From 96f0f0d7068736a33372d037bca88c143b7afefa Mon Sep 17 00:00:00 2001 From: rpoplin Date: Mon, 4 Apr 2011 01:12:00 +0000 Subject: [PATCH] Fixing use of String != String git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5568 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/utils/sam/AlignmentUtils.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 399e96e1b..f05d4ec9d 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -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; }