From cb28875c2a07ec706b774ac3a3bb91a7fe54e718 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Tue, 9 Aug 2011 00:46:39 -0400
Subject: [PATCH] Updated rod binding syntax usage on CombineVariants from
 .rodBind to .variants.

---
 .../sting/queue/extensions/gatk/VcfGatherFunction.scala         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
index 27e186585..fcb3e690a 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
@@ -43,7 +43,7 @@ class VcfGatherFunction extends CombineVariants with GatherFunction {
     this.intervals = this.originalGATK.intervals
     this.intervalsString = this.originalGATK.intervalsString
 
-    this.rodBind = this.gatherParts.zipWithIndex map { case (input, index) => new RodBind("input"+index, "VCF", input) }
+    this.variants = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input"+index) }
     this.rod_priority_list = (0 until this.gatherParts.size).map("input"+_).mkString(",")
     this.out = this.originalOutput
     this.assumeIdenticalSamples = true