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

[olivier sallou]

Le jeu. 8 déc. 2016 01:04, Sascha Steinbiss <satta at tetrinetsucht.de> a
écrit :

> Hi Andreas and Andrew,
>
> to address this problem I have taken a shot at patching Debian’s Artemis
> to use the new htsjdk API, avoiding SAMFileReader and using the
> SamReaderFactory instead. This fixed the FTBFS for me.
> I tested BAM file reading by opening MAL1.embl.gz from the test/data
> directory and adding MAL1_8h.bam via ‘File->Read BAM/VCF...'. One of the
> genes has some mapped reads that are indeed shown. Comparing the displayed
> pile of mapped reads to the one shown by the recent Artemis version I have
> on Mac OS X, the result seems to be correct, but given my lack of practical
> experience with the BAM/VCF/‘anything-to-do-with-reads' components of
> Artemis I can’t say if I caught everything.
>
If you compile and can view the bam, i would consider the api call is
correct and so your patch

Olivier




> I also updated the Debian version to 16.0.17, the latest release from
> Sanger. This allowed me to drop a couple of patches that I already merged
> earlier with my part-time-upstream hat on.
> For now I have pushed my work into the ’6_0_17’ branch in git and I would
> like to kindly ask for some more testing. I don’t have suitable test data
> here and don’t really feel like an expert to test the right usage patterns.
>
> Cheers
> Sascha
>
> > On 5 Dec 2016, at 15:56, Andrew Page <ap13 at sanger.ac.uk> wrote:
> >
> > 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.
> >>
> >> --
> >> You are receiving this because you authored the thread.
> >> Reply to this email directly or view it on GitHub:
> >> https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910
> >>
> >> ----- End forwarded message -----
> >>
> >> --
> >> http://fam-tille.de
> >>
> >> ----- End forwarded message -----
> >>
> >> --
> >> http://fam-tille.de
> >
> >
> >
> > --
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> > Limited, a charity registered in England with number 1021457 and a
> > company registered in England with number 2742969, whose registered
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> >
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