Computes two format (genotype) level annotations: total read depth in the given sample (DP format field) and fraction of reads supporting alt allele(s) in the given sample (FA format field)
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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.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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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.ExtendedEventPileupElement;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.Allele;
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import org.broad.tribble.vcf.VCFFormatHeaderLine;
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import org.broad.tribble.vcf.VCFCompoundHeaderLine;
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import org.broad.tribble.vcf.VCFHeaderLineType;
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import java.util.Map;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Arrays;
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/**
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* Created by IntelliJ IDEA.
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* User: asivache
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* Date: Feb 4, 2011
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* Time: 3:59:27 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class DepthAndFractionBySample implements 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, ReferenceContext ref,
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StratifiedAlignmentContext 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(StratifiedAlignmentContext stratifiedContext, VariantContext vc) {
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if ( ! stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).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.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
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int totalDepth = pileup.size();
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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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for ( PileupElement p : pileup ) {
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if ( alleleCounts.containsKey(p.getBase()) ) // 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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// 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);
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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(StratifiedAlignmentContext
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stratifiedContext, VariantContext
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vc) {
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if ( ! stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).hasExtendedEventPileup() ) {
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return null;
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}
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ReadBackedExtendedEventPileup pileup = stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getExtendedEventPileup();
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//ReadBackedPileup pileup = stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup();
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if ( pileup == null )
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return null;
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int totalDepth = pileup.size();
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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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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.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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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(getAlleleRepresentation(vc.getAlternateAllele(i))))/totalDepth);
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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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VCFCompoundHeaderLine.UNBOUNDED,
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VCFHeaderLineType.Integer,
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"Total read depth per sample"),
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new VCFFormatHeaderLine(getKeyNames().get(1),
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VCFCompoundHeaderLine.UNBOUNDED,
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VCFHeaderLineType.Float,
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"Fractions of reads supporting each reported alternative allele, per sample"));
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}
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}
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