[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))

[Andreas Tille]

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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