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fix bug in read clipper: output bam can be null, so check for it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3005 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-15 18:49:26 +00:00
parent 411d25c8d1
commit 035d4170aa
1 changed files with 2 additions and 1 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java
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@ -123,6 +123,7 @@ public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, Cli
} }
} }
if (outputBam != null)
outputBam.setPresorted(clippingRepresentation != ClippingRepresentation.SOFTCLIP_BASES); outputBam.setPresorted(clippingRepresentation != ClippingRepresentation.SOFTCLIP_BASES);
} }