[med-svn] [SCM] tophat branch, master, updated. upstream/1.3.3-24-g7be6412

[Carlos Borroto]

The following commit has been merged in the master branch:
commit 7be64124ab8cff3f2d261460dd52bee283f8d79c
Author: Carlos Borroto <carlos.borroto at gmail.com>
Date:   Tue Jan 10 12:01:31 2012 -0500

    New upstream release, patches updated

diff --git a/debian/changelog b/debian/changelog
index b079260..20d9bc8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+tophat (1.4.0-1) UNRELEASED; urgency=low
+
+  * New upstream release
+
+ -- Carlos Borroto <carlos.borroto at gmail.com>  Tue, 10 Jan 2012 11:49:39 -0500
+
 tophat (1.3.3-1) UNRELEASED; urgency=low
 
   TODO:
diff --git a/debian/patches/bam2samtools b/debian/patches/bam2samtools
index 1270a71..ed67b2e 100644
--- a/debian/patches/bam2samtools
+++ b/debian/patches/bam2samtools
@@ -6,11 +6,9 @@ Subject: bam2samtools
  ax_bam.m4 |    2 +-
  1 files changed, 1 insertions(+), 1 deletions(-)
 
-diff --git a/ax_bam.m4 b/ax_bam.m4
-index 7d463b7..8641172 100644
---- a/ax_bam.m4
-+++ b/ax_bam.m4
-@@ -102,7 +102,7 @@ if test "x$want_bam" = "xyes"; then
+--- tophat.orig/ax_bam.m4
++++ tophat/ax_bam.m4
+@@ -102,7 +102,7 @@
  
  	AC_LANG_PUSH(C++)
       	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
@@ -19,4 +17,3 @@ index 7d463b7..8641172 100644
  	]], [[
  	]])],[
          AC_MSG_RESULT(yes)
--- 
diff --git a/debian/patches/debian_seqan.patch b/debian/patches/debian_seqan.patch
index e4eac3a..e308bf5 100644
--- a/debian/patches/debian_seqan.patch
+++ b/debian/patches/debian_seqan.patch
@@ -15,15 +15,15 @@ reverse and convertInPlace to convert
  AC_SUBST(AM_CXXFLAGS)
 --- tophat.orig/src/segment_juncs.cpp
 +++ tophat/src/segment_juncs.cpp
-@@ -2674,12 +2674,12 @@
+@@ -2670,12 +2670,12 @@
  	if(color){
- 	  fullRead = read_seq + 1;
+ 	  fullRead = read.seq.c_str() + 1;
  	  rcRead = fullRead;
 -	  seqan::reverseInPlace(rcRead);
 +	  seqan::reverse(rcRead);
  	}else{
- 	  fullRead = read_seq;
- 	  rcRead = read_seq;
+ 	  fullRead = read.seq;
+ 	  rcRead = read.seq;
 -	  seqan::convertInPlace(rcRead, seqan::FunctorComplement<Dna>());
 -	  seqan::reverseInPlace(rcRead);
 +	  seqan::convert(rcRead, seqan::FunctorComplement<Dna>());
@@ -31,3 +31,14 @@ reverse and convertInPlace to convert
  	}
  
  	size_t read_length = seqan::length(fullRead);
+@@ -2878,8 +2878,8 @@
+       seqan::String<char> fullRead, rcRead;
+       fullRead = read.seq;
+       rcRead = read.seq;
+-      seqan::convertInPlace(rcRead, seqan::FunctorComplement<Dna>());
+-      seqan::reverseInPlace(rcRead);
++      seqan::convert(rcRead, seqan::FunctorComplement<Dna>());
++      seqan::reverse(rcRead);
+       size_t read_length =  read.seq.length();
+ 
+       for (size_t l = 0; l < left_segment_hits.hits.size(); ++l)
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index b05b3fc..620311f 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -24,8 +24,8 @@ Subject: Corrected location for samtools .h files
 +#include "samtools/bam.h"
 +#include "samtools/sam.h"
  
- static bool is_fastq=true; //default is fastq
- static char qseq[2048];
+ bool is_fastq=true; //default is fastq
+ bool sam_input=false; //default is BAM
 --- tophat.orig/src/bwt_map.h
 +++ tophat/src/bwt_map.h
 @@ -15,7 +15,7 @@
@@ -49,7 +49,7 @@ Subject: Corrected location for samtools .h files
 +#include "samtools/sam.h"
  
  
- #ifdef MEM_DEBUG
+ #define VMAXINT32 0xFFFFFFFF
 --- tophat.orig/src/bam_merge.cpp
 +++ tophat/src/bam_merge.cpp
 @@ -2,8 +2,8 @@
@@ -63,3 +63,16 @@ Subject: Corrected location for samtools .h files
  #include "GBase.h"
  #include "GList.hh"
  
+--- tophat.orig/src/map2gtf.h
++++ tophat/src/map2gtf.h
+@@ -13,8 +13,8 @@
+ #include <sstream>
+ #include <vector>
+ 
+-#include <bam/bam.h>
+-#include <bam/sam.h>
++#include <samtools/bam.h>
++#include <samtools/sam.h>
+ 
+ #include <seqan/sequence.h>
+ 

-- 
A spliced read mapper for RNA-Seq