The following commit has been merged in the master branch:
commit 39a597c5bd9e4440de354c7f7dbdc7af9eb5e95a
Merge: 528140cf82e42b2a7b7ff3e5532bea1529072e36
fedd24b9bf5c659622fa3386243a60f6197a83ac
Author: Alex Mestiashvili <[email protected]>
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 <[email protected]> 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 <[email protected]> Tue, 03 May 2011 13:53:19
+0000
++=======
++ * Initial release (Closes: #627799)
++
++ -- Alex Mestiashvili <[email protected]> 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.
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