[med-svn] [SCM] tophat branch, master, updated. upstream/1.4.0-24-g0a2dc5e

[Carlos Borroto]

The following commit has been merged in the master branch:
commit 0a2dc5edd18dbc4614daf31e6b6f5c51f4f3782d
Author: Carlos Borroto <carlos.borroto at gmail.com>
Date:   Wed Jan 18 11:08:01 2012 -0500

    refreshs debian/patches/fix_undefined_reference.patch to include
    author's recommendations and DEP 3 header

diff --git a/debian/patches/fix_undefined_reference.patch b/debian/patches/fix_undefined_reference.patch
index 4bcfd12..41872fb 100644
--- a/debian/patches/fix_undefined_reference.patch
+++ b/debian/patches/fix_undefined_reference.patch
@@ -1,3 +1,9 @@
+From: Carlos Borroto <carlos.borroto at gmail.com>
+Date: 2012-01-18
+Subject: Fixs header files missind inclusion of "config.h" causing "undefined
+reference to" errors.
+Forwarded: by email to the author
+Applied-Upstream: to be included in next upstream release
 --- tophat.orig/src/GTFToFasta.h
 +++ tophat/src/GTFToFasta.h
 @@ -9,6 +9,10 @@
@@ -5,9 +11,44 @@
  #define GTFToFasta_H
  
 +#ifdef HAVE_CONFIG_H
-+#include "config.h"
++#include <config.h>
 +#endif
 +
  #include <cassert>
  #include <cstdlib>
  #include <cstring>
+--- tophat.orig/src/FastaTools.h
++++ tophat/src/FastaTools.h
+@@ -8,6 +8,10 @@
+ #ifndef TopHat_FastaTools_h
+ #define TopHat_FastaTools_h
+ 
++#ifdef HAVE_CONFIG_H
++#include <config.h>
++#endif
++
+ #include <cassert>
+ #include <cstdlib>
+ #include <cstring>
+--- tophat.orig/src/map2gtf.h
++++ tophat/src/map2gtf.h
+@@ -4,6 +4,13 @@
+  * Date: June 10, 2011
+  */
+ 
++#ifndef _MAP2GTF_H_
++#define _MAP2GTF_H_
++
++#ifdef HAVE_CONFIG_H
++#include <config.h>
++#endif
++
+ #include <cassert>
+ #include <cstdlib>
+ #include <cstring>
+@@ -83,3 +90,5 @@
+ 
+ void print_trans(GffObj* trans, const BowtieHit& in, size_t rem_len,
+         size_t match_len, size_t cur_pos, size_t start_pos);
++
++#endif /* _MAP2GTF_H_ */

-- 
A spliced read mapper for RNA-Seq