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Added REVERT SOFTCLIPPED bases to ClipReads

This commit is contained in:
Mauricio Carneiro 2013-09-06 09:30:01 -04:00
parent add17dc463
commit b6c3ed0295
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
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@ -305,7 +305,7 @@ public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipRea
*/
public ReadClipperWithData map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES )
if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES || clippingRepresentation == ClippingRepresentation.REVERT_SOFTCLIPPED_BASES )
read = ReadClipper.revertSoftClippedBases(read);
ReadClipperWithData clipper = new ReadClipperWithData(read, sequencesToClip);
@ -600,4 +600,4 @@ public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipRea
}
}
}