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

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1 parent 74c9db9 commit d1f076f3afe1edc2c7bd7c51e4c8e41f78a3e8eb @rpoplin rpoplin committed Nov 26, 2012
@@ -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);

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