academic/tophat/fix_build_w_seqan1.4.patch


1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24

Description: Resolves build failure with seqan 1.4
Bug-Closed: http://bugs.debian.org/733352
Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
--- 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");