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Fix for IDs 5zP7jJeffK2sdPH1BH4JBVSrQztVEDKP and nX0cuBjoqBW4NQFpM6dE13KpkCuYFpZu 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4550 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-22 14:05:27 +00:00
parent d4feb99d9a
commit 9f76aed515
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
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@ -44,6 +44,8 @@ import java.util.*;
@Requires(value={},referenceMetaData=@RMD(name="variant",type= VariantContext.class)) @Requires(value={},referenceMetaData=@RMD(name="variant",type= VariantContext.class))
public class FilterLiftedVariants extends RodWalker<Integer, Integer> { public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
private static final int MAX_VARIANT_SIZE = 100;
@Output(doc="File to which variants should be written",required=true) @Output(doc="File to which variants should be written",required=true)
protected VCFWriter writer = null; protected VCFWriter writer = null;
@ -64,6 +66,8 @@ 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++) {
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;