[med-svn] [SCM] cufflinks branch, master, updated. upstream/1.1.0-32-g57c0153

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 57c01532f69df994e9be3c04feee4a66cb6eb14c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Dec 2 21:19:37 2011 +0000

    bam.h located in /usr/include/samtools and not /usr/include/bam on Debian systems

diff --git a/debian/changelog b/debian/changelog
index eacccfa..a74d5a3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,13 @@
 cufflinks (1.2.1-1) unstable; urgency=low
-
+  
+  [ Alex Mestiashvili ]
   * New upstream release
+  * added patch to fix bam.h localtion . 
+  * [TODO] 
+   - building process modifies some files in the source 
+     dh_auto_clean can't clean the source correctly . 
 
- -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 01 Dec 2011 14:19:13 +0000
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Fri, 02 Dec 2011 21:41:53 +0000
 
 cufflinks (1.0.3-1) unstable; urgency=low
 
diff --git a/debian/patches/0001-bam2samtools.patch b/debian/patches/0001-bam2samtools.patch
new file mode 100644
index 0000000..201c0d8
--- /dev/null
+++ b/debian/patches/0001-bam2samtools.patch
@@ -0,0 +1,36 @@
+From: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Date: Fri, 2 Dec 2011 21:21:17 +0000
+Subject: bam2samtools
+
+---
+ ax_bam.m4 |    2 +-
+ configure |    2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/ax_bam.m4 b/ax_bam.m4
+index 7d463b7..8641172 100644
+--- a/ax_bam.m4
++++ b/ax_bam.m4
+@@ -102,7 +102,7 @@ if test "x$want_bam" = "xyes"; then
+ 
+ 	AC_LANG_PUSH(C++)
+      	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+-	@%:@include <bam/bam.h>
++	@%:@include <samtools/bam.h>
+ 	]], [[
+ 	]])],[
+         AC_MSG_RESULT(yes)
+diff --git a/configure b/configure
+index 67b63f7..88939e9 100755
+--- a/configure
++++ b/configure
+@@ -4206,7 +4206,7 @@ cat confdefs.h >>conftest.$ac_ext
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h.  */
+ 
+-	#include <bam/bam.h>
++	#include <samtools/bam.h>
+ 
+ int
+ main ()
+-- 
diff --git a/debian/patches/0002-fix_includes_path.patch b/debian/patches/0002-fix_includes_path.patch
new file mode 100644
index 0000000..dfd5a55
--- /dev/null
+++ b/debian/patches/0002-fix_includes_path.patch
@@ -0,0 +1,22 @@
+From: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Date: Fri, 2 Dec 2011 21:21:17 +0000
+Subject: fix_includes_path.patch
+
+---
+ src/hits.h |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/src/hits.h b/src/hits.h
+index ee1331e..6aefc9c 100644
+--- a/src/hits.h
++++ b/src/hits.h
+@@ -16,7 +16,7 @@
+ 
+ #include <boost/shared_ptr.hpp>
+ 
+-#include <bam/sam.h>
++#include <samtools/sam.h>
+ 
+ #include "common.h"
+ #include "multireads.h"
+-- 
diff --git a/debian/patches/fix_configure.patch b/debian/patches/fix_configure.patch
deleted file mode 100644
index ae191cd..0000000
--- a/debian/patches/fix_configure.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Description: force configure script to looks for bam.h in /usr/include/samtools
-Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
-Last-Update: 2011-05-24
---- cufflinks-1.0.2.orig/configure
-+++ cufflinks-1.0.2/configure
-@@ -4206,7 +4206,7 @@
- cat >>conftest.$ac_ext <<_ACEOF
- /* end confdefs.h.  */
- 
--	#include <bam/bam.h>
-+	#include <samtools/bam.h>
- 
- int
- main ()
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
deleted file mode 100644
index dafde04..0000000
--- a/debian/patches/fix_includes_path.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Description: sam.h is located in /usr/include/samtools
-Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
-Last-Update: 2011-05-24
---- cufflinks-1.0.2.orig/src/hits.h
-+++ cufflinks-1.0.2/src/hits.h
-@@ -16,7 +16,7 @@
- 
- #include <boost/shared_ptr.hpp>
- 
--#include <bam/sam.h>
-+#include <samtools/sam.h>
- 
- #include "common.h"
- #include "multireads.h"
diff --git a/debian/patches/series b/debian/patches/series
index 08ef98b..bf40253 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-fix_includes_path.patch
-fix_configure.patch
+0001-bam2samtools.patch
+0002-fix_includes_path.patch

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