[med-svn] [SCM] tophat branch, oneiric-ppa, updated. oneiric-ppa/1.4.0-1_oneiric3

[Carlos Borroto]

The following commit has been merged in the oneiric-ppa branch:
commit e87448c1f1d1e2e9922d0c64e071dbc0ac65e852
Author: Carlos Borroto <carlos.borroto at gmail.com>
Date:   Thu Jan 12 11:41:23 2012 -0500

    use seqan 1.2 name space

diff --git a/debian/patches/debian_seqan.patch b/debian/patches/debian_seqan.patch
index e308bf5..e17e23f 100644
--- a/debian/patches/debian_seqan.patch
+++ b/debian/patches/debian_seqan.patch
@@ -13,32 +13,3 @@ reverse and convertInPlace to convert
  
  AC_SUBST(CC)
  AC_SUBST(AM_CXXFLAGS)
---- tophat.orig/src/segment_juncs.cpp
-+++ tophat/src/segment_juncs.cpp
-@@ -2670,12 +2670,12 @@
- 	if(color){
- 	  fullRead = read.seq.c_str() + 1;
- 	  rcRead = fullRead;
--	  seqan::reverseInPlace(rcRead);
-+	  seqan::reverse(rcRead);
- 	}else{
- 	  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 = 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)

-- 
A spliced read mapper for RNA-Seq