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status on picard-tools and issue with libsnappy-java



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.

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....

Olivier


-------- Message original --------
Sujet: Re: [Samtools-help] support of snappy-1.0.4
Date : Thu, 09 Aug 2012 10:27:11 -0400
De : Alec Wysoker <alecw@broadinstitute.org>
Pour : olivier.sallou <olivier.sallou@laposte.net>
Copie à : samtools-help@lists.sourceforge.net


Hi Olivier,

I assume you are referring to Picard library rather than samtools, because I don't think samtools uses Snappy.

I am reluctant to fiddle with Snappy or get a new version, because we had lots of problems when we released it, some of which did not happen on our configuration but only for other users, which made it difficult to test and debug.  It took several iterations for this to settle down.

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
  • 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.

-Alec


On 8/8/12 10:02 AM, olivier.sallou wrote:
Hi,
I am part of the DebianMed team, we package some programs for Debian.
When trying to compile sam-tools, we got an issue because current snappy
version is 1.0.4 and it is not compatible with previous ones.

Indeed, LoadSnappy class is not present anymore, and has been replaced
by SnappyLoader (same name as one of your classes).
Furthermore, public method load is not present anymore.

With hacks, I could get it compile, but I do not know if my hacks are
correct (if needed I can send you what I did).

Do you plan to support new snappy version ?

Thanks

Olivier

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