94ce537eac
* 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.
25 lines
1 KiB
Diff
25 lines
1 KiB
Diff
This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4.
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This is the relevant part of a patch originally posted here:
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https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html
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--- a/src/segment_juncs.cpp
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+++ b/src/segment_juncs.cpp
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@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
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typedef map<uint32_t, IntronMotifs> MotifMap;
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MotifMap ims;
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-
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- seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
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- seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
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-
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+
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+ typedef seqan::ModifiedString<
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+ seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,
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+ seqan::ModReverse> ConstDnaStringReverseComplement;
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+ ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
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+ ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
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+
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if (talkative)
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fprintf(stderr, "Collecting potential splice sites in islands\n");
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