From 49dd02f4090b525beba735fc9ff16e32388b3fcd Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 11 Jan 2018 14:10:49 +0100
Subject: [PATCH] Keep header when converting sam to bam

Otherwise the converted datasets are not valid BAM files.
---
 lib/galaxy/datatypes/converters/sam_to_bam_native.xml | 1 +
 test/functional/tools/sam_to_bam_native.xml           | 1 +
 2 files changed, 2 insertions(+)

diff --git a/lib/galaxy/datatypes/converters/sam_to_bam_native.xml b/lib/galaxy/datatypes/converters/sam_to_bam_native.xml
index 363a3b57b68..5e8475ea52a 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bam_native.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bam_native.xml
@@ -6,6 +6,7 @@
     <command><![CDATA[
         samtools view
             -b
+            -h
             -@ \${GALAXY_SLOTS:-2}
             -o '${output}'
             '$input'
diff --git a/test/functional/tools/sam_to_bam_native.xml b/test/functional/tools/sam_to_bam_native.xml
index df3a728d4a0..b960bb4c87a 100644
--- a/test/functional/tools/sam_to_bam_native.xml
+++ b/test/functional/tools/sam_to_bam_native.xml
@@ -6,6 +6,7 @@
     #if $input1:
         samtools view
             -b
+            -h
             -@ \${GALAXY_SLOTS:-2}
             -o '${output}'
             '$input1'