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Fixing use of String != String 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5568 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-04-04 01:12:00 +00:00
parent 095125152b
commit 96f0f0d706
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
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@ -518,7 +518,7 @@ public class AlignmentUtils {
// we do not call the read "unmapped" when it has only reference name set with ref. index missing
// or vice versa.
if ( ( r.getReferenceIndex() != null && r.getReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX
|| r.getReferenceName() != null && r.getReferenceName() != SAMRecord.NO_ALIGNMENT_REFERENCE_NAME )
|| r.getReferenceName() != null && !r.getReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME) )
&& r.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START ) return false ;
return true;
}
@ -540,7 +540,7 @@ public class AlignmentUtils {
// we do not call the read "unmapped" when it has only reference name set with ref. index missing
// or vice versa.
if ( ( r.getMateReferenceIndex() != null && r.getMateReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX
|| r.getMateReferenceName() != null && r.getMateReferenceName() != SAMRecord.NO_ALIGNMENT_REFERENCE_NAME )
|| r.getMateReferenceName() != null && !r.getMateReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME) )
&& r.getMateAlignmentStart() != SAMRecord.NO_ALIGNMENT_START ) return false ;
return true;
}