From 5ffeddd3b1ac5f83d6018dad0a178ae785a4dc39 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 14 Jul 2011 14:45:16 -0400
Subject: [PATCH] better to use _ instead of ., as this is a special case
 later.

---
 .../sting/gatk/walkers/diffengine/VCFDiffableReader.java      | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index 5677574bd..a812babaf 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -56,7 +56,9 @@ public class VCFDiffableReader implements DiffableReader {
             // must be read as state is stored in reader itself
             VCFHeader header = (VCFHeader)vcfCodec.readHeader(lineReader);
             for ( VCFHeaderLine headerLine : header.getMetaData() ) {
-                final String key = (headerLine instanceof VCFNamedHeaderLine ? headerLine.getKey() + "." + ((VCFNamedHeaderLine) headerLine).getName() : headerLine.getKey());
+                String key = headerLine.getKey();
+                if ( headerLine instanceof VCFNamedHeaderLine )
+                    key += "_" + ((VCFNamedHeaderLine) headerLine).getName();
                 root.add(key, headerLine.toString());
             }