This is an automated email from the git hooks/post-receive script. malex-guest pushed a commit to branch master in repository tophat.
commit dfb42f593b1459c3f06b145956a769a7c51b62db Author: Alexandre Mestiashvili <[email protected]> Date: Mon Jul 7 11:39:14 2014 +0200 d/patches: added patch from Manuel Holtgrewe resolving #733352 removed const_ness_part1.patch as the new patch solves the problem completely --- debian/patches/fix4seqan1.4.patch | 40 +++++++++++++++++++++++++++++++++++++++ debian/patches/series | 2 +- 2 files changed, 41 insertions(+), 1 deletion(-) diff --git a/debian/patches/fix4seqan1.4.patch b/debian/patches/fix4seqan1.4.patch new file mode 100644 index 0000000..e9091be --- /dev/null +++ b/debian/patches/fix4seqan1.4.patch @@ -0,0 +1,40 @@ +Author: Manuel Holtgrewe <[email protected]> +Bug-Closed: http://bugs.debian.org/733352 +Descriptions: resolves build failure with seqan 1.4 +--- tophat.orig/src/segment_juncs.cpp ++++ tophat/src/segment_juncs.cpp +@@ -2055,10 +2055,13 @@ + 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"); + +@@ -2602,12 +2605,14 @@ + { + const Score<int> globalScore(0, -5, -1, -10); // (match, mismatch, gapextend, gapopen) + Align<String<char> > align; +- appendValue(rows(align), read); + ++ resize(rows(align), 2); ++ setSource(row(align, 0), const_cast<seqan::String<char> &>(read)); ++ + String<char> genomicSequence; + assign(genomicSequence, leftReference); + append(genomicSequence, rightReference); +- appendValue(rows(align), genomicSequence); ++ setSource(row(align, 0), genomicSequence); + // int score = globalAlignment(align, globalScore); + + Row<Align<String<char> > >::Type& row0 = row(align, 0); diff --git a/debian/patches/series b/debian/patches/series index 8b5c581..2ef3aff 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,3 @@ +fix4seqan1.4.patch fix_includes_path.patch bashism_in_shell_script.patch -const_ness_part1.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/tophat.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
