A correct bug fix for the mateIsReverseStrand error I was seeing.

broadinstitute · Sep 3, 2015 · 7e267cd · 7e267cd
1 parent cae741e
commit 7e267cd
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Showing 2 changed files with 5 additions and 7 deletions.
diff --git a/...in/java/org/broadinstitute/hellbender/utils/read/GoogleGenomicsReadToGATKReadAdapter.java b/...in/java/org/broadinstitute/hellbender/utils/read/GoogleGenomicsReadToGATKReadAdapter.java
@@ -190,7 +190,7 @@ public void setPosition( final String contig, final int start ) {
 
         genomicsRead.getAlignment().getPosition().setReferenceName(contig);
         // Convert from a 1-based to a 0-based position
-        genomicsRead.getAlignment().getPosition().setPosition((long) start - 1);
+        genomicsRead.getAlignment().getPosition().setPosition((long)start - 1);
     }
 
     @Override
@@ -249,7 +249,7 @@ public void setMatePosition( final String contig, final int start ) {
         makeMatePositionIfNecessary();
         genomicsRead.getNextMatePosition().setReferenceName(contig);
         // Convert from a 1-based to a 0-based position
-        genomicsRead.getNextMatePosition().setPosition((long) start - 1);
+        genomicsRead.getNextMatePosition().setPosition((long)start - 1);
     }
 
     @Override
@@ -448,10 +448,8 @@ public boolean mateIsReverseStrand() {
         if ( ! isPaired() ) {
             throw new IllegalStateException("Cannot get mate information for an unpaired read");
         }
-        final Position matePosition = genomicsRead.getNextMatePosition();
-        if ( matePosition == null ) { // @dr, is this right?
-            return false;
-        }
+
+        final Position matePosition = assertFieldValueNotNull(genomicsRead.getNextMatePosition(), "mate position");
         return assertFieldValueNotNull(matePosition.getReverseStrand(), "mate strand");
     }
 

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/read/ReadUtils.java
@@ -270,7 +270,7 @@ public static int getSAMFlagsForRead( final GATKRead read ) {
         if ( read.isReverseStrand() ) {
             samFlags |= SAM_READ_STRAND_FLAG;
         }
-        if ( read.mateIsReverseStrand() ) {
+        if ( ! read.mateIsUnmapped() && read.mateIsReverseStrand() ) {
             samFlags |= SAM_MATE_STRAND_FLAG;
         }
         if ( read.isFirstOfPair() ) {