From 66838a073e15c891d8f122efbe98259be102a0c8 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 7 May 2012 12:20:11 -0400
Subject: [PATCH] Very annoying: we have been emitting an extra TAB in the
 header of the VCF (which breaks some parsers) for sites-only file.  Hopefully
 not too many integration tests will need to be fixed...

---
 .../sting/utils/codecs/vcf/StandardVCFWriter.java           | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
index ac1da7110..665a4ae0a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
@@ -108,9 +108,13 @@ public class StandardVCFWriter extends IndexingVCFWriter {
 
             // write out the column line
             mWriter.write(VCFHeader.HEADER_INDICATOR);
+            boolean isFirst = true;
             for ( VCFHeader.HEADER_FIELDS field : mHeader.getHeaderFields() ) {
+                if ( isFirst )
+                    isFirst = false; // don't write out a field separator
+                else
+                    mWriter.write(VCFConstants.FIELD_SEPARATOR);
                 mWriter.write(field.toString());
-                mWriter.write(VCFConstants.FIELD_SEPARATOR);
             }
 
             if ( mHeader.hasGenotypingData() ) {