<Allele> alleleList = readLikelihoods.alleleCount() == vcAlleles.size() ? readLikelihoods : new IndexedAlleleList<>(vcAlleles);
|
||||
final GenotypingLikelihoods<Allele> likelihoods = genotypingModel.calculateLikelihoods(alleleList,new GenotypingData<>(ploidyModel,readLikelihoods));
|
||||
final int sampleCount = samples.sampleCount();
|
||||
final GenotypesContext result = GenotypesContext.create(sampleCount);
|
||||
for (int s = 0; s < sampleCount; s++)
|
||||
result.add(new GenotypeBuilder(samples.sampleAt(s)).alleles(NO_CALL).PL(likelihoods.sampleLikelihoods(s).getAsPLs()).make());
|
||||
result.add(new GenotypeBuilder(samples.sampleAt(s)).alleles(noCallAlleles).PL(likelihoods.sampleLikelihoods(s).getAsPLs()).make());
|
||||
return result;
|
||||
}
|
||||
|
||||
|
|
@ -769,23 +750,6 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<HaplotypeC
|
|||
return eventMapper;
|
||||
}
|
||||
|
||||
@Ensures({"result.size() == haplotypeAllelesForSample.size()"})
|
||||
protected static List<Allele> findEventAllelesInSample( final List<Allele> eventAlleles, final List<Allele> haplotypeAlleles, final List<Allele> haplotypeAllelesForSample, final List<List<Haplotype>> alleleMapper, final List<Haplotype> haplotypes ) {
|
||||
if( haplotypeAllelesForSample.contains(Allele.NO_CALL) ) { return NO_CALL; }
|
||||
final List<Allele> eventAllelesForSample = new ArrayList<>();
|
||||
for( final Allele a : haplotypeAllelesForSample ) {
|
||||
final Haplotype haplotype = haplotypes.get(haplotypeAlleles.indexOf(a));
|
||||
for( int iii = 0; iii < alleleMapper.size(); iii++ ) {
|
||||
final List<Haplotype> mappedHaplotypes = alleleMapper.get(iii);
|
||||
if( mappedHaplotypes.contains(haplotype) ) {
|
||||
eventAllelesForSample.add(eventAlleles.get(iii));
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
return eventAllelesForSample;
|
||||
}
|
||||
|
||||
@Deprecated
|
||||
protected static Map<Integer,VariantContext> generateVCsFromAlignment( final Haplotype haplotype, final byte[] ref, final GenomeLoc refLoc, final String sourceNameToAdd ) {
|
||||
return new EventMap(haplotype, ref, refLoc, sourceNameToAdd);
|
||||
|
|
|
|||
|
|
@ -48,6 +48,7 @@ package org.broadinstitute.gatk.tools.walkers.validation;
|
|||
|
||||
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
|
||||
import org.broadinstitute.gatk.engine.walkers.*;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider;
|
||||
import org.broadinstitute.gatk.utils.commandline.*;
|
||||
import org.broadinstitute.gatk.engine.CommandLineGATK;
|
||||
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
|
||||
|
|
@ -352,12 +353,15 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
|
|||
|
||||
final GenomeAnalysisEngine toolkit = getToolkit();
|
||||
uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP;
|
||||
snpEngine = new UnifiedGenotypingEngine(uac,toolkit);
|
||||
snpEngine = new UnifiedGenotypingEngine(uac,
|
||||
FixedAFCalculatorProvider.createThreadSafeProvider(toolkit, uac, logger),toolkit);
|
||||
|
||||
|
||||
// Adding the INDEL calling arguments for UG
|
||||
UnifiedArgumentCollection uac_indel = uac.clone();
|
||||
uac_indel.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
|
||||
indelEngine = new UnifiedGenotypingEngine(uac_indel,toolkit);
|
||||
indelEngine = new UnifiedGenotypingEngine(uac_indel,
|
||||
FixedAFCalculatorProvider.createThreadSafeProvider(toolkit, uac, logger),toolkit);
|
||||
|
||||
// make sure we have callConf set to the threshold set by the UAC so we can use it later.
|
||||
callConf = uac.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING;
|
||||
|
|
|
|||
|
|
@ -46,18 +46,20 @@
|
|||
|
||||
package org.broadinstitute.gatk.tools.walkers.validation.validationsiteselector;
|
||||
|
||||
import htsjdk.variant.variantcontext.VariantContext;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalc;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcResult;
|
||||
import htsjdk.variant.variantcontext.VariantContext;
|
||||
import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
|
||||
|
||||
import java.util.TreeSet;
|
||||
|
||||
|
||||
public class GLBasedSampleSelector extends SampleSelector {
|
||||
private static final int MAX_ALT_ALLELES = 4;
|
||||
double[] flatPriors = null;
|
||||
final double referenceLikelihood;
|
||||
AFCalc AFCalculator;
|
||||
AFCalc afCalculator;
|
||||
|
||||
public GLBasedSampleSelector(TreeSet<String> sm, double refLik) {
|
||||
super(sm);
|
||||
|
|
@ -78,9 +80,9 @@ public class GLBasedSampleSelector extends SampleSelector {
|
|||
// do we want to apply a prior? maybe user-spec?
|
||||
if ( flatPriors == null ) {
|
||||
flatPriors = new double[1+2*samples.size()];
|
||||
AFCalculator = AFCalcFactory.createAFCalc(samples.size(), 4, 2);
|
||||
afCalculator = AFCalcFactory.createCalculator(samples.size(), MAX_ALT_ALLELES, HomoSapiensConstants.DEFAULT_PLOIDY);
|
||||
}
|
||||
final AFCalcResult result = AFCalculator.getLog10PNonRef(subContext, flatPriors);
|
||||
final AFCalcResult result = afCalculator.getLog10PNonRef(subContext, HomoSapiensConstants.DEFAULT_PLOIDY, MAX_ALT_ALLELES, flatPriors);
|
||||
// do we want to let this qual go up or down?
|
||||
if ( result.getLog10LikelihoodOfAFEq0() < referenceLikelihood ) {
|
||||
return true;
|
||||
|
|
|
|||
|
|
@ -63,11 +63,11 @@ import org.broadinstitute.gatk.engine.walkers.Window;
|
|||
import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
|
||||
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.*;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyFailOverAFCalculatorProvider;
|
||||
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller;
|
||||
import org.broadinstitute.gatk.utils.GenomeLoc;
|
||||
import org.broadinstitute.gatk.utils.SampleUtils;
|
||||
import org.broadinstitute.gatk.utils.commandline.*;
|
||||
import org.broadinstitute.gatk.utils.exceptions.UserException;
|
||||
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
|
||||
import org.broadinstitute.gatk.utils.help.HelpConstants;
|
||||
import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
|
||||
|
|
@ -166,7 +166,8 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
|
|||
final Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(toolkit, variants);
|
||||
final SampleList samples = new IndexedSampleList(SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
|
||||
// create the genotyping engine
|
||||
genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(), toolkit.getArguments().BAQMode);
|
||||
genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(), GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit, genotypeArgs, logger),
|
||||
toolkit.getArguments().BAQMode);
|
||||
// create the annotation engine
|
||||
annotationEngine = new VariantAnnotatorEngine(Arrays.asList("none"), annotationsToUse, Collections.<String>emptyList(), this, toolkit);
|
||||
|
||||
|
|
@ -182,6 +183,8 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
|
|||
final Set<String> sampleNameSet = SampleListUtils.asSet(samples);
|
||||
final VCFHeader vcfHeader = new VCFHeader(headerLines, sampleNameSet);
|
||||
vcfWriter.writeHeader(vcfHeader);
|
||||
|
||||
logger.info("Notice that the -ploidy parameter is ignored in " + getClass().getSimpleName() + " tool as this is automatically determined by the input variant files");
|
||||
}
|
||||
|
||||
public VariantContext map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
|
||||
|
|
@ -192,23 +195,9 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
|
|||
final VariantContext combinedVC = ReferenceConfidenceVariantContextMerger.merge(tracker.getPrioritizedValue(variants, loc), loc, INCLUDE_NON_VARIANTS ? ref.getBase() : null, true);
|
||||
if ( combinedVC == null )
|
||||
return null;
|
||||
|
||||
checkPloidy(combinedVC);
|
||||
|
||||
return regenotypeVC(tracker, ref, combinedVC);
|
||||
}
|
||||
|
||||
private void checkPloidy(final VariantContext combinedVC) {
|
||||
final int requiredPloidy = genotypeArgs.samplePloidy;
|
||||
for (final Genotype g : combinedVC.getGenotypes()) {
|
||||
if (g.getPloidy() != requiredPloidy) {
|
||||
throw new UserException.BadArgumentValue("ploidy",
|
||||
"the input variant data contains calls with a different ploidy than the one specified (" + requiredPloidy
|
||||
+ "). For example sample (" + g.getSampleName() + ") at (" + combinedVC.getChr() + ":" + combinedVC.getStart() + ")");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Re-genotype (and re-annotate) a combined genomic VC
|
||||
*
|
||||
|
|
|
|||
|
|
@ -50,6 +50,7 @@ import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
|
|||
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider;
|
||||
import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
|
||||
import org.broadinstitute.gatk.utils.commandline.Output;
|
||||
import org.broadinstitute.gatk.engine.CommandLineGATK;
|
||||
|
|
@ -129,7 +130,9 @@ public class RegenotypeVariants extends RodWalker<Integer, Integer> implements T
|
|||
final SampleList samples =
|
||||
new IndexedSampleList(SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)));
|
||||
final Set<String> sampleNameSet = SampleListUtils.asSet(samples);
|
||||
UG_engine = new UnifiedGenotypingEngine(UAC, samples,toolkit.getGenomeLocParser(),toolkit.getArguments().BAQMode);
|
||||
UG_engine = new UnifiedGenotypingEngine(UAC, samples,toolkit.getGenomeLocParser(),
|
||||
FixedAFCalculatorProvider.createThreadSafeProvider(toolkit,UAC,logger),
|
||||
toolkit.getArguments().BAQMode);
|
||||
|
||||
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
|
||||
hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(trackName)));
|
||||
|
|
|
|||
|
|
@ -293,11 +293,12 @@ public class MathUtils {
|
|||
|
||||
public static double log10sumLog10(final double[] log10p, final int start, final int finish) {
|
||||
|
||||
if (start >= finish)
|
||||
return Double.NEGATIVE_INFINITY;
|
||||
final int maxElementIndex = MathUtils.maxElementIndex(log10p, start, finish);
|
||||
double maxValue = log10p[maxElementIndex];
|
||||
if(maxValue == Double.NEGATIVE_INFINITY) {
|
||||
final double maxValue = log10p[maxElementIndex];
|
||||
if(maxValue == Double.NEGATIVE_INFINITY)
|
||||
return maxValue;
|
||||
}
|
||||
double sum = 1.0;
|
||||
for (int i = start; i < finish; i++) {
|
||||
double curVal = log10p[i];
|
||||
|
|
@ -888,6 +889,7 @@ public class MathUtils {
|
|||
if (start > endIndex) {
|
||||
throw new IllegalArgumentException("Start cannot be after end.");
|
||||
}
|
||||
|
||||
int maxI = start;
|
||||
for (int i = (start+1); i < endIndex; i++) {
|
||||
if (array[i] > array[maxI])
|
||||
|
|
|
|||
|
|
@ -47,7 +47,14 @@ public class GATKVariantContextUtils {
|
|||
|
||||
public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
|
||||
|
||||
/**
|
||||
* Diploid NO_CALL allele list...
|
||||
*
|
||||
* @deprecated you should use {@link #noCallAlleles(int)} instead. It indicates the presence of a hardcoded diploid assumption which is bad.
|
||||
*/
|
||||
@Deprecated
|
||||
public final static List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
|
||||
|
||||
public final static String NON_REF_SYMBOLIC_ALLELE_NAME = "NON_REF";
|
||||
public final static Allele NON_REF_SYMBOLIC_ALLELE = Allele.create("<"+NON_REF_SYMBOLIC_ALLELE_NAME+">", false); // represents any possible non-ref allele at this site
|
||||
|
||||
|
|
@ -143,6 +150,26 @@ public class GATKVariantContextUtils {
|
|||
return ref;
|
||||
}
|
||||
|
||||
/**
|
||||
* Calculates the total ploidy of a variant context as the sum of all plodies across genotypes.
|
||||
* @param vc the target variant context.
|
||||
* @param defaultPloidy the default ploidy to be assume when there is no ploidy information for a genotype.
|
||||
* @return never {@code null}.
|
||||
*/
|
||||
public static int totalPloidy(final VariantContext vc, final int defaultPloidy) {
|
||||
if (vc == null)
|
||||
throw new IllegalArgumentException("the vc provided cannot be null");
|
||||
if (defaultPloidy < 0)
|
||||
throw new IllegalArgumentException("the default ploidy must 0 or greater");
|
||||
int result = 0;
|
||||
for (final Genotype genotype : vc.getGenotypes()) {
|
||||
final int declaredPloidy = genotype.getPloidy();
|
||||
result += declaredPloidy <= 0 ? declaredPloidy : declaredPloidy;
|
||||
}
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
public enum GenotypeMergeType {
|
||||
/**
|
||||
* Make all sample genotypes unique by file. Each sample shared across RODs gets named sample.ROD.
|
||||
|
|
@ -1322,6 +1349,28 @@ public class GATKVariantContextUtils {
|
|||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Cached NO_CALL immutable lists where the position ith contains the list with i elements.
|
||||
*/
|
||||
private static List<Allele>[] NOCALL_LISTS = new List[] {
|
||||
Collections.emptyList(),
|
||||
Collections.singletonList(Allele.NO_CALL),
|
||||
Collections.nCopies(2,Allele.NO_CALL)
|
||||
};
|
||||
|
||||
/**
|
||||
* Synchronized code to ensure that {@link #NOCALL_LISTS} has enough entries beyod the requested ploidy
|
||||
* @param capacity the requested ploidy.
|
||||
*/
|
||||
private static synchronized void ensureNoCallListsCapacity(final int capacity) {
|
||||
final int currentCapacity = NOCALL_LISTS.length - 1;
|
||||
if (currentCapacity >= capacity)
|
||||
return;
|
||||
NOCALL_LISTS = Arrays.copyOf(NOCALL_LISTS,Math.max(capacity,currentCapacity << 1) + 1);
|
||||
for (int i = currentCapacity + 1; i < NOCALL_LISTS.length; i++)
|
||||
NOCALL_LISTS[i] = Collections.nCopies(i,Allele.NO_CALL);
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns a {@link Allele#NO_CALL NO_CALL} allele list provided the ploidy.
|
||||
*
|
||||
|
|
@ -1331,16 +1380,9 @@ public class GATKVariantContextUtils {
|
|||
* might or might not be mutable.
|
||||
*/
|
||||
public static List<Allele> noCallAlleles(final int ploidy) {
|
||||
if (ploidy <= 0)
|
||||
return Collections.EMPTY_LIST;
|
||||
else if (ploidy == 1)
|
||||
return Collections.singletonList(Allele.NO_CALL);
|
||||
else {
|
||||
final List<Allele> result = new ArrayList<>(ploidy);
|
||||
for (int i = 0; i < ploidy; i++)
|
||||
result.add(Allele.NO_CALL);
|
||||
return result;
|
||||
}
|
||||
if (NOCALL_LISTS.length <= ploidy)
|
||||
ensureNoCallListsCapacity(ploidy);
|
||||
return NOCALL_LISTS[ploidy];
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue