CAP_BASE_QUALITY needs to be included in the clone() method for it to be usable in UG

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4516 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-18 03:11:03 +00:00 · 2010-10-18 03:11:03 +00:00 · 80e5ac65b4
parent f962039273
commit 80e5ac65b4
1 changed files with 1 additions and 0 deletions
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@ -117,6 +117,7 @@ public class UnifiedArgumentCollection {
        uac.MAX_MISMATCHES = MAX_MISMATCHES;
        uac.USE_BADLY_MATED_READS = USE_BADLY_MATED_READS;
        uac.MAX_DELETION_FRACTION = MAX_DELETION_FRACTION;
+        uac.CAP_BASE_QUALITY = CAP_BASE_QUALITY;

        return uac;
    }