diff options
Diffstat (limited to 'academic/tophat/fix_build_w_seqan1.4.patch')
| -rw-r--r-- | academic/tophat/fix_build_w_seqan1.4.patch | 24 |
1 files changed, 24 insertions, 0 deletions
diff --git a/academic/tophat/fix_build_w_seqan1.4.patch b/academic/tophat/fix_build_w_seqan1.4.patch new file mode 100644 index 0000000000..f51b833c1e --- /dev/null +++ b/academic/tophat/fix_build_w_seqan1.4.patch @@ -0,0 +1,24 @@ +Description: Resolves build failure with seqan 1.4 +Bug-Closed: http://bugs.debian.org/733352 +Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de> +--- a/src/segment_juncs.cpp ++++ b/src/segment_juncs.cpp +@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl + 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"); + + |