[med-svn] [SCM] cufflinks branch, master, updated. upstream/0.9.3-21-g7df8ccc

[Alex Mestiashvili]

The following commit has been merged in the master branch:
commit 39a597c5bd9e4440de354c7f7dbdc7af9eb5e95a
Merge: 528140cf82e42b2a7b7ff3e5532bea1529072e36 fedd24b9bf5c659622fa3386243a60f6197a83ac
Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed May 25 09:42:52 2011 +0200

    Merge git+ssh://git.debian.org/git/debian-med/cufflinks
    
    Conflicts:
    	configure
    	debian/changelog
    	src/hits.h

diff --combined configure.orig
index e2ed49d,f3bbd5c..ae66f5e
--- a/configure.orig
+++ b/configure.orig
@@@ -4206,7 -4206,7 +4206,11 @@@ cat confdefs.h >>conftest.$ac_ex
  cat >>conftest.$ac_ext <<_ACEOF
  /* end confdefs.h.  */
  
++<<<<<<< HEAD
 +	#include <bam/bam.h>
++=======
+ 	#include <samtools/bam.h>
++>>>>>>> fedd24b9bf5c659622fa3386243a60f6197a83ac
  
  int
  main ()
diff --combined debian/changelog.orig
index 0000000,0000000..fe60738
new file mode 100644
--- /dev/null
+++ b/debian/changelog.orig
@@@ -1,0 -1,0 +1,17 @@@
++cufflinks (1.0.2-1) unstable; urgency=low
++
++<<<<<<< HEAD
++  * Upstream release 
++
++ -- Alex Mestiashvili <alex at biotec.tu-dresden.de>  Tue, 24 May 2011 13:43:09 +0200
++
++cufflinks (0.9.3-1) unstable; urgency=low
++
++  * Initial release (Closes: #nnnn)  <nnnn is the bug number of your ITP>
++
++ -- Alex Mestiashvili <alex at biotec.tu-dresden.de>  Tue, 03 May 2011 13:53:19 +0000
++=======
++  * Initial release (Closes: #627799)
++
++ -- Alex Mestiashvili <alex at biotec.tu-dresden.de>  Tue, 24 May 2011 13:43:09 +0200
++>>>>>>> fedd24b9bf5c659622fa3386243a60f6197a83ac
diff --combined src/hits.h.orig
index adf30ed,38779b2..56b791a
--- a/src/hits.h.orig
+++ b/src/hits.h.orig
@@@ -16,7 -16,7 +16,11 @@@
  
  #include <boost/shared_ptr.hpp>
  
++<<<<<<< HEAD
 +#include <bam/sam.h>
++=======
+ #include <samtools/sam.h>
++>>>>>>> fedd24b9bf5c659622fa3386243a60f6197a83ac
  
  #include "common.h"
  #include "multireads.h"

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