zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

All the zero quality N bases in the solid reads are adding lots of extra paths in the assembly graph. We now require a minimum base quality for every base in the kmer before adding it to the graph. The large number of solid reads with unmapped mates was also triggering the active region traversal at every base. We now ignore that check for solid reads.

This commit is contained in:
Ryan Poplin 2012-03-29 16:14:29 -04:00
parent 9684a2efb0
commit ca96544ed0
1 changed files with 0 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.traversals;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.WalkerManager;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;