Bug#753485: Status of samtools
Hi, Andreas Only some parts of the patches were accepted. https://github.com/samtools/htslib/commit/e8806c71f3408d2cbff8caa8df17eef848d33a02 The pull request (https://github.com/samtools/htslib/pull/99/) contains two patches, one dealing with endianness related issues and the other one dealing with unaligned access issues. Most of the changes that fix endianness related issues were accepted, except the ones that fix detection of system endiannes on mips (mips big endian is not detected). This is still an issue in htslib and consequently in samtools. I will contact upstream to see if they would be willing to reconsider including these changes at least. On the other hand, most of the changes regarding unaligned access issues weren't accepted and upstream developers suggested this should be fixed in another way, that is by implementing a standard set of functions for accessing memory in both cases (where architecture supports unaligned access and for architectures which don't) and using these functions for accessing memory throughout the code. One of the samtools developers has done some work to implement this (https://github.com/jkbonfield/htslib/tree/SPARC), but changes from this experimental branch haven't been merged to the main branch yet. Best Regards Aleksandar Zlicic
Bug#753485: [Debian-med-packaging] Bug#753485: Status of samtools
Le Fri, Oct 10, 2014 at 06:42:34PM +, Aleksandar Zlicic a écrit : On the other hand, most of the changes regarding unaligned access issues weren't accepted and upstream developers suggested this should be fixed in another way, that is by implementing a standard set of functions for accessing memory in both cases (where architecture supports unaligned access and for architectures which don't) and using these functions for accessing memory throughout the code. One of the samtools developers has done some work to implement this (https://github.com/jkbonfield/htslib/tree/SPARC), but changes from this experimental branch haven't been merged to the main branch yet. Hi Aleksandar and Andreas, I was contacted by one of the upstream developers about getting access to a SPARC porter box, and just asked for it to the DSA. Let's see how it goes. Cheers, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#753485: [Debian-med-packaging] Bug#753485: Status of samtools
Le Wed, Sep 03, 2014 at 09:36:02AM +0200, Andreas Tille a écrit : currently we have samtools/0.1.19-1 with bug #753485 tagged patch but are missing a confirmation from upstream for this patch. We also have a new upstream version of samtools (1.0) in experimental (that might or might have not applied this patch). Can anybody give some status update what the plan for samtools regarding the Jessie release might be? Hi Andreas, unless there are major problems of backwards compatibility, I think that we should release with the new version of SAMtools based on the HTSlib, which introduces support for the new CRAM format. I uploaded version 1.0 in experimental for only two reasons: - first, I wanted to test it more, and give opportunity to others to test it as well, - second, I was not sure if dynamic linking was fully supported since it requires patching the makefile. My current plan is to wait a bit more if there is a new upstream version that would solve all of this (and include our patches that I forwarded on GitHub). But if such an update does not come soon, then I (or others) should upload samtools to Unstable. Regarding the portability, I do not know if the 1.x line will induce regressions or not, but if this is the case, I would like to solve the problem by dropping support for the failing architectures, unless the upstream developers show interest for them. Have a nice day, -- Charles -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#753485: Status of samtools
Hi, currently we have samtools/0.1.19-1 with bug #753485 tagged patch but are missing a confirmation from upstream for this patch. We also have a new upstream version of samtools (1.0) in experimental (that might or might have not applied this patch). Can anybody give some status update what the plan for samtools regarding the Jessie release might be? Alexander, in [1] you wrote: I am currently adapting changes to the latest version of samtools. When I'm done I will contact upstream. Did you succeeded to contact upstream or should we ping again? Thanks a lot to Alexander for his effort to provide a patch Andreas. [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=753485#27 -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
