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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<tr><td><span title='2024-03-04 15:49:30 +0100'>2024-03-04</span></td><td><a href='/guix/commit/gnu/packages/dezyne.scm?id=ff3c592710120de2ac05972a85892cdf4b1db101'>gnu: dezyne: Update to 2.18.1.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/packages/dezyne.scm (dezyne): Update to 2.18.1.

Change-Id: I8750035237cd0784ab4244af034dc28549e54dd5
</span></span></td><td>Janneke Nieuwenhuizen</td></tr>
<tr><td><span title='2023-12-15 12:01:57 +0100'>2023-12-15</span></td><td><a href='/guix/commit/gnu/packages/dezyne.scm?id=05c2afc5cb29399465def02a1c1dff14609aadda'>gnu: dezyne: Update to 2.18.0.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/packages/dezyne.scm (dezyne): Update to 2.18.0.
[inputs]: Add boost.
[arguments]: Change assoc-ref memes to use gexps.

Change-Id: I1212de52db6c2b07122e756c68597b1f8ddbb313
</span></span></td><td>Janneke Nieuwenhuizen</td></tr>
<tr><td><span title='2023-12-15 12:01:55 +0100'>2023-12-15</span></td><td><a href='/guix/commit/gnu/packages/dezyne.scm?id=e11b57de7368315d3fdc038c904e9d0e58db22d7'>gnu: Add scmackerel.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/packages/dezyne.scm (scmackerel): New variable.
</span></span></td><td>Janneke Nieuwenhuizen</td></tr>
<tr><td><span title='2023-11-08 16:48:51 +0100'>2023-11-08</span></td><td><a href='/guix/commit/gnu/packages/dezyne.scm?id=00fd6895322d0b1fd774e79494cfcad721b50b8d'>gnu: dezyne: Update to 2.17.8.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/packages/dezyne.scm (dezyne): Update to 2.17.8.

Change-Id: I0982bb987986e59ac5e5d5d874147ec684a27101
</span></span></td><td>Janneke Nieuwenhuizen</td></tr>
<tr><td><span title='2023-10-30 10:14:37 +0100'>2023-10-30</span></td><td><a href='/guix/commit/gnu/packages/dezyne.scm?id=db6b00795a21cce987c844bc440081d06f99ce5e'>gnu: dezyne: Update to 2.17.7.</a><span class='msg-avail'>...<span class='msg-tooltip'>* gnu/packages/dezyne.scm (dezyne): Update to 2.17.7.

Change-Id: I278e4e17f49b15600689cebda04298de6bbc8a65
</span></span></td><td>Janneke Nieuwenhuizen</td></tr>