[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 e0aeb8c69adb0b85bd7c24b33666987a23142248
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Dec 15 18:14:58 2011 +0100

    src/bam_merge.cpp contains bam/bam.h bam/sam.h headers ,
    changed to samtools/bam.h samtools/sam.h

diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index 474e4f6..f9ceae3 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -1,10 +1,8 @@
 ## Description: add some description
 ## Origin/Author: add some origin or author
 ## Bug: bug URL
-Index: tophat-1.3.1/src/align_status.h
-===================================================================
---- tophat-1.3.1.orig/src/align_status.h	2011-06-23 11:11:39.503108250 -0400
-+++ tophat-1.3.1/src/align_status.h	2011-06-23 11:10:04.553107491 -0400
+--- tophat.orig/src/align_status.h
++++ tophat/src/align_status.h
 @@ -14,7 +14,7 @@
  #include <cassert>
  #include <cstring>
@@ -14,10 +12,8 @@ Index: tophat-1.3.1/src/align_status.h
  #include "common.h"
  #include "junctions.h"
  
-Index: tophat-1.3.1/src/bam2fastx.cpp
-===================================================================
---- tophat-1.3.1.orig/src/bam2fastx.cpp	2011-06-23 11:11:39.563108250 -0400
-+++ tophat-1.3.1/src/bam2fastx.cpp	2011-06-23 11:10:24.003108252 -0400
+--- tophat.orig/src/bam2fastx.cpp
++++ tophat/src/bam2fastx.cpp
 @@ -3,8 +3,8 @@
  #include <cstring>
  #include <getopt.h>
@@ -29,10 +25,8 @@ Index: tophat-1.3.1/src/bam2fastx.cpp
  
  static bool is_fastq=true; //default is fastq
  static char qseq[2048];
-Index: tophat-1.3.1/src/bwt_map.h
-===================================================================
---- tophat-1.3.1.orig/src/bwt_map.h	2011-06-23 11:11:39.463108250 -0400
-+++ tophat-1.3.1/src/bwt_map.h	2011-06-23 11:10:49.823108272 -0400
+--- tophat.orig/src/bwt_map.h
++++ tophat/src/bwt_map.h
 @@ -15,7 +15,7 @@
  #include <cstring>
  #include <seqan/sequence.h>
@@ -42,10 +36,8 @@ Index: tophat-1.3.1/src/bwt_map.h
  using namespace std;
  
  #include "common.h"
-Index: tophat-1.3.1/src/common.h
-===================================================================
---- tophat-1.3.1.orig/src/common.h	2011-06-23 11:11:38.843108248 -0400
-+++ tophat-1.3.1/src/common.h	2011-06-23 11:11:31.993108496 -0400
+--- tophat.orig/src/common.h
++++ tophat/src/common.h
 @@ -15,8 +15,8 @@
  #include <cstdio>
  #include <string>
@@ -57,3 +49,16 @@ Index: tophat-1.3.1/src/common.h
  
  
  #ifdef MEM_DEBUG
+--- tophat.orig/src/bam_merge.cpp
++++ tophat/src/bam_merge.cpp
+@@ -2,8 +2,8 @@
+ #include <cstdio>
+ #include <cstring>
+ 
+-#include "bam/bam.h"
+-#include "bam/sam.h"
++#include "samtools/bam.h"
++#include "samtools/sam.h"
+ #include "GBase.h"
+ #include "GList.hh"
+ 

-- 
A spliced read mapper for RNA-Seq