Re: Replacement of SAMtools 0.19 by SAMtools 1.0.

[Olivier Sallou <olivier.sallou@irisa.fr>]

----- Mail original -----
> De: "Charles Plessy" <plessy@debian.org>
> À: debian-med@lists.debian.org
> Envoyé: Lundi 18 Août 2014 08:05:00
> Objet: Replacement of SAMtools 0.19 by SAMtools 1.0.
> 
> Dear all,
> 
> A few days ago, SAMtools was updated to upstream version 1.0 and is now built
> on the HTSlib.

Hi Charles,

do you know, by chance, what is the difference between samtools and the net.sf.samtools Java lib of picard-tools ?
They look quite the same.

The HTSlib fix an issue forigv (on SAMFileWriterFactory), but SAMFileWriterFactory class in picard-tools is not the same than the one in HTSlib.

Thanks

Olivier


> 
> With such an extensive change, on might worry about subtle breakages of
> existing
> toolschains.
> 
> SAMtools users are welcome to try to build packages from Git
> (http://anonscm.debian.org/cgit/debian-med/samtools.git) and to report
> problems.
> 
> I hope to updload an update to Experimental after the HTSlib 1.0 makes it in
> our archive (and it is not yet uploaded to NEW…).
> 
> Have a nice day,
> 
> Charles
> 
> --
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
> 
> 
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