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guix/gnu/packages/patches/tophat-build-with-later-seqan.patch
Ricardo Wurmus 94ce537eac gnu: Add TopHat.
* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2016-01-23 08:53:10 +01:00

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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");