From c0e998621c30bc7e631d7e72d7d22c7661478ef0 Mon Sep 17 00:00:00 2001 From: asivache Date: Fri, 4 Feb 2011 21:23:55 +0000 Subject: [PATCH] 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) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5193 348d0f76-0448-11de-a6fe-93d51630548a --- .../annotator/DepthAndFractionBySample.java | 193 ++++++++++++++++++ 1 file changed, 193 insertions(+) create mode 100644 java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthAndFractionBySample.java diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthAndFractionBySample.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthAndFractionBySample.java new file mode 100644 index 000000000..4c5fede64 --- /dev/null +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthAndFractionBySample.java @@ -0,0 +1,193 @@ +/* + * Copyright (c) 2010 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +package org.broadinstitute.sting.gatk.walkers.annotator; + +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation; +import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation; +import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; +import org.broadinstitute.sting.gatk.contexts.ReferenceContext; +import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; +import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; +import org.broadinstitute.sting.utils.pileup.PileupElement; +import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; +import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement; +import org.broad.tribble.util.variantcontext.VariantContext; +import org.broad.tribble.util.variantcontext.Genotype; +import org.broad.tribble.util.variantcontext.Allele; +import org.broad.tribble.vcf.VCFFormatHeaderLine; +import org.broad.tribble.vcf.VCFCompoundHeaderLine; +import org.broad.tribble.vcf.VCFHeaderLineType; + +import java.util.Map; +import java.util.HashMap; +import java.util.List; +import java.util.Arrays; + +/** + * Created by IntelliJ IDEA. + * User: asivache + * Date: Feb 4, 2011 + * Time: 3:59:27 PM + * To change this template use File | Settings | File Templates. + */ +public class DepthAndFractionBySample implements GenotypeAnnotation { + + private static String REF_ALLELE = "REF"; + + private static String DEL = "DEL"; // constant, for speed: no need to create a key string for deletion allele every time + + public Map annotate(RefMetaDataTracker tracker, ReferenceContext ref, + StratifiedAlignmentContext stratifiedContext, VariantContext vc, Genotype g) { + if ( g == null || !g.isCalled() ) + return null; + + if ( vc.isSNP() ) + return annotateSNP(stratifiedContext, vc); + if ( vc.isIndel() ) + return annotateIndel(stratifiedContext, vc); + + return null; + } + + private Map annotateSNP(StratifiedAlignmentContext stratifiedContext, VariantContext vc) { + + if ( ! stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).hasBasePileup() ) return null; + + HashMap alleleCounts = new HashMap(); + for ( Allele allele : vc.getAlternateAlleles() ) + alleleCounts.put(allele.getBases()[0], 0); + + ReadBackedPileup pileup = stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(); + int totalDepth = pileup.size(); + + Map map = new HashMap(); + map.put(getKeyNames().get(0), totalDepth); // put total depth in right away + + if ( totalDepth == 0 ) return map; // done, can not compute FA at 0 coverage!! + + for ( PileupElement p : pileup ) { + if ( alleleCounts.containsKey(p.getBase()) ) // it's an alt + alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+1); + } + + // we need to add counts in the correct order + String[] fracs = new String[alleleCounts.size()]; + for (int i = 0; i < vc.getAlternateAlleles().size(); i++) { + fracs[i] = String.format("%.3f", ((float)alleleCounts.get(vc.getAlternateAllele(i).getBases()[0]))/totalDepth); + } + + map.put(getKeyNames().get(1), fracs); + return map; + } + + private Map annotateIndel(StratifiedAlignmentContext + stratifiedContext, VariantContext + vc) { + + if ( ! stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).hasExtendedEventPileup() ) { + return null; + } + + ReadBackedExtendedEventPileup pileup = stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getExtendedEventPileup(); + //ReadBackedPileup pileup = stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(); + if ( pileup == null ) + return null; + int totalDepth = pileup.size(); + + Map map = new HashMap(); + map.put(getKeyNames().get(0), totalDepth); // put total depth in right away + + if ( totalDepth == 0 ) return map; + + HashMap alleleCounts = new HashMap(); + Allele refAllele = vc.getReference(); + + for ( Allele allele : vc.getAlternateAlleles() ) { + + if ( allele.isNoCall() ) { + continue; // this does not look so good, should we die??? + } + + alleleCounts.put(getAlleleRepresentation(allele), 0); + } + + for ( ExtendedEventPileupElement e : pileup.toExtendedIterable() ) { + if ( e.isInsertion() ) { + + final String b = e.getEventBases(); + if ( alleleCounts.containsKey(b) ) { + alleleCounts.put(b, alleleCounts.get(b)+1); + } + + } else { + if ( e.isDeletion() ) { + if ( e.getEventLength() == refAllele.length() ) { + // this is indeed the deletion allele recorded in VC + final String b = DEL; + if ( alleleCounts.containsKey(b) ) { + alleleCounts.put(b, alleleCounts.get(b)+1); + } + } +// else { +// System.out.print(" deletion of WRONG length found"); +// } + } + } + } + + String[] fracs = new String[alleleCounts.size()]; + for (int i = 0; i < vc.getAlternateAlleles().size(); i++) + fracs[i] = String.format("%.3f", ((float)alleleCounts.get(getAlleleRepresentation(vc.getAlternateAllele(i))))/totalDepth); + + map.put(getKeyNames().get(1), fracs); + + //map.put(getKeyNames().get(0), counts); + return map; + } + + private String getAlleleRepresentation(Allele allele) { + if ( allele.isNull() ) { // deletion wrt the ref + return DEL; + } else { // insertion, pass actual bases + return allele.getBaseString(); + } + + } + + // public String getIndelBases() + public List getKeyNames() { return Arrays.asList("DP","FA"); } + + public List getDescriptions() { + return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), + VCFCompoundHeaderLine.UNBOUNDED, + VCFHeaderLineType.Integer, + "Total read depth per sample"), + new VCFFormatHeaderLine(getKeyNames().get(1), + VCFCompoundHeaderLine.UNBOUNDED, + VCFHeaderLineType.Float, + "Fractions of reads supporting each reported alternative allele, per sample")); + } +}