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It never fails to amaze me that aligners can find so many different ways to place indels off the ends of contigs 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5503 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2011-03-24 04:17:23 +00:00
parent 48b15d42e0
commit 18271aa1f4
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
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@ -722,7 +722,7 @@ public class AlignmentUtils {
byte[] alt = new byte[refSeq.length + (indelLength * (indel.getOperator() == CigarOperator.D ? -1 : 1))]; byte[] alt = new byte[refSeq.length + (indelLength * (indel.getOperator() == CigarOperator.D ? -1 : 1))];
// add the bases before the indel, making sure it's not aligned off the end of the reference // add the bases before the indel, making sure it's not aligned off the end of the reference
if ( refIndex > alt.length ) if ( refIndex > alt.length || refIndex > refSeq.length )
return null; return null;
System.arraycopy(refSeq, 0, alt, 0, refIndex); System.arraycopy(refSeq, 0, alt, 0, refIndex);
int currentPos = refIndex; int currentPos = refIndex;