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Now annotates indels as well. Probably can also annotate mixed vcf with indels +snps, but not tested in that mode... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5192 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-02-04 20:28:03 +00:00
parent cd6ace1b47
commit 8700b74640
1 changed files with 71 additions and 11 deletions
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82
java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -13,6 +13,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnota
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
import java.util.Arrays;
import java.util.HashMap;
@ -22,6 +24,10 @@ import java.util.Map;
public class DepthPerAlleleBySample implements GenotypeAnnotation, StandardAnnotation {
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<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, StratifiedAlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
if ( g == null || !g.isCalled() )
return null;
@ -36,6 +42,8 @@ public class DepthPerAlleleBySample implements GenotypeAnnotation, StandardAnnot
private Map<String,Object> annotateSNP(StratifiedAlignmentContext stratifiedContext, VariantContext vc) {
if ( ! stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).hasBasePileup() ) return null;
HashMap<Byte, Integer> alleleCounts = new HashMap<Byte, Integer>();
for ( Allele allele : vc.getAlleles() )
alleleCounts.put(allele.getBases()[0], 0);
@ -58,29 +66,81 @@ public class DepthPerAlleleBySample implements GenotypeAnnotation, StandardAnnot
}
private Map<String,Object> annotateIndel(StratifiedAlignmentContext stratifiedContext, VariantContext vc) {
// ReadBackedExtendedEventPileup pileup = stratifiedContext.getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getExtendedEventPileup();
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 )
if ( pileup == null )
return null;
//Integer[] counts = new Integer[2];
HashMap<String, Integer> alleleCounts = new HashMap<String, Integer>();
alleleCounts.put(REF_ALLELE,0);
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);
}
// TODO -- fix me
/*
for ( ExtendedEventPileupElement e : pileup.toExtendedIterable() ) {
if ( countsBySize.keySet().contains(e.getEventLength()) ) { // if proper length
if ( e.isDeletion() && vc.isDeletion() || e.isInsertion() && vc.isInsertion() ) {
countsBySize.put(e.getEventLength(),countsBySize.get(e.getEventLength())+1);
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");
// }
}
else {
if ( e.getRead().getAlignmentEnd() <= vc.getStart() ) {
continue;
}
alleleCounts.put(REF_ALLELE,alleleCounts.get(REF_ALLELE)+1);
}
}
}
*/
//Map<String,Object> map = new HashMap<String,Object>();
Integer[] counts = new Integer[alleleCounts.size()];
counts[0] = alleleCounts.get(REF_ALLELE);
for (int i = 0; i < vc.getAlternateAlleles().size(); i++)
counts[i+1] = alleleCounts.get( getAlleleRepresentation(vc.getAlternateAllele(i)) );
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), counts);
//map.put(getKeyNames().get(0), counts);
//return map;
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<String> getKeyNames() { return Arrays.asList("AD"); }
public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), VCFCompoundHeaderLine.UNBOUNDED, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed")); }