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Behave intelligently in the deepest levels of GATK record filtration when 

we find a read flagged as 'mapped' in the unmapped region at the end of the 
file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5365 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-03 04:52:55 +00:00
parent 7a22f19366
commit 5d4bbf41fb
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
View File

@ -974,11 +974,11 @@ public class SAMDataSource {
}
}
else {
// Unmapped read filter; just check getReadUnmappedFlag().
if(!candidateRead.getReadUnmappedFlag())
continue;
nextRead = candidateRead;
break;
// Found an unmapped read. We're done.
if(candidateRead.getReadUnmappedFlag()) {
nextRead = candidateRead;
break;
}
}
// No more reads available. Stop the search.