[med-svn] [tophat] 04/07: d/patches: added patch from Manuel Holtgrewe resolving #733352 removed const_ness_part1.patch as the new patch solves the problem completely

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
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commit dfb42f593b1459c3f06b145956a769a7c51b62db
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Jul 7 11:39:14 2014 +0200

     d/patches: added patch from Manuel Holtgrewe resolving #733352
      removed const_ness_part1.patch as the new patch solves the problem completely
---
 debian/patches/fix4seqan1.4.patch | 40 +++++++++++++++++++++++++++++++++++++++
 debian/patches/series             |  2 +-
 2 files changed, 41 insertions(+), 1 deletion(-)

diff --git a/debian/patches/fix4seqan1.4.patch b/debian/patches/fix4seqan1.4.patch
new file mode 100644
index 0000000..e9091be
--- /dev/null
+++ b/debian/patches/fix4seqan1.4.patch
@@ -0,0 +1,40 @@
+Author: Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
+Bug-Closed: http://bugs.debian.org/733352
+Descriptions: resolves build failure with seqan 1.4
+--- tophat.orig/src/segment_juncs.cpp
++++ tophat/src/segment_juncs.cpp
+@@ -2055,10 +2055,13 @@
+     typedef map<uint32_t, IntronMotifs> MotifMap;
+     
+     MotifMap ims;
+-	
+-    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
+-    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
+-    
++
++    typedef seqan::ModifiedString<
++                    seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,  
++                    seqan::ModReverse>   ConstDnaStringReverseComplement;
++    ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
++    ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
++     
+     if (talkative)
+         fprintf(stderr, "Collecting potential splice sites in islands\n");
+ 
+@@ -2602,12 +2605,14 @@
+ {
+   const Score<int> globalScore(0, -5, -1, -10);  // (match, mismatch, gapextend, gapopen)
+   Align<String<char> > align;
+-  appendValue(rows(align), read);
+   
++  resize(rows(align), 2);
++  setSource(row(align, 0), const_cast<seqan::String<char> &>(read));
++
+   String<char> genomicSequence;
+   assign(genomicSequence, leftReference);
+   append(genomicSequence, rightReference);
+-  appendValue(rows(align), genomicSequence);
++  setSource(row(align, 0), genomicSequence);
+   // int score = globalAlignment(align, globalScore);
+ 
+   Row<Align<String<char> > >::Type& row0 = row(align, 0);
diff --git a/debian/patches/series b/debian/patches/series
index 8b5c581..2ef3aff 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
+fix4seqan1.4.patch
 fix_includes_path.patch
 bashism_in_shell_script.patch
-const_ness_part1.patch

-- 
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