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Don't left-align complex indels because it's too complicated.

This commit is contained in:
Eric Banks 2011-08-03 12:03:50 -04:00
parent 5dc324ff35
commit f6648e0144
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
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@ -90,7 +90,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
private int alignAndWrite(VariantContext vc, final ReferenceContext ref) { private int alignAndWrite(VariantContext vc, final ReferenceContext ref) {
if ( vc.isBiallelic() && vc.isIndel() ) if ( vc.isBiallelic() && vc.isIndel() && !vc.isComplexIndel() )
return writeLeftAlignedIndel(vc, ref); return writeLeftAlignedIndel(vc, ref);
else { else {
writer.add(vc); writer.add(vc);