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Potential corner condition bug fix: protect against null pointer exceptions when computing consensus indel bases when UG is discovering alt alleles. If an alt allele has non-standard bases, skip allele gracefully instead of adding null object into list

This commit is contained in:
Guillermo del Angel 2012-03-22 10:06:22 -04:00
parent 58245bfa2f
commit b8cd959461
1 changed files with 2 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -240,6 +240,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
refAllele = Allele.create(refBases, true); refAllele = Allele.create(refBases, true);
altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false); altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false);
} }
else continue; // don't go on with this allele if refBases are non-standard
} else { } else {
// insertion case // insertion case
if (Allele.acceptableAlleleBases(s)) { if (Allele.acceptableAlleleBases(s)) {
@ -247,6 +248,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
altAllele = Allele.create(s, false); altAllele = Allele.create(s, false);
stop = loc.getStart(); stop = loc.getStart();
} }
else continue; // go on to next allele if consensus insertion has any non-standard base.
} }