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Don't try to genotype an indel even bigger than the reference window size, or else we'll be out of bounds. Necessary to handle Phase 1 integrated callset with large deletions. Better error indication when validating a GenomeLoc.

This commit is contained in:
Guillermo del Angel 2011-12-08 12:54:08 -05:00
parent cb284eebde
commit 1bfe28067f
2 changed files with 5 additions and 1 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -361,6 +361,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
final int hsize = (int)ref.getWindow().size()-Math.abs(eventLength)-1; final int hsize = (int)ref.getWindow().size()-Math.abs(eventLength)-1;
final int numPrefBases= ref.getLocus().getStart()-ref.getWindow().getStart()+1; final int numPrefBases= ref.getLocus().getStart()-ref.getWindow().getStart()+1;
if (hsize <=0) {
logger.warn(String.format("Warning: event at location %s can't be genotyped, skipping",loc.toString()));
return null;
}
haplotypeMap = Haplotype.makeHaplotypeListFromAlleles(alleleList, loc.getStart(), haplotypeMap = Haplotype.makeHaplotypeListFromAlleles(alleleList, loc.getStart(),
ref, hsize, numPrefBases); ref, hsize, numPrefBases);

2
public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -285,7 +285,7 @@ public class GenomeLocParser {
return vglHelper(exceptOnError, String.format("Unknown contig %s", contig)); return vglHelper(exceptOnError, String.format("Unknown contig %s", contig));
if (stop < start) if (stop < start)
return vglHelper(exceptOnError, String.format("The stop position %d is less than start %d", stop, start)); return vglHelper(exceptOnError, String.format("The stop position %d is less than start %d in contig %s", stop, start, contig));
if (contigIndex < 0) if (contigIndex < 0)
return vglHelper(exceptOnError, String.format("The contig index %d is less than 0", contigIndex)); return vglHelper(exceptOnError, String.format("The contig index %d is less than 0", contigIndex));