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Fix for reads that have insertion as their last (mapped) cigar elements (i.e. not followed by M) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2476 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-12-29 21:13:16 +00:00
parent 05deb8796b
commit e286313b67
1 changed files with 14 additions and 2 deletions
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16
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -160,8 +160,20 @@ public class LocusIteratorByState extends LocusIterator {
// we reenter in order to re-check cigarElementCounter against curElement's length // we reenter in order to re-check cigarElementCounter against curElement's length
return stepForwardOnGenome(); return stepForwardOnGenome();
} else { } else {
genomeOffset++; // extended events need that. Logically, it's legal to advance the genomic offset here: if ( generateExtendedEvents && eventDelayedFlag > 0 ) {
// we do step forward on the ref, and by returning null we also indicate that we are past the read end. genomeOffset++; // extended events need that. Logically, it's legal to advance the genomic offset here:
// we do step forward on the ref, and by returning null we also indicate that we are past the read end.
// if we had an indel right before the read ended (i.e. insertion was the last cigar element),
// we keep it until next reference base; then we discard it and this will allow the LocusIterator to
// finally discard this read
eventDelayedFlag--;
if ( eventDelayedFlag == 0 ) {
eventLength = -1; // reset event when we are past it
insertedBases = null;
eventStart = -1;
}
}
return null; return null;
} }
} }