diff options
Diffstat (limited to 'gnu/packages/patches/tophat-build-with-later-seqan.patch')
| -rw-r--r-- | gnu/packages/patches/tophat-build-with-later-seqan.patch | 24 |
1 files changed, 0 insertions, 24 deletions
diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch deleted file mode 100644 index fc742e2a7d..0000000000 --- a/gnu/packages/patches/tophat-build-with-later-seqan.patch +++ /dev/null @@ -1,24 +0,0 @@ -This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4. -This is the relevant part of a patch originally posted here: -https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html - ---- 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"); - |