[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))

[Simon Andrews]

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.

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