[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-26-g3b790e2

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 67f4e8162b71be8a202d7aa1accee99dc0f21443
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Sat Jun 9 11:09:49 2012 +0200

    refreshed debian/patches/fix_includes_path.patch

diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index 1fa080f..1819ef3 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -15,8 +15,8 @@ Subject: Corrected location for samtools .h files
  #include "bwt_map.h"
 --- tophat.orig/src/bam2fastx.cpp
 +++ tophat/src/bam2fastx.cpp
-@@ -4,8 +4,8 @@
- #include <getopt.h>
+@@ -5,8 +5,8 @@
+ #include <assert.h>
  #include <string>
  
 -#include "bam/bam.h"

-- 
A spliced read mapper for RNA-Seq