[Debian-med-packaging] Bug#753485: Bug#753485: Status of samtools

[Charles Plessy]

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