This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4.
This is the relevant part of a patch originally posted here:
https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html

--- 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");
 
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