Removing dependence on extended events for the remaining Variant Annotator modules.
This commit is contained in:
Eric Banks
parent
b21889812d
commit
b467cd1dae
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@ -34,6 +34,7 @@ import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
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import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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@ -67,18 +68,19 @@ public class AlleleBalance extends InfoFieldAnnotation {
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continue;
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AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
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if ( context == null )
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if ( context == null || !context.hasBasePileup() )
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continue;
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if ( vc.isSNP() && context.hasBasePileup() ) {
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final String bases = new String(context.getBasePileup().getBases());
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final ReadBackedPileup pileup = context.getBasePileup();
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if ( vc.isSNP() ) {
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final String bases = new String(pileup.getBases());
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if ( bases.length() == 0 )
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return null;
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char refChr = vc.getReference().toString().charAt(0);
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char altChr = vc.getAlternateAllele(0).toString().charAt(0);
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final char refChr = vc.getReference().toString().charAt(0);
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final char altChr = vc.getAlternateAllele(0).toString().charAt(0);
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int refCount = MathUtils.countOccurrences(refChr, bases);
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int altCount = MathUtils.countOccurrences(altChr, bases);
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final int refCount = MathUtils.countOccurrences(refChr, bases);
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final int altCount = MathUtils.countOccurrences(altChr, bases);
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// sanity check
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if ( refCount + altCount == 0 )
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@ -87,22 +89,10 @@ public class AlleleBalance extends InfoFieldAnnotation {
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// weight the allele balance by genotype quality so that e.g. mis-called homs don't affect the ratio too much
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ratio += genotype.getLog10PError() * ((double)refCount / (double)(refCount + altCount));
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totalWeights += genotype.getLog10PError();
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} else if ( vc.isIndel() && context.hasExtendedEventPileup() ) {
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final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
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if ( indelPileup == null ) {
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continue;
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}
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// todo -- actually care about indel length from the pileup (agnostic at the moment)
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int refCount = indelPileup.getNumberOfElements();
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int altCount = vc.isSimpleInsertion() ? indelPileup.getNumberOfInsertions() : indelPileup.getNumberOfDeletions();
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if ( refCount + altCount == 0 ) {
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continue;
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}
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ratio += /* todo -- make not uniform */ 1 * ((double) refCount) / (double) (refCount + altCount);
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totalWeights += 1;
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}
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// Allele Balance for indels was not being computed correctly (since there was no allele matching). Instead of
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// prolonging the life of imperfect code, I've decided to delete it. If someone else wants to try again from
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// scratch, be my guest - but make sure it's done correctly! [EB]
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}
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// make sure we had a het genotype
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@ -245,24 +245,16 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
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for ( String sample : stratifiedContexts.keySet() ) {
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final AlignmentContext context = stratifiedContexts.get(sample);
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if ( context == null )
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if ( context == null || !context.hasBasePileup() )
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continue;
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ReadBackedPileup pileup = null;
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if (context.hasExtendedEventPileup())
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pileup = context.getExtendedEventPileup();
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else if (context.hasBasePileup())
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pileup = context.getBasePileup();
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if (pileup == null)
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continue;
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for (final PileupElement p: pileup) {
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final ReadBackedPileup pileup = context.getBasePileup();
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for ( final PileupElement p : pileup ) {
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if ( p.getRead().isReducedRead() ) // ignore reduced reads
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continue;
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if ( p.getRead().getMappingQuality() < 20)
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if ( p.getRead().getMappingQuality() < 20 )
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continue;
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if (indelLikelihoodMap.containsKey(p)) {
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if ( indelLikelihoodMap.containsKey(p) ) {
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// to classify a pileup element as ref or alt, we look at the likelihood associated with the allele associated to this element.
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// A pileup element then has a list of pairs of form (Allele, likelihood of this allele).
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// To classify a pileup element as Ref or Alt, we look at the likelihood of corresponding alleles.
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@ -30,14 +30,9 @@ public class MappingQualityZero extends InfoFieldAnnotation implements StandardA
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int mq0 = 0;
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for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
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AlignmentContext context = sample.getValue();
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ReadBackedPileup pileup = null;
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if (context.hasExtendedEventPileup())
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pileup = context.getExtendedEventPileup();
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else if (context.hasBasePileup())
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pileup = context.getBasePileup();
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if (pileup != null) {
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final AlignmentContext context = sample.getValue();
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if ( context.hasBasePileup() ) {
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final ReadBackedPileup pileup = context.getBasePileup();
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for (PileupElement p : pileup ) {
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if ( p.getMappingQual() == 0 )
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mq0++;
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@ -53,14 +53,8 @@ public class MappingQualityZeroBySample extends GenotypeAnnotation {
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return null;
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int mq0 = 0;
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ReadBackedPileup pileup = null;
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if (vc.isIndel() && context.hasExtendedEventPileup())
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pileup = context.getExtendedEventPileup();
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else if (context.hasBasePileup())
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pileup = context.getBasePileup();
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else return null;
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if (pileup != null) {
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if ( context.hasBasePileup() ) {
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final ReadBackedPileup pileup = context.getBasePileup();
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for (PileupElement p : pileup ) {
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if ( p.getMappingQual() == 0 )
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mq0++;
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@ -31,13 +31,8 @@ public class MappingQualityZeroFraction extends InfoFieldAnnotation implements E
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for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
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AlignmentContext context = sample.getValue();
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depth += context.size();
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ReadBackedPileup pileup = null;
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if (context.hasExtendedEventPileup())
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pileup = context.getExtendedEventPileup();
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else if (context.hasBasePileup())
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pileup = context.getBasePileup();
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if (pileup != null) {
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if ( context.hasBasePileup() ) {
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final ReadBackedPileup pileup = context.getBasePileup();
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for (PileupElement p : pileup ) {
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if ( p.getMappingQual() == 0 )
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mq0++;
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@ -45,7 +45,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
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if ( context == null )
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continue;
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depth += context.hasBasePileup() ? context.getBasePileup().depthOfCoverage() : context.getExtendedEventPileup().depthOfCoverage();
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depth += context.hasBasePileup() ? context.getBasePileup().depthOfCoverage() : 0;
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}
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if ( depth == 0 )
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@ -39,13 +39,8 @@ public class RMSMappingQuality extends InfoFieldAnnotation implements StandardAn
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for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
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AlignmentContext context = sample.getValue();
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ReadBackedPileup pileup = null;
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if (context.hasExtendedEventPileup())
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pileup = context.getExtendedEventPileup();
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else if (context.hasBasePileup())
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pileup = context.getBasePileup();
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if (pileup != null) {
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if ( context.hasBasePileup() ) {
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final ReadBackedPileup pileup = context.getBasePileup();
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for (PileupElement p : pileup ) {
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if ( p.getMappingQual() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE )
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qualities[index++] = p.getMappingQual();
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@ -1,207 +0,0 @@
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.commandline.Hidden;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
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import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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/**
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* Unsupported
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*/
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@Hidden
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public class ReadDepthAndAllelicFractionBySample extends GenotypeAnnotation {
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private static String REF_ALLELE = "REF";
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private static String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time
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public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref,
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AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
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if ( g == null || !g.isCalled() )
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return null;
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if ( vc.isSNP() )
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return annotateSNP(stratifiedContext, vc);
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if ( vc.isIndel() )
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return annotateIndel(stratifiedContext, vc);
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return null;
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}
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private Map<String,Object> annotateSNP(AlignmentContext stratifiedContext, VariantContext vc) {
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if ( ! stratifiedContext.hasBasePileup() ) return null;
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HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>();
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for ( Allele allele : vc.getAlternateAlleles() )
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alleleCounts.put(allele.getBases()[0], 0);
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ReadBackedPileup pileup = stratifiedContext.getBasePileup();
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int totalDepth = pileup.getNumberOfElements();
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Map<String, Object> map = new HashMap<String, Object>();
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map.put(getKeyNames().get(0), totalDepth); // put total depth in right away
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if ( totalDepth == 0 ) return map; // done, can not compute FA at 0 coverage!!
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int mq0 = 0; // number of "ref" reads that are acually mq0
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for ( PileupElement p : pileup ) {
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if ( p.getMappingQual() == 0 ) {
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mq0++;
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continue;
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}
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if ( alleleCounts.containsKey(p.getBase()) ) // non-mq0 read and it's an alt
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alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+1);
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}
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if ( mq0 == totalDepth ) return map; // if all reads are mq0, there is nothing left to do
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// we need to add counts in the correct order
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String[] fracs = new String[alleleCounts.size()];
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for (int i = 0; i < vc.getAlternateAlleles().size(); i++) {
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fracs[i] = String.format("%.3f", ((float)alleleCounts.get(vc.getAlternateAllele(i).getBases()[0]))/(totalDepth-mq0));
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}
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map.put(getKeyNames().get(1), fracs);
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return map;
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}
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private Map<String,Object> annotateIndel(AlignmentContext
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stratifiedContext, VariantContext
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vc) {
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if ( ! stratifiedContext.hasExtendedEventPileup() ) {
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return null;
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}
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ReadBackedExtendedEventPileup pileup = stratifiedContext.getExtendedEventPileup();
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if ( pileup == null )
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return null;
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int totalDepth = pileup.getNumberOfElements();
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Map<String, Object> map = new HashMap<String, Object>();
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map.put(getKeyNames().get(0), totalDepth); // put total depth in right away
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if ( totalDepth == 0 ) return map;
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int mq0 = 0; // number of "ref" reads that are acually mq0
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HashMap<String, Integer> alleleCounts = new HashMap<String, Integer>();
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Allele refAllele = vc.getReference();
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for ( Allele allele : vc.getAlternateAlleles() ) {
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if ( allele.isNoCall() ) {
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continue; // this does not look so good, should we die???
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}
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alleleCounts.put(getAlleleRepresentation(allele), 0);
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}
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for ( ExtendedEventPileupElement e : pileup.toExtendedIterable() ) {
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if ( e.getMappingQual() == 0 ) {
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mq0++;
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continue;
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}
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if ( e.isInsertion() ) {
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final String b = e.getEventBases();
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if ( alleleCounts.containsKey(b) ) {
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alleleCounts.put(b, alleleCounts.get(b)+1);
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}
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} else {
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if ( e.isDeletion() ) {
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if ( e.getEventLength() == refAllele.length() ) {
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// this is indeed the deletion allele recorded in VC
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final String b = DEL;
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if ( alleleCounts.containsKey(b) ) {
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alleleCounts.put(b, alleleCounts.get(b)+1);
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}
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}
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// else {
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// System.out.print(" deletion of WRONG length found");
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// }
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}
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}
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}
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if ( mq0 == totalDepth ) return map;
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String[] fracs = new String[alleleCounts.size()];
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for (int i = 0; i < vc.getAlternateAlleles().size(); i++)
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fracs[i] = String.format("%.3f",
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((float)alleleCounts.get(getAlleleRepresentation(vc.getAlternateAllele(i))))/(totalDepth-mq0));
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map.put(getKeyNames().get(1), fracs);
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//map.put(getKeyNames().get(0), counts);
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return map;
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}
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private String getAlleleRepresentation(Allele allele) {
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if ( allele.isNull() ) { // deletion wrt the ref
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return DEL;
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} else { // insertion, pass actual bases
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return allele.getBaseString();
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}
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}
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// public String getIndelBases()
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public List<String> getKeyNames() { return Arrays.asList("DP","FA"); }
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public List<VCFFormatHeaderLine> getDescriptions() {
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return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0),
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1,
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VCFHeaderLineType.Integer,
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"Total read depth per sample, including MQ0"),
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new VCFFormatHeaderLine(getKeyNames().get(1),
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VCFHeaderLineCount.UNBOUNDED,
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VCFHeaderLineType.Float,
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"Fractions of reads (excluding MQ0 from both ref and alt) supporting each reported alternative allele, per sample"));
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}
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}
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@ -35,13 +35,8 @@ public class SpanningDeletions extends InfoFieldAnnotation implements StandardAn
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int depth = 0;
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for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
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AlignmentContext context = sample.getValue();
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ReadBackedPileup pileup = null;
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if (context.hasExtendedEventPileup())
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pileup = context.getExtendedEventPileup();
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else if (context.hasBasePileup())
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pileup = context.getBasePileup();
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if (pileup != null) {
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if ( context.hasBasePileup() ) {
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final ReadBackedPileup pileup = context.getBasePileup();
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deletions += pileup.getNumberOfDeletions();
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depth += pileup.getNumberOfElements();
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}
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@ -39,15 +39,9 @@ public class TechnologyComposition extends InfoFieldAnnotation implements Experi
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for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
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AlignmentContext context = sample.getValue();
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ReadBackedPileup pileup = null;
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if (context.hasExtendedEventPileup())
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pileup = context.getExtendedEventPileup();
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else if (context.hasBasePileup())
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pileup = context.getBasePileup();
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if (pileup != null) {
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for (PileupElement p : pileup ) {
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if ( context.hasBasePileup() ) {
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final ReadBackedPileup pileup = context.getBasePileup();
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for ( PileupElement p : pileup ) {
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if(ReadUtils.is454Read(p.getRead()))
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reads454++;
|
||||
else if (ReadUtils.isSOLiDRead(p.getRead()))
|
||||
|
|
|
|||
|
|
@ -304,12 +304,8 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
|
|||
// if the reference base is not ambiguous, we can annotate
|
||||
Map<String, AlignmentContext> stratifiedContexts;
|
||||
if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
|
||||
if ( ! context.hasExtendedEventPileup() ) {
|
||||
if ( context.hasBasePileup() ) {
|
||||
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup());
|
||||
} else {
|
||||
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getExtendedEventPileup());
|
||||
}
|
||||
if ( stratifiedContexts != null ) {
|
||||
annotatedVCs = new ArrayList<VariantContext>(VCs.size());
|
||||
for ( VariantContext vc : VCs )
|
||||
annotatedVCs.add(engine.annotateContext(tracker, ref, stratifiedContexts, vc));
|
||||
|
|
|
|||
Loading…
Reference in New Issue