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Better fix for earlier bug. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4484 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-12 19:21:33 +00:00
parent ff0df1a2da
commit fe9f128631
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -924,9 +924,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// for reads that end in an insertion // for reads that end in an insertion
if ( myPosOnAlt + aRead.getReadLength() < endOfFirstBlock + indelCE.getLength() ) { if ( myPosOnAlt + aRead.getReadLength() < endOfFirstBlock + indelCE.getLength() ) {
int partialInsertionLength = myPosOnAlt + aRead.getReadLength() - endOfFirstBlock; int partialInsertionLength = myPosOnAlt + aRead.getReadLength() - endOfFirstBlock;
// if we also started inside the insertion, then we need to modify the length by 1 base // if we also started inside the insertion, then we need to modify the length
if ( !sawAlignmentStart ) if ( !sawAlignmentStart )
partialInsertionLength--; partialInsertionLength = aRead.getReadLength();
readCigar.add(new CigarElement(partialInsertionLength, CigarOperator.I)); readCigar.add(new CigarElement(partialInsertionLength, CigarOperator.I));
aRead.setCigar(readCigar); aRead.setCigar(readCigar);
return true; return true;