Re: help needed for #733352
On 04/11/2014 12:29 AM, Diane Trout wrote: 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_castDnaString(donor_dinuc)); +seqan::DnaStringReverseComplement rev_acceptor_dinuc(const_castDnaString(acceptor_dinuc)); if (talkative) fprintf(stderr, Collecting potential splice sites in islands\n); Hi Diane, Cool, thank you a lot, we are one step further! Still I think that the upstream should try to fix it or we should reintroduce back SeqAn-1.3. Best regards, Alex -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/5347b9a7.1020...@biotec.tu-dresden.de
Re: help needed for #733352
Hi Diane, On Thu, Apr 10, 2014 at 03:29:38PM -0700, Diane Trout wrote: 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. Great. At least I have injected the patch into the Git repository. Many thanks Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140411214740.gc8...@an3as.eu
Re: help needed for #733352
Hi Alex, On Fri, Apr 11, 2014 at 11:45:11AM +0200, Alex Mestiashvili wrote: Cool, thank you a lot, we are one step further! Perhaps it makes sense to contact upstream and propose the patch (in Git) and ask for further help. Would you volunteer to do this? Still I think that the upstream should try to fix it or we should reintroduce back SeqAn-1.3. This should be the last resort - but yes, if nothing else helps we should probably do this. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140411215215.gd8...@an3as.eu
Re: help needed for #733352
On 04/11/2014 11:52 PM, Andreas Tille wrote: Hi Alex, On Fri, Apr 11, 2014 at 11:45:11AM +0200, Alex Mestiashvili wrote: Cool, thank you a lot, we are one step further! Perhaps it makes sense to contact upstream and propose the patch (in Git) and ask for further help. Would you volunteer to do this? Done: https://groups.google.com/forum/#!topic/tuxedo-tools-users/TCyKinjd2Wc though my English skills for a polite message are not very good :) Forgot to CC to debian-med, but if there will be any activity I'll forward. Still I think that the upstream should try to fix it or we should reintroduce back SeqAn-1.3. This should be the last resort - but yes, if nothing else helps we should probably do this. Kind regards Andreas. but may be than we simply can leave seqan-1.3 in the tophat's source ? I think at some point tophat will switch to seqan-1.4 too ( probably when seqan devs vill release 1.6 :) ), but we can win the time and have working tophat in the distribution before this happens. Best regards, Alex -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/53486fe2.2010...@biotec.tu-dresden.de
