Re: [Seqan-dev] help needed to build tophat with seqan >=1.4

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

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);