[Debian-med-packaging] Bug#846671: Artemis should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))]

[Andrew Page]

Hi Andreas,
Thanks for letting us know.  We are actively trying to hire a Java developer who will take over the maintenance and development of Artemis. So unfortunately it will be at least a few months before we will have anyone in post to work on it.  If you happen to know of anyone looking for a job, please send them our way!
Regards,
Andrew



> On 5 Dec 2016, at 14:40, Andreas Tille <tille at debian.org> wrote:
> 
> Hi,
> 
> after uploading htsjdk 2.7.0 Artemis failed to build from source[1].  I
> relised that the file src/main/java/htsjdk/samtools/SAMFileReader.java
> was removed from htsjdk source and assumed that this was by accident.
> However, upstream has dropped this interface intentionally as you can
> read below.  In issue #767[2] an htsjdk author gives advise to use the
> new API version.
> 
> Kind regards
> 
>       Andreas.
> 
> 
> [1] https://bugs.debian.org/846671
> [2] https://github.com/samtools/htsjdk/issues/767
> 
> 
> ----- Forwarded message from Daniel Gómez-Sánchez <notifications at github.com> -----
> 
> Date: Mon, 05 Dec 2016 06:18:16 -0800
> From: Daniel Gómez-Sánchez <notifications at github.com>
> To: samtools/htsjdk <htsjdk at noreply.github.com>
> Cc: Andreas Tille <tille at debian.org>, Author <author at noreply.github.com>
> Subject: Re: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767)
> 
> The file was removed in #699 because it was deprecated. I guess that either 1) fastqc/artemis should be updated to use the new API version, or 2) the classpath for them in Debian should include an older version.
> 
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> https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910
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