[Biojava-l] AMOScmp problem

[Michael Heuer]

Hello Spencer, Janier

I suppose there will be a biojava-legacy 1.8.3 release as soon as we figure
out the configuration changes necessary to support the release process due
to the svn --> github switch.

   michael


On Tue, May 7, 2013 at 3:27 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> Janier,
>
> Biojava 1 is only receiving bug fixes currently. There are a couple changes
> since 1.8.2, which can be incorporated by using the 1.8.3-SNAPSHOT from the
> maven repository. There is no release date for 3.0.6 yet, but again you can
> use the latest SNAPSHOT from maven if you need new features.
>
>
> -Spencer
>
>
> On Tue, May 7, 2013 at 12:31 PM, Janier J. Ramírez <
> jjramirez at estudiantes.uci.cu> wrote:
>
> > When Biojaba 1.8.3 will be released ?
> >
> > cheers
> >
> >
> > ----- Mensaje original -----
> > De: "Spencer Bliven" <sbliven at ucsd.edu>
> > Para: "Janier J. Ramírez" <jjramirez at estudiantes.uci.cu>
> > CC: "Biojava-l at lists.open-bio.org" <biojava-l at lists.open-bio.org>
> > Enviados: Martes, 7 de Mayo 2013 21:00:44
> > Asunto: Re: [Biojava-l] AMOScmp problem
> >
> >
> >
> >
> > Hey Janier,
> >
> > Sorry no one responded to your last question. Biojava doesn't currently
> do
> > full-blown assembly, although the basic pairwise alignment algorithms are
> > there.
> >
> > I've never used AMOScmp myself, and so can't advise you on your problem.
> >
> > -Spencer
> >
> >
> >
> >
> > On Mon, May 6, 2013 at 6:41 PM, Janier J. Ramírez <
> > jjramirez at estudiantes.uci.cu > wrote:
> >
> >
> > Hi !
> > I'm interested in the reference based assemblies using AMOScmp, I used
> > tarchive2Amos to obtain the .afg file an I have the reference (.fasta
> > file), but the problem is that the output files (.fasta and .contig) are
> > empty. In the log files there is a WARNING which says that the file
> FRG.ifo
> > was not found and could not retrieve mate pairs information.
> > This is very important to me and won't have many time for that.
> >
> > Please any sugestion for this proble ?
> >
> > Thanks in advance
> >
> > --
> >
> >
> > Universidad de las Ciencias Informáticas
> > Janier J. Ramírez Landaburo
> > Facultad - 6
> > Tel-837-3121
> > http://www.uci.cu
> >
> > _______________________________________________
> > Biojava-l mailing list - Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> > http://www.uci.cu
> >
>
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