Merge pull request #1326 from broadinstitute/sl_issue_1293
Added maxNumPLValues argument to allow users to set maximum number of PL values in output.
This commit is contained in:
samuelklee
commit
aa0c76a166
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@ -51,6 +51,7 @@
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package org.broadinstitute.gatk.engine.arguments;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculator;
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import org.broadinstitute.gatk.utils.commandline.Advanced;
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import org.broadinstitute.gatk.utils.commandline.Argument;
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import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
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@ -113,7 +114,7 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{
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public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;
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/**
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* If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
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* If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN_ALLELES),
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* then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
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* scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend
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* that you not play around with this parameter.
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@ -124,6 +125,15 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{
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@Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
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public int MAX_ALTERNATE_ALLELES = 6;
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/**
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* Determines the maximum number of PL values that will be logged in the output. If the number of genotypes
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* (which is determined by the ploidy and the number of alleles) exceeds the value provided by this argument,
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* then output of all of the PL values will be suppressed.
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*/
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@Advanced
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@Argument(fullName = "max_num_PL_values", shortName = "maxNumPLValues", doc = "Maximum number of PL values to output", required = false)
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public int MAX_NUM_PL_VALUES = AFCalculator.MAX_NUM_PL_VALUES_DEFAULT;
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/**
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* By default, the prior specified with the argument --heterozygosity/-hets is used for variant discovery at a particular locus, using an infinite sites model,
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* see e.g. Waterson (1975) or Tajima (1996).
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@ -56,22 +56,22 @@ import com.google.java.contract.Requires;
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import htsjdk.variant.variantcontext.*;
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import htsjdk.variant.vcf.VCFInfoHeaderLine;
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import org.apache.log4j.Logger;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils;
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import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
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import org.broadinstitute.gatk.utils.genotyper.SampleList;
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import org.broadinstitute.gatk.utils.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.AFCalculator;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationResult;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculator;
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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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import org.broadinstitute.gatk.utils.QualityUtils;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils;
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import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
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import org.broadinstitute.gatk.utils.exceptions.UserException;
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import org.broadinstitute.gatk.utils.genotyper.SampleList;
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import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils;
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import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
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import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
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import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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@ -85,7 +85,7 @@ import java.util.*;
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*/
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public abstract class GenotypingEngine<Config extends StandardCallerArgumentCollection> {
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protected final AFCalculatorProvider afCalculatorProvider ;
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protected final AFCalculatorProvider afCalculatorProvider;
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protected Logger logger;
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@ -104,6 +104,9 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
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protected final GenomeLocParser genomeLocParser;
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protected static int maxNumPLValuesObserved = 0;
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protected static int numTimesMaxNumPLValuesExceeded = 0;
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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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@ -226,7 +229,8 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
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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 AFCalculator afCalculator = afCalculatorProvider.getInstance(vc,defaultPloidy,maxAltAlleles);
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final int maxNumPLValues = configuration.genotypeArgs.MAX_NUM_PL_VALUES;
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final AFCalculator afCalculator = afCalculatorProvider.getInstance(vc,defaultPloidy,maxAltAlleles).setMaxNumPLValues(maxNumPLValues);
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final AFCalculationResult AFresult = afCalculator.getLog10PNonRef(vc, defaultPloidy,maxAltAlleles, getAlleleFrequencyPriors(vc,defaultPloidy,model));
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final OutputAlleleSubset outputAlternativeAlleles = calculateOutputAlleleSubset(AFresult);
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@ -730,4 +734,15 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
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return 1.0 - Math.pow(10.0, normalizedLog10ACeq0Posterior);
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}
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}
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/**
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* Logs the number of times the maximum allowed number of PLs was exceeded and the largest number of PLs observed. The corresponding counters are reset.
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*/
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public void printFinalMaxNumPLValuesWarning() {
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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 int maxNumPLValues = configuration.genotypeArgs.MAX_NUM_PL_VALUES;
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final AFCalculator afCalculator = afCalculatorProvider.getInstance(defaultPloidy,maxAltAlleles).setMaxNumPLValues(maxNumPLValues);
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afCalculator.printFinalMaxNumPLValuesWarning();
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}
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}
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@ -56,22 +56,22 @@ import htsjdk.variant.variantcontext.GenotypesContext;
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import htsjdk.variant.variantcontext.VariantContext;
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import org.apache.log4j.Logger;
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import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils;
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import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
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import org.broadinstitute.gatk.utils.genotyper.SampleList;
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import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
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import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculationResult;
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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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import org.broadinstitute.gatk.utils.classloader.PluginManager;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils;
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import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
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import org.broadinstitute.gatk.utils.exceptions.UserException;
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import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.gatk.utils.genotyper.SampleList;
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import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils;
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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 org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import java.io.PrintStream;
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@ -470,7 +470,9 @@ public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArgumentCol
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allAllelesToUse, false, model, perReadAlleleLikelihoodMap);
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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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final int maxNumPLValues = configuration.genotypeArgs.MAX_NUM_PL_VALUES;
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return afCalculatorProvider.getInstance(vc, defaultPloidy, maxAltAlleles).setMaxNumPLValues(maxNumPLValues)
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.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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@ -53,11 +53,12 @@ package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
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import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import org.apache.log4j.Logger;
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import org.broadinstitute.gatk.utils.SimpleTimer;
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import htsjdk.variant.variantcontext.Allele;
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import htsjdk.variant.variantcontext.GenotypeBuilder;
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import htsjdk.variant.variantcontext.GenotypesContext;
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import htsjdk.variant.variantcontext.VariantContext;
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import org.apache.log4j.Logger;
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import org.broadinstitute.gatk.utils.SimpleTimer;
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import java.io.File;
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import java.util.List;
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@ -67,10 +68,13 @@ import java.util.List;
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* Generic interface for calculating the probability of alleles segregating given priors and genotype likelihoods
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*/
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public abstract class AFCalculator implements Cloneable {
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private final static Logger defaultLogger = Logger.getLogger(AFCalculator.class);
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private static final Logger defaultLogger = Logger.getLogger(AFCalculator.class);
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public static final int MAX_NUM_PL_VALUES_DEFAULT = 100;
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protected Logger logger = defaultLogger;
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protected int maxNumPLValues = MAX_NUM_PL_VALUES_DEFAULT; // if PL vectors longer than this # of elements, don't log them
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protected static int maxNumPLValuesObserved = 0;
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protected static long numTimesMaxNumPLValuesExceeded = 0;
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private SimpleTimer callTimer = new SimpleTimer();
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private StateTracker stateTracker;
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@ -102,10 +106,19 @@ public abstract class AFCalculator implements Cloneable {
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*
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* @param logger
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*/
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public void setLogger(Logger logger) {
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public void setLogger(final Logger logger) {
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this.logger = logger;
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}
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/**
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* Set the maximum number of PL values to log. If the number of PL values exceeds this, no PL values will be logged.
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* @param maxNumPLValues maximum number of PL values to log
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*/
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public AFCalculator setMaxNumPLValues(final int maxNumPLValues) {
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this.maxNumPLValues = maxNumPLValues;
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return this;
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}
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/**
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* Compute the probability of the alleles segregating given the genotype likelihoods of the samples in vc
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*
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@ -242,4 +255,50 @@ public abstract class AFCalculator implements Cloneable {
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return getStateTracker(false,allele + 1).getAlleleCountsOfMAP()[allele];
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}
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/**
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* Strips PLs from the specified GenotypeBuilder if their number exceeds the maximum allowed. Corresponding counters are updated.
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* @param gb the GenotypeBuilder to modify
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* @param vc the VariantContext
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* @param sampleName the sample name
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* @param newLikelihoods the PL array
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*/
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protected void removePLsIfMaxNumPLValuesExceeded(final GenotypeBuilder gb, final VariantContext vc, final String sampleName, final double[] newLikelihoods) {
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final int numPLValuesFound = newLikelihoods.length;
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if (numPLValuesFound > maxNumPLValues) {
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logMaxNumPLValuesWarning(vc, sampleName, numPLValuesFound);
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numTimesMaxNumPLValuesExceeded++;
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gb.noPL();
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if (numPLValuesFound > maxNumPLValuesObserved) {
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maxNumPLValuesObserved = numPLValuesFound;
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}
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}
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}
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private void logMaxNumPLValuesWarning(final VariantContext vc, final String sampleName, final int numPLValuesFound) {
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final String message = String.format("Maximum allowed number of PLs (%d) exceeded for sample %s at %s:%d-%d with %d possible genotypes. " +
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"No PLs will be output for these genotypes (which may cause incorrect results in subsequent analyses) " +
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"unless the --max_num_PL_values argument is increased accordingly",
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maxNumPLValues, sampleName, vc.getContig(), vc.getStart(), vc.getEnd(), numPLValuesFound);
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if ( numTimesMaxNumPLValuesExceeded == 0 ) {
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logger.warn(message + ". Unless the DEBUG logging level is used, this warning message is output just once per run and further warnings are suppressed.");
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} else {
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logger.debug(message);
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}
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}
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/**
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* Logs the number of times the maximum allowed number of PLs was exceeded and the largest number of PLs observed. The corresponding counters are reset.
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*/
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public void printFinalMaxNumPLValuesWarning() {
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if ( numTimesMaxNumPLValuesExceeded > 0 ) {
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final String message = String.format("Maximum allowed number of PLs (%d) was exceeded %d time(s); the largest number of PLs found was %d. " +
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"No PLs will be output for these genotypes (which may cause incorrect results in subsequent analyses) " +
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"unless the --max_num_PL_values argument is increased accordingly",
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maxNumPLValues, numTimesMaxNumPLValuesExceeded, maxNumPLValuesObserved);
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logger.warn(message);
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}
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maxNumPLValuesObserved = 0;
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numTimesMaxNumPLValuesExceeded = 0;
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}
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}
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@ -51,10 +51,10 @@
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package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc;
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import htsjdk.variant.variantcontext.*;
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import org.broadinstitute.gatk.utils.MathUtils;
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import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import htsjdk.variant.variantcontext.*;
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import java.util.*;
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@ -65,8 +65,8 @@ abstract class ExactAFCalculator extends AFCalculator {
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protected static final int HOM_REF_INDEX = 0; // AA likelihoods are always first
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// useful so that we don't keep printing out the same warning message
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protected static boolean printedWarning = false;
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// useful so that we don't keep printing out the same warning messages
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protected static boolean printedMaxAltAllelesWarning = false;
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/**
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* Sorts {@link ExactAFCalculator.LikelihoodSum} instances where those with higher likelihood are first.
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@ -168,15 +168,14 @@ abstract class ExactAFCalculator extends AFCalculator {
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if (altAlleleReduction == 0)
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return vc;
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String message = "this tool is currently set to genotype at most " + maximumAlternativeAlleles
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+ " alternate alleles in a given context, but the context at " + vc.getContig() + ":" + vc.getStart()
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+ " has " + (vc.getAlternateAlleles().size())
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+ " alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument";
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final String message = String.format("This tool is currently set to genotype at most %d " +
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"alternate alleles in a given context, but the context at %s: %d has %d " +
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"alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument",
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maximumAlternativeAlleles, vc.getContig(), vc.getStart(), vc.getAlternateAlleles().size());
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if ( !printedWarning ) {
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printedWarning = true;
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message += ". This warning message is output just once per run and further warnings will be suppressed unless the DEBUG logging level is used.";
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logger.warn(message);
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if ( !printedMaxAltAllelesWarning ) {
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printedMaxAltAllelesWarning = true;
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logger.warn(message + ". Unless the DEBUG logging level is used, this warning message is output just once per run and further warnings are suppressed.");
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} else {
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logger.debug(message);
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}
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@ -71,6 +71,8 @@ public class FixedAFCalculatorProvider extends AFCalculatorProvider {
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private final int maximumAltAlleleCount;
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private final int maximumNumPLValues;
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private final int ploidy;
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/**
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@ -125,17 +127,18 @@ public class FixedAFCalculatorProvider extends AFCalculatorProvider {
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final Logger logger, final boolean verifyRequests) {
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if (configuration == null)
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throw new IllegalArgumentException("null configuration");
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if (configuration == null)
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throw new IllegalArgumentException("null configuration genotype arguments");
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throw new IllegalArgumentException("null genotype-arguments configuration");
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if (configuration.samplePloidy < 1)
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throw new IllegalArgumentException("invalid sample ploidy " + configuration.samplePloidy);
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if (configuration.MAX_ALTERNATE_ALLELES < 0)
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throw new IllegalArgumentException("invalid maximum number of alleles " + (configuration.MAX_ALTERNATE_ALLELES + 1));
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if (configuration.MAX_NUM_PL_VALUES < 0)
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throw new IllegalArgumentException("invalid maximum number of PL values " + configuration.MAX_NUM_PL_VALUES);
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ploidy = configuration.samplePloidy;
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maximumAltAlleleCount = configuration.MAX_ALTERNATE_ALLELES;
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singleton = AFCalculatorImplementation.bestValue(ploidy,maximumAltAlleleCount,preferred).newInstance();
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maximumNumPLValues = configuration.MAX_NUM_PL_VALUES;
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singleton = AFCalculatorImplementation.bestValue(ploidy,maximumAltAlleleCount,preferred).newInstance().setMaxNumPLValues(maximumNumPLValues);
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singleton.setLogger(logger);
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this.verifyRequests = verifyRequests;
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}
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@ -58,15 +58,16 @@ import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalcula
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import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators;
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import org.broadinstitute.gatk.utils.MathUtils;
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import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
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import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
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import java.util.*;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.LinkedList;
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import java.util.List;
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public class GeneralPloidyExactAFCalculator extends ExactAFCalculator {
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static final int MAX_LENGTH_FOR_POOL_PL_LOGGING = 100; // if PL vectors longer than this # of elements, don't log them
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protected GeneralPloidyExactAFCalculator() {
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}
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|
|
@ -491,6 +492,7 @@ public class GeneralPloidyExactAFCalculator extends ExactAFCalculator {
|
|||
final boolean assignGenotypes, final double[] newLikelihoods) {
|
||||
|
||||
final GenotypeBuilder gb = new GenotypeBuilder(g);
|
||||
final String sampleName = g.getSampleName();
|
||||
|
||||
// add likelihoods
|
||||
gb.PL(newLikelihoods);
|
||||
|
|
@ -500,7 +502,7 @@ public class GeneralPloidyExactAFCalculator extends ExactAFCalculator {
|
|||
if (newSACs != null)
|
||||
gb.attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, newSACs);
|
||||
if (assignGenotypes)
|
||||
assignGenotype(gb, newLikelihoods, allelesToUse, ploidy);
|
||||
assignGenotype(gb, vc, sampleName, newLikelihoods, allelesToUse, ploidy);
|
||||
else
|
||||
gb.alleles(GATKVariantContextUtils.noCallAlleles(ploidy));
|
||||
|
||||
|
|
@ -528,13 +530,18 @@ public class GeneralPloidyExactAFCalculator extends ExactAFCalculator {
|
|||
}
|
||||
|
||||
/**
|
||||
* Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs
|
||||
* Assign genotypes (GTs) to the samples in the VariantContext greedily based on the PLs
|
||||
*
|
||||
* @param gb the GenotypeBuilder to modify
|
||||
* @param vc the VariantContext
|
||||
* @param sampleName the sample name
|
||||
* @param newLikelihoods the PL array
|
||||
* @param allelesToUse the list of alleles to choose from (corresponding to the PLs)
|
||||
* @param numChromosomes Number of chromosomes per pool
|
||||
*/
|
||||
private void assignGenotype(final GenotypeBuilder gb,
|
||||
final VariantContext vc,
|
||||
final String sampleName,
|
||||
final double[] newLikelihoods,
|
||||
final List<Allele> allelesToUse,
|
||||
final int numChromosomes) {
|
||||
|
|
@ -547,13 +554,10 @@ public class GeneralPloidyExactAFCalculator extends ExactAFCalculator {
|
|||
|
||||
gb.alleles(alleleCounts.asAlleleList(allelesToUse));
|
||||
|
||||
// remove PLs if necessary
|
||||
if (newLikelihoods.length > MAX_LENGTH_FOR_POOL_PL_LOGGING)
|
||||
gb.noPL();
|
||||
removePLsIfMaxNumPLValuesExceeded(gb, vc, sampleName, newLikelihoods);
|
||||
|
||||
// TODO - deprecated so what is the appropriate method to call?
|
||||
if ( numNewAltAlleles > 0 )
|
||||
gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -75,8 +75,6 @@ import java.util.*;
|
|||
*/
|
||||
public class IndependentAllelesExactAFCalculator extends ExactAFCalculator {
|
||||
|
||||
private static final int MAX_LENGTH_FOR_POOL_PL_LOGGING = 100; // if PL vectors longer than this # of elements, don't log them
|
||||
|
||||
/**
|
||||
* Array that caches the allele list that corresponds to the ith ploidy.
|
||||
*
|
||||
|
|
@ -460,78 +458,83 @@ public class IndependentAllelesExactAFCalculator extends ExactAFCalculator {
|
|||
@Override
|
||||
@Requires("vc != null && allelesToUse != null")
|
||||
public GenotypesContext subsetAlleles(VariantContext vc, int defaultPloidy, List<Allele> allelesToUse, boolean assignGenotypes) {
|
||||
// the genotypes with PLs
|
||||
final GenotypesContext oldGTs = vc.getGenotypes();
|
||||
// the genotypes with PLs
|
||||
final GenotypesContext oldGTs = vc.getGenotypes();
|
||||
|
||||
// samples
|
||||
final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();
|
||||
// samples
|
||||
final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();
|
||||
|
||||
// the new genotypes to create
|
||||
final GenotypesContext newGTs = GenotypesContext.create();
|
||||
// the new genotypes to create
|
||||
final GenotypesContext newGTs = GenotypesContext.create();
|
||||
|
||||
// we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
|
||||
final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
|
||||
final int numNewAltAlleles = allelesToUse.size() - 1;
|
||||
// we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
|
||||
final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
|
||||
final int numNewAltAlleles = allelesToUse.size() - 1;
|
||||
|
||||
|
||||
// create the new genotypes
|
||||
for ( int k = 0; k < oldGTs.size(); k++ ) {
|
||||
final Genotype g = oldGTs.get(sampleIndices.get(k));
|
||||
final int declaredPloidy = g.getPloidy();
|
||||
final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy;
|
||||
if ( !g.hasLikelihoods() ) {
|
||||
newGTs.add(GenotypeBuilder.create(g.getSampleName(),GATKVariantContextUtils.noCallAlleles(ploidy)));
|
||||
continue;
|
||||
}
|
||||
|
||||
// create the new likelihoods array from the alleles we are allowed to use
|
||||
final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
|
||||
double[] newLikelihoods;
|
||||
|
||||
// Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization
|
||||
// and subsetting
|
||||
if ( numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) {
|
||||
newLikelihoods = originalLikelihoods;
|
||||
} else {
|
||||
newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse);
|
||||
|
||||
// might need to re-normalize
|
||||
newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
|
||||
}
|
||||
|
||||
// if there is no mass on the (new) likelihoods, then just no-call the sample
|
||||
if ( MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) {
|
||||
newGTs.add(GenotypeBuilder.create(g.getSampleName(), GATKVariantContextUtils.noCallAlleles(ploidy)));
|
||||
}
|
||||
else {
|
||||
final GenotypeBuilder gb = new GenotypeBuilder(g);
|
||||
|
||||
if ( numNewAltAlleles == 0 )
|
||||
gb.noPL();
|
||||
else
|
||||
gb.PL(newLikelihoods);
|
||||
|
||||
// if we weren't asked to assign a genotype, then just no-call the sample
|
||||
if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL )
|
||||
gb.alleles(GATKVariantContextUtils.noCallAlleles(ploidy));
|
||||
else
|
||||
assignGenotype(gb, newLikelihoods, allelesToUse, ploidy);
|
||||
newGTs.add(gb.make());
|
||||
}
|
||||
// create the new genotypes
|
||||
for ( int k = 0; k < oldGTs.size(); k++ ) {
|
||||
final Genotype g = oldGTs.get(sampleIndices.get(k));
|
||||
final int declaredPloidy = g.getPloidy();
|
||||
final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy;
|
||||
if ( !g.hasLikelihoods() ) {
|
||||
newGTs.add(GenotypeBuilder.create(g.getSampleName(),GATKVariantContextUtils.noCallAlleles(ploidy)));
|
||||
continue;
|
||||
}
|
||||
|
||||
return GATKVariantContextUtils.fixADFromSubsettedAlleles(newGTs, vc, allelesToUse);
|
||||
// create the new likelihoods array from the alleles we are allowed to use
|
||||
final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
|
||||
double[] newLikelihoods;
|
||||
|
||||
// Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization
|
||||
// and subsetting
|
||||
if ( numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) {
|
||||
newLikelihoods = originalLikelihoods;
|
||||
} else {
|
||||
newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse);
|
||||
|
||||
// might need to re-normalize
|
||||
newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
|
||||
}
|
||||
|
||||
// if there is no mass on the (new) likelihoods, then just no-call the sample
|
||||
if ( MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) {
|
||||
newGTs.add(GenotypeBuilder.create(g.getSampleName(), GATKVariantContextUtils.noCallAlleles(ploidy)));
|
||||
} else {
|
||||
final GenotypeBuilder gb = new GenotypeBuilder(g);
|
||||
final String sampleName = g.getSampleName();
|
||||
|
||||
if ( numNewAltAlleles == 0 )
|
||||
gb.noPL();
|
||||
else
|
||||
gb.PL(newLikelihoods);
|
||||
|
||||
// if we weren't asked to assign a genotype, then just no-call the sample
|
||||
if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL )
|
||||
gb.alleles(GATKVariantContextUtils.noCallAlleles(ploidy));
|
||||
else
|
||||
assignGenotype(gb, vc, sampleName, newLikelihoods, allelesToUse, ploidy);
|
||||
newGTs.add(gb.make());
|
||||
}
|
||||
}
|
||||
|
||||
return GATKVariantContextUtils.fixADFromSubsettedAlleles(newGTs, vc, allelesToUse);
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs
|
||||
* Assign genotypes (GTs) to the samples in the VariantContext greedily based on the PLs
|
||||
*
|
||||
* @param gb the GenotypeBuilder to modify
|
||||
* @param vc the VariantContext
|
||||
* @param sampleName the sample name
|
||||
* @param newLikelihoods the PL array
|
||||
* @param allelesToUse the list of alleles to choose from (corresponding to the PLs)
|
||||
* @param numChromosomes Number of chromosomes per pool
|
||||
*/
|
||||
private void assignGenotype(final GenotypeBuilder gb,
|
||||
final VariantContext vc,
|
||||
final String sampleName,
|
||||
final double[] newLikelihoods,
|
||||
final List<Allele> allelesToUse,
|
||||
final int numChromosomes) {
|
||||
|
|
@ -544,9 +547,7 @@ public class IndependentAllelesExactAFCalculator extends ExactAFCalculator {
|
|||
|
||||
gb.alleles(alleleCounts.asAlleleList(allelesToUse));
|
||||
|
||||
// remove PLs if necessary
|
||||
if (newLikelihoods.length > MAX_LENGTH_FOR_POOL_PL_LOGGING)
|
||||
gb.noPL();
|
||||
removePLsIfMaxNumPLValuesExceeded(gb, vc, sampleName, newLikelihoods);
|
||||
|
||||
if ( numNewAltAlleles > 0 )
|
||||
gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
|
||||
|
|
|
|||
|
|
@ -55,30 +55,24 @@ import com.google.java.contract.Ensures;
|
|||
import htsjdk.samtools.SAMFileWriter;
|
||||
import htsjdk.variant.variantcontext.*;
|
||||
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
|
||||
import htsjdk.variant.vcf.*;
|
||||
import htsjdk.variant.vcf.VCFConstants;
|
||||
import htsjdk.variant.vcf.VCFHeader;
|
||||
import htsjdk.variant.vcf.VCFHeaderLine;
|
||||
import htsjdk.variant.vcf.VCFStandardHeaderLines;
|
||||
import org.broadinstitute.gatk.engine.CommandLineGATK;
|
||||
import org.broadinstitute.gatk.engine.GATKVCFUtils;
|
||||
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
|
||||
import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
|
||||
import org.broadinstitute.gatk.engine.filters.BadMateFilter;
|
||||
import org.broadinstitute.gatk.engine.io.DirectOutputTracker;
|
||||
import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub;
|
||||
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
|
||||
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardHCAnnotation;
|
||||
import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
|
||||
import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils;
|
||||
import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
|
||||
import org.broadinstitute.gatk.utils.downsampling.AlleleBiasedDownsamplingUtils;
|
||||
import org.broadinstitute.gatk.utils.downsampling.DownsampleType;
|
||||
import org.broadinstitute.gatk.utils.downsampling.DownsamplingUtils;
|
||||
import org.broadinstitute.gatk.engine.filters.BadMateFilter;
|
||||
import org.broadinstitute.gatk.utils.genotyper.*;
|
||||
import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
|
||||
import org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub;
|
||||
import org.broadinstitute.gatk.utils.haplotypeBAMWriter.DroppedReadsTracker;
|
||||
import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
|
||||
import org.broadinstitute.gatk.engine.walkers.*;
|
||||
import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
|
||||
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
|
||||
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
|
||||
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardHCAnnotation;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.*;
|
||||
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.FixedAFCalculatorProvider;
|
||||
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler;
|
||||
|
|
@ -91,21 +85,33 @@ import org.broadinstitute.gatk.utils.activeregion.ActiveRegionReadState;
|
|||
import org.broadinstitute.gatk.utils.activeregion.ActivityProfileState;
|
||||
import org.broadinstitute.gatk.utils.clipping.ReadClipper;
|
||||
import org.broadinstitute.gatk.utils.commandline.*;
|
||||
import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
|
||||
import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils;
|
||||
import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
|
||||
import org.broadinstitute.gatk.utils.downsampling.AlleleBiasedDownsamplingUtils;
|
||||
import org.broadinstitute.gatk.utils.downsampling.DownsampleType;
|
||||
import org.broadinstitute.gatk.utils.downsampling.DownsamplingUtils;
|
||||
import org.broadinstitute.gatk.utils.exceptions.UserException;
|
||||
import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
|
||||
import org.broadinstitute.gatk.utils.fragments.FragmentCollection;
|
||||
import org.broadinstitute.gatk.utils.fragments.FragmentUtils;
|
||||
import org.broadinstitute.gatk.utils.genotyper.*;
|
||||
import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils;
|
||||
import org.broadinstitute.gatk.utils.gvcf.GVCFWriter;
|
||||
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
|
||||
import org.broadinstitute.gatk.utils.haplotypeBAMWriter.DroppedReadsTracker;
|
||||
import org.broadinstitute.gatk.utils.haplotypeBAMWriter.HaplotypeBAMWriter;
|
||||
import org.broadinstitute.gatk.utils.help.DocumentedGATKFeature;
|
||||
import org.broadinstitute.gatk.utils.help.HelpConstants;
|
||||
import org.broadinstitute.gatk.utils.pairhmm.PairHMM;
|
||||
import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.gatk.utils.sam.AlignmentUtils;
|
||||
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
|
||||
import org.broadinstitute.gatk.utils.sam.ReadUtils;
|
||||
import org.broadinstitute.gatk.utils.variant.*;
|
||||
import org.broadinstitute.gatk.utils.variant.GATKVCFConstants;
|
||||
import org.broadinstitute.gatk.utils.variant.GATKVCFHeaderLines;
|
||||
import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
|
||||
import org.broadinstitute.gatk.utils.variant.HomoSapiensConstants;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
|
|
@ -1154,6 +1160,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
|
|||
|
||||
@Override
|
||||
public void onTraversalDone(Integer result) {
|
||||
genotypingEngine.printFinalMaxNumPLValuesWarning();
|
||||
if ( HCAC.emitReferenceConfidence == ReferenceConfidenceMode.GVCF ) ((GVCFWriter)vcfWriter).close(false); // GROSS -- engine forces us to close our own VCF writer since we wrapped it
|
||||
referenceConfidenceModel.close();
|
||||
//TODO remove the need to call close here for debugging, the likelihood output stream should be managed
|
||||
|
|
|
|||
|
|
@ -51,13 +51,18 @@
|
|||
|
||||
package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.log4j.Level;
|
||||
import org.broadinstitute.gatk.engine.GATKVCFUtils;
|
||||
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
|
||||
import org.broadinstitute.gatk.utils.exceptions.UserException;
|
||||
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType;
|
||||
import org.testng.Assert;
|
||||
import org.testng.annotations.DataProvider;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
|
@ -352,4 +357,60 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
|
|||
executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerMaxNumPLValues() {
|
||||
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 70",
|
||||
b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7ea93210277fa4b590790a81c4b3994b"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testHaplotypeCallerMaxNumPLValues", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel() throws IOException {
|
||||
// Need to see log WARN messages
|
||||
final Level level = logger.getLevel();
|
||||
logger.setLevel(Level.WARN);
|
||||
|
||||
final File logFile = createTempFile("testMaxNumPLValuesExceededWithWarnLogLevel.log", ".tmp");
|
||||
final String logFileName = logFile.getAbsolutePath();
|
||||
|
||||
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s",
|
||||
b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals",
|
||||
GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9d69cb9dc67e0d0ee9863767428e6841"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec);
|
||||
// Make sure the "Maximum allowed number of PLs exceeded" messages are in the log
|
||||
Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) exceeded for sample NA12878 at 20:10097101-10097101 with 35 possible genotypes. " +
|
||||
"No PLs will be output for these genotypes (which may cause incorrect results in subsequent analyses) unless the --max_num_PL_values argument is increased accordingly. " +
|
||||
"Unless the DEBUG logging level is used, this warning message is output just once per run and further warnings are suppressed."));
|
||||
Assert.assertFalse(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) exceeded for sample NA12878 at 20:10316239-10316241 with 70 possible genotypes."));
|
||||
Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) was exceeded 2 time(s); the largest number of PLs found was 70."));
|
||||
// Set the log level back
|
||||
logger.setLevel(level);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel() throws IOException {
|
||||
// Need to see log DEBUG messages
|
||||
final Level level = logger.getLevel();
|
||||
logger.setLevel(Level.DEBUG);
|
||||
|
||||
final File logFile = createTempFile("testMaxNumPLValuesExceededWithDebugLogLevel.log", ".tmp");
|
||||
final String logFileName = logFile.getAbsolutePath();
|
||||
|
||||
final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s",
|
||||
b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals",
|
||||
GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName);
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9d69cb9dc67e0d0ee9863767428e6841"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec);
|
||||
// Make sure the "Maximum allowed number of PLs exceeded" messages are in the log
|
||||
Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) exceeded for sample NA12878 at 20:10097101-10097101 with 35 possible genotypes."));
|
||||
Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) exceeded for sample NA12878 at 20:10316239-10316241 with 70 possible genotypes."));
|
||||
Assert.assertTrue(FileUtils.readFileToString(logFile).contains("Maximum allowed number of PLs (30) was exceeded 2 time(s); the largest number of PLs found was 70."));
|
||||
// Set the log level back
|
||||
logger.setLevel(level);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue