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Bug: ExpandedSAMRecord did not treat hard-clipped bases ('H') correctly. Fixed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2680 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-01-25 19:23:44 +00:00
parent 4990139b60
commit 6cf413e630
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -1105,13 +1105,13 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
int eventPosition = posOnRef;
switch(ce.getOperator()) {
case H: break; // hard clipped reads do not have clipped bases in their sequence, so we just ignore the H element...
case I:
type = IndelVariant.Type.I;
bases = readBases.substring(posOnRead,posOnRead+ce.getLength());
// will increment position on the read below, there's no 'break' statement yet...
case H:
case S:
// here we also skip hard and soft-clipped bases on the read; according to SAM format specification,
// here we also skip soft-clipped bases on the read; according to SAM format specification,
// alignment start position on the reference points to where the actually aligned
// (not clipped) bases go, so we do not need to increment reference position here
posOnRead += ce.getLength();