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
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