[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 45d35bf897f7e58698cbb5ea0f73767400ea2ab8
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Dec 15 18:09:59 2011 +0100

    added patch to fix ax_bam.m4 , changed rules to use autoreconf

diff --git a/debian/patches/bam2samtools b/debian/patches/bam2samtools
new file mode 100644
index 0000000..1270a71
--- /dev/null
+++ b/debian/patches/bam2samtools
@@ -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: bam2samtools
+
+---
+ ax_bam.m4 |    2 +-
+ 1 files changed, 1 insertions(+), 1 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/debian/patches/series b/debian/patches/series
index 08ef98b..e101519 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
 fix_includes_path.patch
-fix_configure.patch
+bam2samtools
diff --git a/debian/rules b/debian/rules
index 736b14e..94a9b7e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,4 +4,15 @@
 #export DH_VERBOSE=1
 
 %:
-	dh $@ 
+	dh $@ --with autoreconf
+
+override_dh_auto_clean:
+	dh_quilt_patch
+	dh_auto_clean
+
+override_dh_clean:
+	dh_quilt_unpatch
+	dh_clean
+
+override_dh_builddeb:
+	dh_builddeb -- -Z xz

-- 
A spliced read mapper for RNA-Seq