From d828eba7f4ce126eeddb68266a1fe38909ed3336 Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Wed, 9 Nov 2011 15:27:38 -0500
Subject: [PATCH] Allow comments in a table-formatted file to precede the
 header line.

---
 .../broadinstitute/sting/utils/codecs/table/TableCodec.java   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
index fac926587..4082a5597 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java
@@ -89,10 +89,10 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
             boolean isFirst = true;
             while ((line = reader.readLine()) != null) {
                 System.out.println(line);
-                if ( isFirst && ! line.startsWith(headerDelimiter) ) {
+                if ( isFirst && ! line.startsWith(headerDelimiter) && ! line.startsWith(commentDelimiter)) {
                     throw new UserException.MalformedFile("TableCodec file does not have a header");
                 }
-                isFirst &= false;
+		isFirst &= line.startsWith(commentDelimiter);
                 if (line.startsWith(headerDelimiter)) {
                     if (header.size() > 0) throw new IllegalStateException("Input table file seems to have two header lines.  The second is = " + line);
                     String spl[] = line.split(delimiterRegex);