Re: About pysam
Hi Charles,
thanks for your comments. Just an explanation for my engagement. I'd like to
package
http://blends.debian.org/med/tasks/bio#gasic
http://blends.debian.org/med/tasks/bio#fitgpc
and my reasons are given in the according remarks there.
On Tue, Feb 11, 2014 at 01:43:16PM +0900, Charles Plessy wrote:
> Hi Andreas,
>
> I see that you are working on pysam, thank you for this !
>
> If you are wondering why it was never uploaded, it is because of the extensive
> code duplications with the samtools and tabix packages, which I could not try
> to resolve because of my lack of understanding on how the C code is used in
> python (in particular the relation between original code and the pxd or pyx
> files).
This became obvious in the according remarks you have given in debian/DRAFT.
> See also https://lists.debian.org/debian-med/2012/12/msg00112.html, it looks
> like Diane prepared a patch.
I can confirm that I checked out Diane's repository (Diane in CC) but I
do not see any patch for dealing with the code duplication. Diane, am I
missing something?
> Maybe I was overzealous, so if you feel like uploading, I definitely do not
> mind ! I am using Debian and pysam in one of my tutorials for transcriptome
> analysis (https://github.com/charles-plessy/tutorial/search?q=pysam&ref=cmdform).
My main goal was to get all tests working first. Once the tests are
properly working I could try to get rid of code copies and if I manage
to reproduce the tests this could be considered successful. I will keep
you updated about the progress.
Thanks for your input
Andreas.
--
http://fam-tille.de
Reply to: