Re: [Seqan-dev] help needed to build tophat with seqan >=1.4
Hi Alex,
attached is a patch that circumvents the problems in TopHat with SeqAn 1.4.1.
I had problems building tophat from your git repository so I had to hack the Makefiles a bit.
Do not hesitate to send another email in case the problem remains.
HTH,
Manuel
________________________________________
From: Alex Mestiashvili [alex@biotec.tu-dresden.de]
Sent: Friday, July 04, 2014 11:31 AM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] help needed to build tophat with seqan >=1.4
Dear SeqAn Developers,
We distribute SeqAn in Debian and recently packaged SeqAn version 1.4.
However after switching to the new version, tophat [0] fails to build.
Here are the build errors which we couldn't solve:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=733352#45
It would be really great if you would give us a hint.
Debianized tophat lives here:
http://anonscm.debian.org/gitweb/?p=debian-med/tophat.git
Thank you,
Alex
[0] http://ccb.jhu.edu/software/tophat/index.shtml
Please also CC to 733352@bugs.debian.org
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diff --git a/src/segment_juncs.cpp b/src/segment_juncs.cpp
index e3acc46..383394b 100644
--- a/src/segment_juncs.cpp
+++ b/src/segment_juncs.cpp
@@ -2055,9 +2055,12 @@ void juncs_from_ref_segs(RefSequenceTable& rt,
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 +2605,13 @@ void gappedAlignment(const seqan::String<char>& read,
{
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);