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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 --------
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:
-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 Indeed, LoadSnappy class is not present anymore, and has been replaced by SnappyLoader (same name as one of your classes).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 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help |