[med-svn] [SCM] tophat branch, master, updated. upstream/1.4.0-38-ga7aaa86

[Charles Plessy]

The following commit has been merged in the master branch:
commit fc8aa2225c89485297a930901e462547fa4dfb90
Author: Charles Plessy <plessy at debian.org>
Date:   Mon Feb 6 14:51:58 2012 +0900

    Merged bam2samtools and fix_includes_path.patch (same purpose).

diff --git a/debian/patches/bam2samtools b/debian/patches/bam2samtools
deleted file mode 100644
index ed67b2e..0000000
--- a/debian/patches/bam2samtools
+++ /dev/null
@@ -1,19 +0,0 @@
-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 +-
- 1 files changed, 1 insertions(+), 1 deletions(-)
-
---- tophat.orig/ax_bam.m4
-+++ tophat/ax_bam.m4
-@@ -102,7 +102,7 @@
- 
- 	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/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index 620311f..526b4f1 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -76,3 +76,14 @@ Subject: Corrected location for samtools .h files
  
  #include <seqan/sequence.h>
  
+--- tophat.orig/ax_bam.m4
++++ tophat/ax_bam.m4
+@@ -102,7 +102,7 @@
+ 
+ 	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/debian/patches/series b/debian/patches/series
index a3d0eb4..9c36db4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 debian_seqan.patch
 fix_includes_path.patch
-bam2samtools

-- 
A spliced read mapper for RNA-Seq