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Er, here's the right fix 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4552 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-22 15:08:25 +00:00
parent 181f901126
commit c0b4317311
1 changed files with 1 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
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@ -65,9 +65,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
boolean failed = false; boolean failed = false;
byte[] recordRef = vc.getReference().getBases(); byte[] recordRef = vc.getReference().getBases();
for (int i = 0; i < recordRef.length; i++) { for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) {
if ( i > MAX_VARIANT_SIZE )
break;
if ( recordRef[i] != ref[i + (vc.isSNP() ? 0 : 1)] ) { if ( recordRef[i] != ref[i + (vc.isSNP() ? 0 : 1)] ) {
failed = true; failed = true;
break; break;