Hi Diane,
thanks for your update.
On Tue, Feb 11, 2014 at 11:07:39AM -0800, Diane Trout wrote:
> I made an effort to try and clean up the code duplication mess of pysam /
> samtools. My first attempt was to provide upstream with a suggestion on how
> to
> build tabix as a shared library.[1] (As a step toward convincing them to make
> samtools build libbam as a shared library)
>
> However I don't think they took advantage of it.
After I inspected the code I also came to the conclusion that only
upstream could find a sensible way to make profit from official samtools
code instead of the copy.
> I then discovered a worse code duplication problem in pysam & samtools with
> the attractivechaos/klib "library" [2] as far as I can tell a number of
> bioinformatics packages just periodically copy the source from that
> repository
> into their own projects.
+1
> At that point I gave up, and just built a package for my lab.
And I decided to upload to new and see what ftpmaster might think. I
need python-pysam for (at least) two other packages. So I simply tried.
> I recall seeing something about an improved libbam or samtools? (I can't
> quickly find Charles' posts on the list about it though)
>
> I could try cleaning the package up a bit for Debian, but I don't think I
> could resolve the code duplication issues. (I could at least get the
> copyright
> / README.Debian to acknowledge and point to where all the code is being
> duplicated from).
I hope I got the copyright right. Any enhancement in
git://anonscm.debian.org/debian-med/python-pysam.git
would be perfectly welcome at any time.
Kind regards
Andreas.
> [1] my patch https://github.com/detrout/tabix/tree/dynamic-makefile
> [2] https://github.com/attractivechaos/klib
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