[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))]

[Andrew Page]

Hi Sascha,
Thanks a million for patching this issue.
Regards,
Andrew

> On 8 Dec 2016, at 08:11, Andreas Tille <andreas at fam-tille.de> wrote:
> 
> Ahh, I've found branch 6_0_17_fix - I can do the merge ...
> 
> On Thu, Dec 08, 2016 at 09:06:52AM +0100, Andreas Tille wrote:
>> 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.
>> 
>> -- 
>> http://fam-tille.de
> 
> -- 
> http://fam-tille.de



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