Le jeu. 8 déc. 2016 01:04, Sascha Steinbiss <sa...@tetrinetsucht.de> a écrit :
> Hi Andreas and Andrew, > > 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. > If you compile and can view the bam, i would consider the api call is correct and so your patch Olivier > 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. > > Cheers > Sascha > > > On 5 Dec 2016, at 15:56, Andrew Page <a...@sanger.ac.uk> wrote: > > > > Hi Andreas, > > Thanks for letting us know. We are actively trying to hire a Java > developer who will take over the maintenance and development of Artemis. So > unfortunately it will be at least a few months before we will have anyone > in post to work on it. If you happen to know of anyone looking for a job, > please send them our way! > > Regards, > > Andrew > > > > > > > >> On 5 Dec 2016, at 14:40, Andreas Tille <ti...@debian.org> wrote: > >> > >> Hi, > >> > >> after uploading htsjdk 2.7.0 Artemis failed to build from source[1]. I > >> relised that the file src/main/java/htsjdk/samtools/SAMFileReader.java > >> was removed from htsjdk source and assumed that this was by accident. > >> However, upstream has dropped this interface intentionally as you can > >> read below. In issue #767[2] an htsjdk author gives advise to use the > >> new API version. > >> > >> Kind regards > >> > >> Andreas. > >> > >> > >> [1] https://bugs.debian.org/846671 > >> [2] https://github.com/samtools/htsjdk/issues/767 > >> > >> > >> ----- Forwarded message from Daniel Gómez-Sánchez < > notificati...@github.com> ----- > >> > >> Date: Mon, 05 Dec 2016 06:18:16 -0800 > >> From: Daniel Gómez-Sánchez <notificati...@github.com> > >> To: samtools/htsjdk <hts...@noreply.github.com> > >> Cc: Andreas Tille <ti...@debian.org>, Author <aut...@noreply.github.com > > > >> Subject: Re: [samtools/htsjdk] SAMFileReader vanished in Version 2.7.0 > (#767) > >> > >> The file was removed in #699 because it was deprecated. I guess that > either 1) fastqc/artemis should be updated to use the new API version, or > 2) the classpath for them in Debian should include an older version. > >> > >> -- > >> You are receiving this because you authored the thread. > >> Reply to this email directly or view it on GitHub: > >> https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910 > >> > >> ----- End forwarded message ----- > >> > >> -- > >> http://fam-tille.de > >> > >> ----- End forwarded message ----- > >> > >> -- > >> http://fam-tille.de > > > > > > > > -- > > The Wellcome Trust Sanger Institute is operated by Genome Research > > Limited, a charity registered in England with number 1021457 and a > > company registered in England with number 2742969, whose registered > > office is 215 Euston Road, London, NW1 2BE. > > > > _______________________________________________ > > Debian-med-packaging mailing list > > debian-med-packag...@lists.alioth.debian.org > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > >
