From 6684cb8bc9999fe63d688494bc769c17c2bc9880 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Jul 2009 12:55:51 +0000
Subject: [PATCH] copySamFileHeader() utility function

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1154 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/Utils.java | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java
index 179fd3122..ea7463e20 100755
--- a/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -65,6 +65,20 @@ public class Utils {
         logger.warn(String.format("* %s", builder));
     }
 
+    public static SAMFileHeader copySAMFileHeader( SAMFileHeader toCopy ) {
+        SAMFileHeader copy = new SAMFileHeader();
+
+        copy.setSortOrder(toCopy.getSortOrder());
+        copy.setGroupOrder(toCopy.getGroupOrder());
+        copy.setProgramRecords(toCopy.getProgramRecords());
+        copy.setReadGroups(toCopy.getReadGroups());
+        copy.setSequenceDictionary(toCopy.getSequenceDictionary());
+
+        for ( Map.Entry<String, Object> e : toCopy.getAttributes())
+            copy.setAttribute(e.getKey(), e.getValue());
+        
+        return copy;
+    }
 
     public static SAMFileWriter createSAMFileWriterWithCompression(SAMFileHeader header, boolean presorted, String file, int compression) {
         if (file.endsWith(".bam"))