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Check for null platform (even when the read group isn't null) and assign it the default platform if it is 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2420 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-21 07:01:41 +00:00
parent 87e5a41964
commit e06dfe44c4
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
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@ -250,9 +250,13 @@ public class RecalDataManager {
((GATKSAMRecord)read).setReadGroup( readGroup ); ((GATKSAMRecord)read).setReadGroup( readGroup );
} }
if( RAC.FORCE_PLATFORM != null && !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM)) { if( RAC.FORCE_PLATFORM != null && (readGroup.getPlatform() == null || !readGroup.getPlatform().equals(RAC.FORCE_PLATFORM))) {
readGroup.setPlatform( RAC.FORCE_PLATFORM ); readGroup.setPlatform( RAC.FORCE_PLATFORM );
} }
if ( readGroup.getPlatform() == null ) {
readGroup.setPlatform( RAC.DEFAULT_PLATFORM );
}
} }
/** /**