[Debian-med-packaging] Bug#846708: FastQC should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))

[Andreas Tille]

Hi Olivier,

On Mon, Dec 12, 2016 at 10:50:00AM +0000, olivier sallou wrote:
> > For me currently the most urgend Java tasks are:
> >
> >  * Upgrade BioJava 1.x series to its latest version
> >
> ithnk it is a difficult task (reason I did not update before). As version
> is quite old and nobody requested for an upgrade, I think we should keep
> old version or drop if no program depends on it

We have several rdepends of libbiojava-java.
 
> >  * Decide whether we can drop BioJava 3 since it conflicts
> >    with latest Jmol
> 
> keeping all old releases in sync with new dependencies can be quite time
> consuming. It is indeed worth the effort as new releases come out?

Nothing except med-bio-dev depends from libbiojava3-java so we could
drop this.
 
>  * Make BioJava 4.x compatible with Jmol 14
> >
> if upstream is working on it, let's wait if something comes.
> Is latest jmol in experimental?

Yes, latest jmol is in experimental and we should try to move it to
unstable as soon as possible.

Kind regards

     Andreas.
 
> > [1] https://lists.debian.org/debian-med/2016/12/msg00103.html

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