Hi Sascha, Thanks a million for patching this issue. Regards, Andrew > On 8 Dec 2016, at 08:11, Andreas Tille <andr...@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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