hanna c1ecf75dd5 Update to the latest rev of the picard sharding patch. Includes updates reflecting ... the imminent move of IlluminaUtil into picard public. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-06 20:33:21 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Update to the latest rev of the picard sharding patch. Includes updates reflecting	2010-06-06 20:33:21 +00:00
test/org/broadinstitute/sting	No more new Allele() -- must use create. Allelel simple alleles are now cached for efficiency reasons. VCF4 codec optimizations -- 4x performance in general. Now working in general but hooked up to the ROD system now as VCF4. WARNING -- does not actually work with indels, genotype filters, etc.	2010-06-04 23:03:55 +00:00