[med-svn] [SCM] tophat branch, master, updated. upstream/1.3.3-8-g1067240

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 1067240bbf50de263bf3723a6442e7a622ae0a8f
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Dec 15 18:23:54 2011 +0100

    No need in fix_configure.patch patch , replaced by bam2samtools.

diff --git a/debian/patches/fix_configure.patch b/debian/patches/fix_configure.patch
deleted file mode 100644
index b822436..0000000
--- a/debian/patches/fix_configure.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-## Description: add some description
-## Origin/Author: add some origin or author
-## Bug: bug URL
-Index: tophat-1.3.1/configure
-===================================================================
---- tophat-1.3.1.orig/configure	2011-06-23 11:13:09.343108260 -0400
-+++ tophat-1.3.1/configure	2011-06-23 11:13:02.553108267 -0400
-@@ -4110,7 +4110,7 @@
- cat >>conftest.$ac_ext <<_ACEOF
- /* end confdefs.h.  */
- 
--	#include <bam/bam.h>
-+	#include <samtools/bam.h>
- 
- int
- main ()

-- 
A spliced read mapper for RNA-Seq