[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))]

[Andreas Tille]

Hi Sascha,

On Thu, Dec 08, 2016 at 01:04:34AM +0100, Sascha Steinbiss wrote:
> to address this problem I have taken a shot at patching Debian’s Artemis to use the new htsjdk API, avoiding SAMFileReader and using the SamReaderFactory instead. This fixed the FTBFS for me.
> I tested BAM file reading by opening MAL1.embl.gz from the test/data directory and adding MAL1_8h.bam via ‘File->Read BAM/VCF...'. One of the genes has some mapped reads that are indeed shown. Comparing the displayed pile of mapped reads to the one shown by the recent Artemis version I have on Mac OS X, the result seems to be correct, but given my lack of practical experience with the BAM/VCF/‘anything-to-do-with-reads' components of Artemis I can’t say if I caught everything.

Thanks for this.  That's probably very helpful for upstream as well as
the Debian package.
 
> I also updated the Debian version to 16.0.17, the latest release from Sanger. This allowed me to drop a couple of patches that I already merged earlier with my part-time-upstream hat on.
> For now I have pushed my work into the ’6_0_17’ branch in git and I would like to kindly ask for some more testing. I don’t have suitable test data here and don’t really feel like an expert to test the right usage patterns. 

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.  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.

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.

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.

Thanks again for your very helpful contribution

     Andreas.

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