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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable

This commit is contained in:
Mauricio Carneiro 2011-06-29 16:06:14 -04:00
parent 1085df8b7b 70ba851478
commit 2ad4d2f0bb
1 changed files with 2 additions and 0 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -1010,6 +1010,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
for ( byte b : indelStr ) for ( byte b : indelStr )
sb.append((char)b); sb.append((char)b);
cigar.add(new CigarElement(indelStr.length, CigarOperator.I)); cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
} else {
throw new ReviewedStingException("Creating an alternate consensus from a complex indel is not allowed");
} }
if ( reference.length - refIdx > 0 ) if ( reference.length - refIdx > 0 )