From 6f2c3d676183ee5b24d8ea41930b9182231bfeb4 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 11 Jun 2012 15:52:36 -0400
Subject: [PATCH] Have Bowtie2 wrapper produce BAM rather than SAM output.

---
 tools/sr_mapping/bowtie2_wrapper.py  | 2 +-
 tools/sr_mapping/bowtie2_wrapper.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/sr_mapping/bowtie2_wrapper.py b/tools/sr_mapping/bowtie2_wrapper.py
index 78e21c1bc1a..259fd067efe 100644
--- a/tools/sr_mapping/bowtie2_wrapper.py
+++ b/tools/sr_mapping/bowtie2_wrapper.py
@@ -65,7 +65,7 @@ def __main__():
         index_path = options.index_path
 
     # Build bowtie command.
-    cmd = 'bowtie2 %s -x %s %s -S %s'
+    cmd = 'bowtie2 %s -x %s %s | samtools view -Sb - > %s'
     
     # Set up reads.
     if options.single_paired == 'paired':
diff --git a/tools/sr_mapping/bowtie2_wrapper.xml b/tools/sr_mapping/bowtie2_wrapper.xml
index 3cb79ff35f5..416fdc0f0bf 100644
--- a/tools/sr_mapping/bowtie2_wrapper.xml
+++ b/tools/sr_mapping/bowtie2_wrapper.xml
@@ -112,7 +112,7 @@
     </inputs>
 
     <outputs>
-        <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
+        <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
           <actions>
             <conditional name="refGenomeSource.genomeSource">
               <when value="indexed">