Re: help needed for #733352

[Diane Trout <diane@ghic.org>]

On Thursday, April 10, 2014 15:30:21 Alex Mestiashvili wrote:
> Dear mentors,
> 
> I would greatly appreciate if somebody would help with the #733352, I've
> spent a couple of hours trying to resolve the issue but my cpp skills
> are rather poor.
> 
> Thank you,
> Alex

The patch below deals with one of the compile errors. I don't know if just 
hiding the const modifier is better than pushing const-ness further into 
tophat.

Unfortunately the next const error I get is even worse. Const-ness seems to 
get flipped between appendValue and trying to create a seqan::Gaps...

Diane


diff --git a/src/segment_juncs.cpp b/src/segment_juncs.cpp
index e3acc46..d73e0d6 100644
--- a/src/segment_juncs.cpp
+++ b/src/segment_juncs.cpp
@@ -2056,8 +2056,8 @@ void juncs_from_ref_segs(RefSequenceTable& rt,
 
     MotifMap ims;
 
-    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
-    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
+    seqan::DnaStringReverseComplement 
rev_donor_dinuc(const_cast<DnaString&>(donor_dinuc));
+    seqan::DnaStringReverseComplement 
rev_acceptor_dinuc(const_cast<DnaString&>(acceptor_dinuc));
 
     if (talkative)
         fprintf(stderr, "Collecting potential splice sites in islands\n");