On Mon, Aug 13, 2012 at 09:27:50AM +0200, [email protected] wrote: > I copy below the answer from upstream team. > They will not go to latest snappy version. Seems it was quite difficult > to integrate it and faced issues. > > The problem is snappy-java 1.0.4 breaks its API and is not compatible > with version 1.0.3 used by picard-tools.
This is what we also learned (the hard way). > At runtime, picard-tools tries to detect snappy. If not present, it will > be ok. However we still face the problem for Debian for compilation.... > > -------- Message original -------- > Sujet: Re: [Samtools-help] support of snappy-1.0.4 > Date : Thu, 09 Aug 2012 10:27:11 -0400 > De : Alec Wysoker <[email protected]> > Pour : olivier.sallou <[email protected]> > Copie à : [email protected] > > ... > > Could you try one of the following alternatives to using latest snappy-java: > > * Use the same version Picard uses, i.e. 1.0.3-rc3 It somehow came to my mind to package this older version. Finally we started packaging libsnappy-java for the only purpose to support picard ... and currently this purpose is not fullfilled. > * Omit snappy-java classes completely. > net.sf.samtools.util.SnappyLoader is written so that if > org.xerial.snappy.SnappyInputStream and > org.xerial.snappy.SnappyOutputStream are not found on the classpath, > then the code should work without using Snappy. Hmmm, I do not know the advantage we would liked to reach and whether this is acceptable. However, it seems to make sense to do not only a check whether the class is available but also to verify the version if there are incompatible versions known. I have no idea whether this is possible - but if yes this would be a reasonable hint to upstream. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
