[Debian-med-packaging] Bug#846671: Bug#846671: Artemis should adapt to new htsjdk API which has dropped SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 (#767))]

[Sascha Steinbiss]

Hi all,

[...]
> I do not find branch 6_0_17 and I do not even think that we need this
> extra branch.  I'd recommend to use master and as far as I understood
> Olivier's comment your test should be sufficient.

Sure. Sorry for the branch naming mixup, it was a little late ;)

> I personally also do not feel able to test but I think under this
> circumstances its a sensible approach to upload and thus enable some
> wider testing rather than expecting people to build a separate
> branch.

Agreed. I just didn't want to break functionality I am not familiar
with, as I never used this part of Artemis myself (still better than
having Artemis removed in the first place though).

> I have unmerged the fastqc and artemis bug since it seems we will be
> able to fix both packages without reintroducing the old API to htsjdk.

Good to hear!

> So I'd recommend you merge your separate branch back to master and push
> these changes.  I can have another look (I'm also currently bumping
> debhelper to compat level 10 and mark those watch files I have verified
> to version=4 just to have a marker even if version=3 works as well). I'm
> perfectly fine if you upload yourself without my additional inspection.

I see -- thanks for the housekeeping work and the upload.
As far as Artemis is concerned, it would have been a shame to have it
drop out of stretch for something like this bug.

@Andrew: I would have prepared a PR againsr sanger-pathogens/Artemis as
well but due to the level of divergence between Sanger's and Debian's
version it wasn't trivial to reduce it to a concise and short patch.
I recommend that the new Artemis developer (fingers crossed) should take
a look at Debian's full patch set, which, among other things, introduces
support for more recent dependencies (e.g. htsjdk).

Kind regards
Sascha