Hi folks,
does anybody feel able to rather patch FactQC than reintroducing the
outdated API to htsjdk? 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:ti...@debian.org]
> Sent: 05 December 2016 14:34
> To: Simon Andrews <simon.andr...@babraham.ac.uk>; 846...@bugs.debian.org
> Cc: Vincent Danjean <vdanj...@debian.org>; Olivier Sallou
> <osal...@debian.org>; Charles Plessy <ple...@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 <notificati...@github.com>
> -----
>
> Date: Mon, 05 Dec 2016 06:18:16 -0800
> From: Daniel Gómez-Sánchez <notificati...@github.com>
> To: samtools/htsjdk <hts...@noreply.github.com>
> Cc: Andreas Tille <ti...@debian.org>, Author <aut...@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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