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Fix up liftover to enable lifting over indels 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4148 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-27 17:55:27 +00:00
parent fb177c4fee
commit 9860db64a3
1 changed files with 3 additions and 2 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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@ -81,11 +81,12 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
private void convertAndWrite(VariantContext vc, ReferenceContext ref) {
final Interval fromInterval = new Interval(vc.getChr(), vc.getStart(), vc.getEnd());
final Interval fromInterval = new Interval(vc.getChr(), vc.getStart(), vc.getStart(), false, String.format("%s:%d", vc.getChr(), vc.getStart()));
final int length = vc.getEnd() - vc.getStart();
final Interval toInterval = liftOver.liftOver(fromInterval);
if ( toInterval != null ) {
vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createPotentiallyInvalidGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getEnd()));
vc = VariantContextUtils.modifyLocation(vc, GenomeLocParser.createPotentiallyInvalidGenomeLoc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length));
writer.add(vc, ref.getBase());
successfulIntervals++;
} else {