HTSlib code copy in python-pysam.

[Charles Plessy <plessy@debian.org>]

Le Tue, Aug 19, 2014 at 07:27:48PM +0000, Andreas Tille a écrit :
> This is an automated email from the git hooks/post-receive script.
> 
> tille pushed a change to branch upstream
> in repository python-pysam.
> 
>       from  a757e53   Imported Upstream version 0.7.7
>        new  547982f   Imported Upstream version 0.8.0
… 
> Summary of changes:
>  INSTALL                                            |    13 +
>  MANIFEST.in                                        |    82 +-
>  PKG-INFO                                           |     4 +-
>  README.rst                                         |    27 +
>  doc/api.rst                                        |     3 +-
>  doc/conf.py                                        |    14 +-
>  doc/developer.rst                                  |    48 +-
>  doc/faq.rst                                        |    10 +-
>  doc/glossary.rst                                   |     4 +-
>  doc/{contents.rst => index.rst}                    |     4 +-
>  doc/release.rst                                    |    26 +
>  doc/usage.rst                                      |    23 +-
>  {tabix => htslib}/__init__.py                      |     0
>  htslib/bgzf.c                                      |  1085 +
>  htslib/bgzip.c                                     |   283 +
>  htslib/config.h                                    |     3 +

(etc)

Hi Andreas,

I guess you spotted the code copy of the HTSlib in python-pysam ?

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…

I opened the following issue on GitHub's upstream tracker.

    https://github.com/pysam-developers/pysam/issues/34

Have a nice day,

-- 
Charles