zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -361,6 +361,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
final int hsize = (int)ref.getWindow().size()-Math.abs(eventLength)-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(),
ref, hsize, numPrefBases);

2
public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
View File

@ -285,7 +285,7 @@ public class GenomeLocParser {
return vglHelper(exceptOnError, String.format("Unknown contig %s", contig));
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)
return vglHelper(exceptOnError, String.format("The contig index %d is less than 0", contigIndex));