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Correct way in which start/stop positions in a VC are computed when creating an indel VC. Old way was incorrect in case GENOTYPE_GIVEN_ALLELES was specified with a complex record. New way should work in general for all cases and is simpler.

This commit is contained in:
Guillermo del Angel 2012-05-23 21:19:30 -04:00
parent 557da77a1a
commit 4bc04e2a9e
1 changed files with 9 additions and 18 deletions
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27
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -106,6 +107,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
Allele refAllele, altAllele;
VariantContext vc = null;
boolean allelesArePadded = true;
if (!ref.getLocus().equals(lastSiteVisited)) {
// starting a new site: clear allele list
alleleList.clear();
@ -139,6 +142,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
for (Allele a : vc.getAlleles())
alleleList.add(a);
}
if (vc.getReference().getBases().length == vc.getEnd()-vc.getStart()+1)
allelesArePadded = false;
} else {
alleleList = computeConsensusAlleles(ref, contexts, contextType, locParser);
@ -184,7 +189,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
ref, hsize, numPrefBases);
// start making the VariantContext
final int endLoc = calculateEndPos(alleleList, refAllele, loc);
// For all non-snp VC types, VC end location is just startLocation + length of ref allele including padding base.
int endLoc = loc.getStart() + refAllele.length()-1;
if (allelesArePadded)
endLoc++;
final VariantContextBuilder builder = new VariantContextBuilder("UG_call", loc.getContig(), loc.getStart(), endLoc, alleleList).referenceBaseForIndel(ref.getBase());
// create the genotypes; no-call everyone for now
@ -222,23 +230,6 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
return builder.genotypes(genotypes).make();
}
private int calculateEndPos(Collection<Allele> alleles, Allele refAllele, GenomeLoc loc) {
// for indels, stop location is one more than ref allele length
boolean hasNullAltAllele = false;
for (Allele a : alleles) {
if (a.isNull()) {
hasNullAltAllele = true;
break;
}
}
int endLoc = loc.getStart() + refAllele.length();
if (!hasNullAltAllele)
endLoc--;
return endLoc;
}
public static HashMap<PileupElement, LinkedHashMap<Allele, Double>> getIndelLikelihoodMap() {
return indelLikelihoodMap.get();
}