From 80e5ac65b424445ca485788eca9f4af3f53471f2 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 18 Oct 2010 03:11:03 +0000
Subject: [PATCH] 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
---
 .../gatk/walkers/genotyper/UnifiedArgumentCollection.java        | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 1438b0a8c..1f66afe83 100755
--- 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;
     }