Patching fermi-lite to enable packaging libSeqLib
Hi,
to package the latest version of freebayes (version 1.0.2 is in new,
latest upstream is 1.1) a new library libSeqLib is needed. I started
with the packaging[1] and managed to build it without the patched code
copy of fermi-lite. SeqLib upstream was doing some patching since bwa
and fermi-lite are using the same variable bseq1_t which is defined
differently. I patched fermi-lite in Git by renaming it to fml_seq1_t
(and some other code changes + additions by libSeqLib author).
I have not yet uploaded fermi-lite since ariba depends from fermi-lite
and needs to be adapted to the patched fermi-lite (as I did in commit
92be90993f020d5d2395f083a42a48cebd5bab49) and wanted to discuss this
here. While I have opened an issue at Github for fermi-lite[2] there
was no response until now.
What do you suggest to do? My proposal would be to upload the patched
fermi-lite as well as the patched ariba to experimental (which is
advisable in freeze anyway) and keep on working with libseqlib. Once
Stretch is released and the Buster release cycle has started we could
make up our mind again whether we want to carry the patched fermi-lite
along or what might be a better solution.
Any other options?
Kind regards
Andreas.
[1] https://anonscm.debian.org/git/debian-med/libseqlib.git
[2] https://github.com/lh3/fermi-lite/issues/5
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