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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.

This commit is contained in:
Ryan Poplin 2012-06-18 08:51:41 -04:00
parent 0c98c34f5f
commit e3147969d9
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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@ -90,7 +90,7 @@ public class ActiveRegion implements HasGenomeLocation, Comparable<ActiveRegion>
public void removeAll( final ArrayList<GATKSAMRecord> 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;