From e3147969d9351cf6f2896577e550b84feb079cad Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Mon, 18 Jun 2012 08:51:41 -0400 Subject: [PATCH] Smith Waterman parameters have somehow gotten too diverged from what it is used in the indel realigner. Results are very dependent on these params. Changes to the assembly to not create long haplotypes out of only small pieces that were properly assembled. --- .../broadinstitute/sting/utils/activeregion/ActiveRegion.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java index 4fcc6a879..7c956b855 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java @@ -90,7 +90,7 @@ public class ActiveRegion implements HasGenomeLocation, Comparable public void removeAll( final ArrayList readsToRemove ) { reads.removeAll( readsToRemove ); } public boolean equalExceptReads(final ActiveRegion other) { - if ( ! activeRegionLoc.equals(other.activeRegionLoc)) return false; + if ( ! activeRegionLoc.equals(other.activeRegionLoc) ) return false; if ( isActive != other.isActive ) return false; if ( genomeLocParser != other.genomeLocParser ) return false; if ( extension != other.extension ) return false;