[med-svn] [SCM] tophat branch, master, updated. upstream/1.3.3-14-g7059312

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit a3b55d563ea95991662c9e6ddddc0e95618a1f46
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Dec 15 22:40:05 2011 +0100

    in new seqan v1.3  function reverseInPlace seems to be renamed to reverse
    and convertInPlace to convert

diff --git a/debian/patches/debian_seqan.patch b/debian/patches/debian_seqan.patch
index e677688..372d80c 100644
--- a/debian/patches/debian_seqan.patch
+++ b/debian/patches/debian_seqan.patch
@@ -9,3 +9,21 @@
  
  AC_SUBST(CC)
  AC_SUBST(AM_CXXFLAGS)
+--- tophat.orig/src/segment_juncs.cpp
++++ tophat/src/segment_juncs.cpp
+@@ -2674,12 +2674,12 @@
+ 	if(color){
+ 	  fullRead = read_seq + 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);

-- 
A spliced read mapper for RNA-Seq