Soft clipped bases shouldn't be counted in the delocalized BQSR.

broadgsa · Nov 26, 2012 · d1f076f · d1f076f
1 parent 74c9db9
commit d1f076f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
@@ -227,7 +227,7 @@ private boolean isLowQualityBase( final GATKSAMRecord read, final int offset ) {
      */
     public Long map( final ReferenceContext ref, final GATKSAMRecord originalRead, final RefMetaDataTracker metaDataTracker ) {
 
-        final GATKSAMRecord read = ReadClipper.hardClipAdaptorSequence(originalRead);
+        final GATKSAMRecord read = ReadClipper.hardClipSoftClippedBases( ReadClipper.hardClipAdaptorSequence(originalRead) );
         if( read.isEmpty() ) { return 0L; } // the whole read was inside the adaptor so skip it
 
         RecalUtils.parsePlatformForRead(read, RAC);