Le lun. 5 déc. 2016 à 17:00, Andreas Tille <ti...@debian.org> a écrit :
> Hi folks, > > does anybody feel able to rather patch FactQC than reintroducing the > outdated API to htsjdk? I have some work on biojava which requires quite a lot of patch updates for the moment, but after this I can try to have a look Olivier > Same is valid for Artemis. I admit while > reintroducing the old API works I'd consider this only the second best > solution for the problem. > > Kind regards > > Andreas. > > On Mon, Dec 05, 2016 at 02:47:16PM +0000, Simon Andrews wrote: > > Hi Andreas, > > > > None of the official FastQC releases has ever used htsjdk - we've been > using the older picard sam.jar API which is substantially different (htsjdk > is a major rewrite and restructure - it's not just a version update). > Internally we have tried the new API, and although it works OK it also > imposes a restriction on the use of java >=8 which wasn't present in the > old version and which would break a lot of our existing installations. > We're therefore not keen to make that change yet - especially since the old > API works just fine for all the types of data we support. > > > > If you're packaging this for Debian and wanted to move to htkjdk then > it's pretty trivial to patch this. It takes a small boilerplate change to > the BAM opening and reading code in the BAMFile class, and a change to the > classpath in the launcher script (which I guess you're already doing). > We'll probably move to the new API eventually, but at the moment the > downsides outweigh the benefits for us. > > > > Cheers > > > > Simon. > > > > > > > > > > -----Original Message----- > > From: Andreas Tille [mailto:ti...@debian.org] > > Sent: 05 December 2016 14:34 > > To: Simon Andrews <simon.andr...@babraham.ac.uk>; 846...@bugs.debian.org > > Cc: Vincent Danjean <vdanj...@debian.org>; Olivier Sallou < > osal...@debian.org>; Charles Plessy <ple...@debian.org> > > Subject: FastQC should adapt to new htsjdk API which has dropped > SAMFileReader (Was: [samtools/htsjdk] SAMFileReader vanished in Version > 2.7.0 (#767)) > > > > Hi Simon, > > > > after uploading htsjdk 2.7.0 FastQC 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/846708 > > [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 > > The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT > Registered Charity No. 1053902. > > The information transmitted in this email is directed only to the > addressee. If you received this in error, please contact the sender and > delete this email from your system. The contents of this e-mail are the > views of the sender and do not necessarily represent the views of the > Babraham Institute. Full conditions at: www.babraham.ac.uk< > http://www.babraham.ac.uk/terms> > > > > _______________________________________________ > > Debian-med-packaging mailing list > > debian-med-packag...@lists.alioth.debian.org > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > > > > -- > http://fam-tille.de >
