gnu/packages/patches/tophat-build-with-later-seqan.patch

   1 This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4.
   2 This is the relevant part of a patch originally posted here:
   3 https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html
   4
   5 --- a/src/segment_juncs.cpp
   6 +++ b/src/segment_juncs.cpp
   7 @@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
   8      typedef map<uint32_t, IntronMotifs> MotifMap;
   9
  10      MotifMap ims;
  11 -
  12 -    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
  13 -    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
  14 -
  15 +
  16 +    typedef seqan::ModifiedString<
  17 +                    seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,
  18 +                    seqan::ModReverse>   ConstDnaStringReverseComplement;
  19 +    ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
  20 +    ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
  21 +
  22      if (talkative)
  23          fprintf(stderr, "Collecting potential splice sites in islands\n");
  24