[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))

[olivier sallou]

Hi,
I have uploaded biojava, do you still need i have a look? Seems sasha did
the job.. :-)

Olivier

Le lun. 5 déc. 2016 22:24, olivier sallou <olivier.sallou at gmail.com> a
écrit :

> Le lun. 5 déc. 2016 à 17:00, Andreas Tille <tille at debian.org> a écrit :
>
> Hi folks,
>
> does anybody feel able to rather patch FactQC than reintroducing the
> outdated API to htsjdk?
>
>
> I have some work on biojava which requires quite a lot of patch updates
> for the moment, but after this I can try to have a look
>
>
>
> Olivier
>
>
>   Same is valid for Artemis.  I admit while
> reintroducing the old API works I'd consider this only the second best
> solution for the problem.
>
> Kind regards
>
>      Andreas.
>
> On Mon, Dec 05, 2016 at 02:47:16PM +0000, Simon Andrews wrote:
> > Hi Andreas,
> >
> > None of the official FastQC releases has ever used htsjdk - we've been
> using the older picard sam.jar API which is substantially different (htsjdk
> is a major rewrite and restructure - it's not just a version update).
> Internally we have tried the new API, and although it works OK it also
> imposes a restriction on the use of java >=8 which wasn't present in the
> old version and which would break a lot of our existing installations.
> We're therefore not keen to make that change yet - especially since the old
> API works just fine for all the types of data we support.
> >
> > If you're packaging this for Debian and wanted to move to htkjdk then
> it's pretty trivial to patch this.  It takes a small boilerplate change to
> the BAM opening and reading code in the BAMFile class, and a change to the
> classpath in the launcher script (which I guess you're already doing).
> We'll probably move to the new API eventually, but at the moment the
> downsides outweigh the benefits for us.
> >
> > Cheers
> >
> > Simon.
> >
> >
> >
> >
> > -----Original Message-----
> > From: Andreas Tille [mailto:tille at debian.org]
> > Sent: 05 December 2016 14:34
> > To: Simon Andrews <simon.andrews at babraham.ac.uk>; 846708 at bugs.debian.org
> > Cc: Vincent Danjean <vdanjean at debian.org>; Olivier Sallou <
> osallou at debian.org>; Charles Plessy <plessy at debian.org>
> > Subject: FastQC should adapt to new htsjdk API which has dropped
> SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version
> 2.7.0 (#767))
> >
> > Hi Simon,
> >
> > after uploading htsjdk 2.7.0 FastQC 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/846708
> > [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 -----
> >
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