[med-svn] [SCM] tophat branch, master, updated. debian/2.0.6-1-18-gb16c75d

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit fe6dee29918a3e18c451b0e16c7a583382d22f44
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Jul 4 14:04:12 2013 +0200

    refresh patches

diff --git a/debian/changelog b/debian/changelog
index 1efd88c..b663b02 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+tophat (2.0.9-1) UNRELEASED; urgency=low
+
+  * d/get-orig-source: place tarballs to ../tarballs/
+  * d/control: use canonical vcs fields, Standards-Version: 3.9.4  
+  * d/changelog: updated source field
+  * refreshed patches
+  * Imported Upstream version 2.0.9
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 04 Jul 2013 13:59:07 +0200
+
 tophat (2.0.8b-1) unstable; urgency=low
 
   * Imported Upstream version 2.0.8b
diff --git a/debian/patches/bashism_in_shell_script.patch b/debian/patches/bashism_in_shell_script.patch
index 9df6b3c..d93b0b8 100644
--- a/debian/patches/bashism_in_shell_script.patch
+++ b/debian/patches/bashism_in_shell_script.patch
@@ -2,10 +2,8 @@ Author: Andreas Tille <tille at debian.org>
 Bug-Closed: http://bugs.debian.org/671813
 Descriptions: Remove bashism from shell script
 
-Index: tophat/src/tophat2.in
-===================================================================
---- tophat.orig/src/tophat2.in	2012-06-21 14:28:32.730584269 -0400
-+++ tophat/src/tophat2.in	2012-06-21 14:28:47.166584998 -0400
+--- a/src/tophat2.in
++++ b/src/tophat2.in
 @@ -1,9 +1,9 @@
  #!/bin/bash
  prefix="__PREFIX__"
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index 1819ef3..0fb35ff 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -2,8 +2,8 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
 Date: 2012-01-05
 Subject: Corrected location for samtools .h files 
 
---- tophat.orig/src/align_status.h
-+++ tophat/src/align_status.h
+--- a/src/align_status.h
++++ b/src/align_status.h
 @@ -14,7 +14,7 @@
  #include <cassert>
  #include <cstring>
@@ -13,8 +13,8 @@ Subject: Corrected location for samtools .h files
  #include "common.h"
  
  #include "bwt_map.h"
---- tophat.orig/src/bam2fastx.cpp
-+++ tophat/src/bam2fastx.cpp
+--- a/src/bam2fastx.cpp
++++ b/src/bam2fastx.cpp
 @@ -5,8 +5,8 @@
  #include <assert.h>
  #include <string>
@@ -26,8 +26,8 @@ Subject: Corrected location for samtools .h files
  
  using namespace std;
  
---- tophat.orig/src/bwt_map.h
-+++ tophat/src/bwt_map.h
+--- a/src/bwt_map.h
++++ b/src/bwt_map.h
 @@ -16,7 +16,7 @@
  #include <algorithm>
  #include <seqan/sequence.h>
@@ -37,8 +37,8 @@ Subject: Corrected location for samtools .h files
  using namespace std;
  
  #include "common.h"
---- tophat.orig/src/common.h
-+++ tophat/src/common.h
+--- a/src/common.h
++++ b/src/common.h
 @@ -15,8 +15,8 @@
  #include <cstdio>
  #include <string>
@@ -48,10 +48,10 @@ Subject: Corrected location for samtools .h files
 +#include "samtools/bam.h"
 +#include "samtools/sam.h"
  
- 
  #define MAX_READ_LEN 1024
---- tophat.orig/src/map2gtf.h
-+++ tophat/src/map2gtf.h
+ 
+--- a/src/map2gtf.h
++++ b/src/map2gtf.h
 @@ -20,8 +20,8 @@
  #include <sstream>
  #include <vector>
@@ -63,8 +63,8 @@ Subject: Corrected location for samtools .h files
  
  #include <seqan/sequence.h>
  
---- tophat.orig/ax_bam.m4
-+++ tophat/ax_bam.m4
+--- a/ax_bam.m4
++++ b/ax_bam.m4
 @@ -102,7 +102,7 @@
  
  	AC_LANG_PUSH(C++)

-- 
A spliced read mapper for RNA-Seq