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The upstream code attemps to use a specific commit id of bwa, which corresponds
to the tip of the Apache2 branch in the Github repository of bwa.
Unfortunately this is somehow different from the version of bwa that is shipped
in Debian. I have opened an issue in the Github repository of gatk-bwamem-jni
to ask if the developers might consider syncing with the master branch of bwa.
Until this could be done, I am embedding the contents of the Apache2 branch tip
in gatk-bwamem using by designing a MUT package. I have added the patches of
the bwa Debian package in the current one.
-- Pierre Gruet <pgt@debian.org> Tue, 05 Jul 2022 22:58:02 +0200
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