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deal with screwy solid reads in the cleaner (no cigar strings) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1171 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-05 16:49:58 +00:00
parent 8bcbf7f18a
commit 338cdbebad
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -225,8 +225,8 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// decide which reads potentially need to be cleaned // decide which reads potentially need to be cleaned
for ( SAMRecord read : reads ) { for ( SAMRecord read : reads ) {
// we currently can not deal with clipped reads correctly // we currently can not deal with clipped reads correctly (or screwy record)
if ( readIsClipped(read) ) { if ( read.getCigar().numCigarElements() == 0 || readIsClipped(read) ) {
refReads.add(read); refReads.add(read);
continue; continue;
} }