From 9dec783a82627f854f7f13b59b7f92c346bafee2 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 18 May 2009 13:34:52 +0000
Subject: [PATCH] Actually writes out a good header now

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@744 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/SimulateReads.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/python/SimulateReads.py b/python/SimulateReads.py
index 565ca8f15..19bd11b40 100755
--- a/python/SimulateReads.py
+++ b/python/SimulateReads.py
@@ -651,7 +651,8 @@ def main():
         raise Exception('Does not support mutation density > 1 for mutations of class', OPTIONS.mutationType)
 
     readLen = OPTIONS.readLen
-    header = SAMHeader( "MarkD", readLen ) 
+    fastaRecords = [seq for seq in readRef(OPTIONS.reference)]
+    header = SAMHeader( fastaRecords[0].id, len(fastaRecords[0].seq) ) 
     SAMout = SAMIO( outputSAM, header, debugging=OPTIONS.debug )
     
     mutationsout = open(root + '.mutations.txt', 'w')
@@ -665,7 +666,7 @@ def main():
 
     counter = 0
     refLen = 0
-    for ref in readRef(OPTIONS.reference):
+    for ref in fastaRecords:
         refLen = len(ref.seq)
         
         # write the crazy ref file info needed by samtools