[med-svn] [reapr] 01/03: support samtools 1.3 sort syntax

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository reapr.

commit c4482a8f4261d3f0771e64767f72036041304892
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Mon Feb 1 12:49:49 2016 +0000

    support samtools 1.3 sort syntax
---
 debian/patches/fix_sort_samtools13 | 16 ++++++++++++++++
 debian/patches/series              |  1 +
 2 files changed, 17 insertions(+)

diff --git a/debian/patches/fix_sort_samtools13 b/debian/patches/fix_sort_samtools13
new file mode 100644
index 0000000..f009223
--- /dev/null
+++ b/debian/patches/fix_sort_samtools13
@@ -0,0 +1,16 @@
+Description: adapt samtools sort usage to 1.3 syntax 
+ Samtools 1.3 changed the syntax of the 'samtools sort' command, breaking
+ REAPR's smaltmap command in the process.
+ Discussed and forwarded to upstream in person, hence no URL.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/src/task_smaltmap.pl
++++ b/src/task_smaltmap.pl
+@@ -155,7 +155,7 @@
+                . " | $samtools view -S -T $assembly -b - > $raw_bam";
+ 
+ # sort the bam by coordinate
+-push @commands, "$samtools sort $raw_bam $raw_bam.sort";
++push @commands, "$samtools sort $raw_bam -O bam -o $raw_bam.sort.bam";
+ 
+ # remove duplicates
+ push @commands, "$samtools rmdup $raw_bam.sort.bam $rmdup_bam";
diff --git a/debian/patches/series b/debian/patches/series
index ffad062..0811d9f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 use_shared_libs
 hardening
+fix_sort_samtools13

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