From 60f88866ddfebd13c4e53160781166ecbb0c1bc5 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 Oct 2010 19:49:01 +0000
Subject: [PATCH] Uses VCFConstants instead of hard-coded constants

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4547 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/contexts/variantcontext/VariantContextUtils.java | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index a473f7c92..ea220d926 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -795,7 +795,7 @@ public class VariantContextUtils {
         String mergedName = VariantContextUtils.mergeVariantContextNames(vc1.getName(), vc2.getName());
         double mergedNegLog10PError = Math.max(vc1.getNegLog10PError(), vc2.getNegLog10PError());
         Set<String> mergedFilters = new HashSet<String>(); // Since vc1 and vc2 were unfiltered, the merged record remains unfiltered
-        Map<String, Object> mergedAttribs = VariantContextUtils.mergeVariantContextAttributes(vc1.getAttributes(), vc2.getAttributes(), allMergedAlleles);
+        Map<String, Object> mergedAttribs = VariantContextUtils.mergeVariantContextAttributes(vc1.getAttributes(), vc2.getAttributes());
         if (mergedAttribs == null)
             return null;
 
@@ -815,7 +815,7 @@ public class VariantContextUtils {
         return name1 + "_" + name2;
     }
 
-    private static Map<String, Object> mergeVariantContextAttributes(Map<String, Object> attribs1, Map<String, Object> attribs2, Set<Allele> allMergedAlleles) {
+    private static Map<String, Object> mergeVariantContextAttributes(Map<String, Object> attribs1, Map<String, Object> attribs2) {
         Map<String, Object> mergedAttribs = new HashMap<String, Object>();
 
         List<Map<String, Object>> attribsList = new LinkedList<Map<String, Object>>();
@@ -829,6 +829,8 @@ public class VariantContextUtils {
                 Boolean val = getBooleanAttribute(attribs, orAttrib);
                 if (val != null)
                     attribVal = (attribVal || val);
+                if (attribVal) // already true, so no reason to continue:
+                    break;
             }
             mergedAttribs.put(orAttrib, attribVal);
         }
@@ -841,7 +843,7 @@ public class VariantContextUtils {
                 if (iDVal == null)
                     iDVal = val;
                 else
-                    iDVal += ";" + val;
+                    iDVal += VCFConstants.ID_FIELD_SEPARATOR + val;
             }
         }
         if (iDVal != null)