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More plumbing: if after the shift window contains indel(s) at the first position, do not throw an exception, just print the warning (we can not deal with this situation!!) and discard those indels without trying to call them. This situation will most probably arise after forced shift over a messy region anyway. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2781 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-02-04 21:06:28 +00:00
parent 1d86dd7fd1
commit 0d347d662a
1 changed files with 5 additions and 2 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -1142,8 +1142,11 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
if ( indels.get(0) != null && indels.get(0).size() != 0 ) {
IndelVariant indel = indels.get(0).get(0);
throw new StingException("Indel found at the first position ("+start+") after a shift was performed: currently not supported: "+
(indel.getType()==IndelVariant.Type.I?"+":"-")+indel.getBases()+"; reads: "+indel.getReadSet().iterator().next().getSAMRecord().getReadName());
System.out.println("WARNING: Indel(s) at first position in the window ("+refName+":"+start+"): currently not supported: "+
(indel.getType()==IndelVariant.Type.I?"+":"-")+indel.getBases()+"; read: "+indel.getReadSet().iterator().next().getSAMRecord().getReadName()+"; site ignored");
indels.get(0).clear();
// throw new StingException("Indel found at the first position ("+start+") after a shift was performed: currently not supported: "+
// (indel.getType()==IndelVariant.Type.I?"+":"-")+indel.getBases()+"; reads: "+indel.getReadSet().iterator().next().getSAMRecord().getReadName());
}
Iterator<ExpandedSAMRecord> read_iter = reads.iterator();