[med-svn] [SCM] cufflinks branch, master, updated. upstream/1.2.1-39-gf82cc58

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit f82cc58acff3a1b099f461b369670c58d0a9e7ee
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Sun Dec 4 12:20:52 2011 +0000

    no need to patch configure because we use dh $@ --with autoreconf

diff --git a/debian/patches/0001-bam2samtools.patch b/debian/patches/0001-bam2samtools.patch
index 201c0d8..884d2e2 100644
--- a/debian/patches/0001-bam2samtools.patch
+++ b/debian/patches/0001-bam2samtools.patch
@@ -4,8 +4,7 @@ Subject: bam2samtools
 
 ---
  ax_bam.m4 |    2 +-
- configure |    2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
+ 1 files changed, 1 insertions(+), 1 deletions(-)
 
 diff --git a/ax_bam.m4 b/ax_bam.m4
 index 7d463b7..8641172 100644
@@ -20,17 +19,3 @@ index 7d463b7..8641172 100644
  	]], [[
  	]])],[
          AC_MSG_RESULT(yes)
-diff --git a/configure b/configure
-index 67b63f7..88939e9 100755
---- a/configure
-+++ b/configure
-@@ -4206,7 +4206,7 @@ cat confdefs.h >>conftest.$ac_ext
- cat >>conftest.$ac_ext <<_ACEOF
- /* end confdefs.h.  */
- 
--	#include <bam/bam.h>
-+	#include <samtools/bam.h>
- 
- int
- main ()
--- 

-- 
Transcript assembly, differential expression, and differential regulation for RNA-Seq.