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Fixed merge conflict deleting a {

This commit is contained in:
Mark DePristo 2011-08-04 18:48:34 -04:00
parent 75632abf88
commit d7f98e5c2a
1 changed files with 6 additions and 4 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
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@ -112,11 +112,13 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
vc = VariantContext.modifyGenotypes(vc, genotypes);
}
// todo - fix me. This may not be the cleanest way to handle features what need correct indel padding
if (fixReferenceBase) {
vc = new VariantContext("Variant",vc.getChr(),vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.getFilters(),vc.getAttributes(), ref.getBase());
// todo - fix me. This may not be the cleanest way to handle features what need correct indel padding
if (fixReferenceBase) {
vc = new VariantContext("Variant",vc.getChr(),vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.getFilters(),vc.getAttributes(), ref.getBase());
}
writeRecord(vc, tracker, ref.getBase());
}
writeRecord(vc, tracker, ref.getBase());
}
return 1;