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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50567e9376986f'>build: Add a Guile custom test driver using SRFI-64.</a><span class='msg-avail'>...</span></td><td>Mathieu Lirzin</td></tr>
<tr><td><span title='2015-09-24 21:21:02 +0200'>2015-09-24</span></td><td><a href='/guix/commit/tests/build-utils.scm?id=12cd4dd3a9052491e3912ffeecbe8854ea9b971a'>tests: Unset 'LOCPATH' before running bootstrap program.</a><span class='msg-avail'>...</span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2014-09-13 21:53:21 -0500'>2014-09-13</span></td><td><a href='/guix/commit/tests/build-utils.scm?id=de61113857d3ebda1f4557c5a8f6bffe63100060'>utils: Allow wrap-program to be called multiple times.</a><span class='msg-avail'>...</span></td><td>Eric Bavier</td></tr>
<tr><td><span title='2013-02-01 13:16:45 +0100'>2013-02-01</span></td><td><a href='/guix/commit/tests/build-utils.scm?id=0bdba772ca2167cdd3acaed81ca8667cb78b266c'>Augment `.dir-locals.el'.</a><span class='msg-avail'>...</span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2013-01-06 00:47:50 +0100'>2013-01-06</span></td><td><a href='/guix/commit/tests/build-utils.scm?id=233e76769ae3a438bff7117c68f2c88739a28db0'>Update license headers.</a><span class='msg-avail'>...</span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2012-10-16 23:01:01 +0200'>2012-10-16</span></td><td><a href='/guix/commit/tests/build-utils.scm?id=91133c2d71960644eeba749027a4141c098ea64c'>utils: Add `fold-port-matches' and `remove-store-references'.</a><span class='msg-avail'>...</span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2012-07-05 00:13:30 +0200'>2012-07-05</span></td><td><a href='/guix/commit/tests/build-utils.scm?id=b0e0d0e99fab04fc374061adc7386b0f3f4b18c5'>Add builder-side utilities for phases, stream editing, &amp; co.</a><span class='msg-avail'>...</span></td><td>Ludovic Courtès</td></tr>