[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 07:01:19AM +0000, olivier sallou wrote:
> I have uploaded biojava, do you still need i have a look? Seems sasha did
> the job.. :-)

Yes, thanks to Sascha for taking over.

For me currently the most urgend Java tasks are:

 * Upgrade BioJava 1.x series to its latest version
 * Decide whether we can drop BioJava 3 since it conflicts
   with latest Jmol
 * Make BioJava 4.x compatible with Jmol 14
 * Care for latest version of Jalview

There are two threads about Jmol on the Debian Med list currently and the
latest status is here[1].  It would be helpful to hear your opinion about
BioJava.

Kind regards

      Andreas.

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

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