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.
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
