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authorRicardo Wurmus <rekado@elephly.net>2018-10-21 11:54:44 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-10-21 23:06:45 +0200
commit9a6808e0c00d6acb00b7be4aa573f252fa7d9635 (patch)
tree4207f7aebf11479910ac902b24741d5cce6f6734 /gnu/packages/patches
parentf7618bf18e00f6ece8e886f2fc6328314d1ed544 (diff)
gnu: tophat: Update to 2.1.1.
* gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1. * gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch.
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r--gnu/packages/patches/tophat-build-with-later-seqan.patch24
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");
-