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 <[email protected]>
-----
Date: Mon, 05 Dec 2016 06:18:16 -0800
From: Daniel Gómez-Sánchez <[email protected]>
To: samtools/htsjdk <[email protected]>
Cc: Andreas Tille <[email protected]>, Author <[email protected]>
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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