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Need to check isBiallelic before calling getSNPSubstitutionType for the allele swap warning 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4909 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-12-27 20:17:14 +00:00
parent 8a0c07b865
commit a31f6e4e99
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -97,7 +97,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
vc = VariantContext.modifyLocation(vc, toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length); vc = VariantContext.modifyLocation(vc, toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length);
VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false); VariantContext newVC = VariantContext.createVariantContextWithPaddedAlleles(vc, ref.getBase(), false);
if ( originalVC.isSNP() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) { if ( originalVC.isSNP() && originalVC.isBiallelic() && VariantContextUtils.getSNPSubstitutionType(originalVC) != VariantContextUtils.getSNPSubstitutionType(newVC) ) {
logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s", logger.warn(String.format("VCF at %s / %d => %s / %d is switching substitution type %s/%s to %s/%s",
originalVC.getChr(), originalVC.getStart(), newVC.getChr(), newVC.getStart(), originalVC.getChr(), originalVC.getStart(), newVC.getChr(), newVC.getStart(),
originalVC.getReference(), originalVC.getAlternateAllele(0), newVC.getReference(), newVC.getAlternateAllele(0))); originalVC.getReference(), originalVC.getAlternateAllele(0), newVC.getReference(), newVC.getAlternateAllele(0)));