Re: HTSlib code copy in python-pysam.
Hi Charles,
On Wed, Aug 20, 2014 at 06:53:49AM +0900, Charles Plessy wrote:
>
> I guess you spotted the code copy of the HTSlib in python-pysam ?
Well, the code copy existed from the beginning of maintaining
python-pysam (at this time compared to the predecessor of htslib). At
this time we decided that it is to hard to link dynamically.
> In theory, it should be easier to build python-pysam on the system's
> copy, compared to the previsous situation with libbam, because
> the HTSlib allows for dynamic linking.
>
> In practice, I do not know how to do it with python modules…
Thanks for the hint - we might rethink the current packaging. However,
my actual approach is targeting at an upgrade and recheck whether we
could fix #753490 (I somehow missed this bug with patch and it does not
apply to the new version ... :-()
> I opened the following issue on GitHub's upstream tracker.
>
> https://github.com/pysam-developers/pysam/issues/34
Cool. May be we get some help from upstream.
Any help / enhancement is more than welcome. BTW, my push was more an
accident since I wanted to write `quilt push` and instead issued `git
push`. The current status in Git is not functional and I have some
local changes here which also do not yet lead to a working package since
the test suite fails. If anybody is interested - I'd be more than happy
to hand over this task to somebody else (as always ;-)).
Thanks again for the hint
Andreas.
--
http://fam-tille.de
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