From ca96544ed02117b28c166a66f851d4c7e7d4677b Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Thu, 29 Mar 2012 16:14:29 -0400 Subject: [PATCH] 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. --- .../sting/gatk/traversals/TraverseActiveRegions.java | 1 - 1 file changed, 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java index f9a185650..22d23f216 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java @@ -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;