[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-13-gfc9cd68

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 45c55eba4f5486191184aeaf21e6c16c9b34b725
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Sat Apr 14 10:41:37 2012 +0200

    updated debian/patches
    updated debian/changelog

diff --git a/debian/changelog b/debian/changelog
index 3ce9c42..7bf50c6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+tophat (2.0.0-1) UNRELEASED; urgency=low
+
+  [ Charles Plessy ]
+  * YAML syntax correction
+
+  [ Alexandre Mestiashvili ]
+  * Imported Upstream version 2.0.0
+  * updated debian/patches
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Sat, 14 Apr 2012 10:47:13 +0200
+
 tophat (1.4.1-2) unstable; urgency=low
 
   [ Carlos Borroto ]
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index 526b4f1..1fa080f 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -11,25 +11,25 @@ Subject: Corrected location for samtools .h files
 -#include <bam/sam.h>
 +#include <samtools/sam.h>
  #include "common.h"
- #include "junctions.h"
  
+ #include "bwt_map.h"
 --- tophat.orig/src/bam2fastx.cpp
 +++ tophat/src/bam2fastx.cpp
-@@ -3,8 +3,8 @@
- #include <cstring>
+@@ -4,8 +4,8 @@
  #include <getopt.h>
+ #include <string>
  
 -#include "bam/bam.h"
 -#include "bam/sam.h"
 +#include "samtools/bam.h"
 +#include "samtools/sam.h"
  
- bool is_fastq=true; //default is fastq
- bool sam_input=false; //default is BAM
+ using namespace std;
+ 
 --- tophat.orig/src/bwt_map.h
 +++ tophat/src/bwt_map.h
-@@ -15,7 +15,7 @@
- #include <cstring>
+@@ -16,7 +16,7 @@
+ #include <algorithm>
  #include <seqan/sequence.h>
  
 -#include <bam/sam.h>
@@ -49,23 +49,10 @@ Subject: Corrected location for samtools .h files
 +#include "samtools/sam.h"
  
  
- #define VMAXINT32 0xFFFFFFFF
---- 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"
- 
+ #define MAX_READ_LEN 1024
 --- tophat.orig/src/map2gtf.h
 +++ tophat/src/map2gtf.h
-@@ -13,8 +13,8 @@
+@@ -20,8 +20,8 @@
  #include <sstream>
  #include <vector>
  
diff --git a/debian/patches/series b/debian/patches/series
index 35999cd..9f30ee6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1 @@
-debian_seqan.patch
 fix_includes_path.patch
-remove_cflag_handling_in_configure.patch

-- 
A spliced read mapper for RNA-Seq