From 9860db64a353230c2d394bc1ceb6022ac80289bc Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 27 Aug 2010 17:55:27 +0000
Subject: [PATCH] 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
---
 .../sting/gatk/walkers/variantutils/LiftoverVariants.java    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 765578776..2fcf5c71d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -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 {