From ade18438184adcb42e5d0df2a93a63bf8ba7de86 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 22 May 2012 16:40:01 -0400
Subject: [PATCH] Bugfix for not setting header in AbstractVCFCodec

---
 .../sting/utils/codecs/vcf/AbstractVCFCodec.java               | 3 ++-
 .../org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java    | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index 75230d00c..67ebf6adc 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -176,7 +176,8 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
             }
         }
 
-        return new VCFHeader(metaData, sampleNames);
+        this.header = new VCFHeader(metaData, sampleNames);
+        return this.header;
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
index 2a8343786..6581c13fc 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
@@ -88,7 +88,7 @@ public class VCFCodec extends AbstractVCFCodec {
                         throw new TribbleException.InvalidHeader("We never saw a header line specifying VCF version");
                     }
                     headerStrings.add(line);
-                    this.header = super.parseHeaderFromLines(headerStrings, version);
+                    super.parseHeaderFromLines(headerStrings, version);
                     if ( headerForRepairs != null )
                         this.header = repairHeader(this.header, headerForRepairs);
                     return this.header;