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Bug fix for HC GGA mode. Shouldn't try to add an indel into the haplotype if that haplotype already contains the event of interest. Misc minor assembly param changes. Turning off capping of base qualities by base indel qualities until we can evaluate that change.

This commit is contained in:
Ryan Poplin 2012-06-28 12:57:51 -04:00
parent 21d5e8a252
commit 5bb0693888
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
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@ -46,7 +46,7 @@ public class ActiveRegion implements HasGenomeLocation, Comparable<ActiveRegion>
}
public void hardClipToActiveRegion() {
final ArrayList<GATKSAMRecord> clippedReads = ReadClipper.hardClipToRegion( reads, activeRegionLoc.getStart(), activeRegionLoc.getStop() );
final ArrayList<GATKSAMRecord> clippedReads = ReadClipper.hardClipToRegion( reads, extendedLoc.getStart(), extendedLoc.getStop() );
reads.clear();
reads.addAll(clippedReads);
}