Hello, 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. 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. At that point I gave up, and just built a package for my lab. 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). Diane [1] my patch https://github.com/detrout/tabix/tree/dynamic-makefile [2] https://github.com/attractivechaos/klib On Tuesday, February 11, 2014 09:08:14 Andreas Tille wrote: > 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. -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/2910761.drh1LTaiLj@myrada
