ebanks 0429301536 Added ability to output just sites (no genotypes) from UG with the --sites_only argument. Note that we do still genotype in this mode so that the INFO annotations are identical, but we strip the genotypes out of the VC right before writing to output. In other words, this is not designed to make UG go faster; the point here is to allow downstream tools not to have to parse GTs if they don't want to. Here you go, Ryan. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5081 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-26 14:52:38 +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	Added ability to output just sites (no genotypes) from UG with the --sites_only argument. Note that we do still genotype in this mode so that the INFO annotations are identical, but we strip the genotypes out of the VC right before writing to output. In other words, this is not designed to make UG go faster; the point here is to allow downstream tools not to have to parse GTs if they don't want to. Here you go, Ryan.	2011-01-26 14:52:38 +00:00
test	An apparently robust implementation of the file locking for distributed computation, using Lucene's file creation locking approach. It is worth trying out for those with large-scale, high-cost data sets. Details and discussion at group meeting on Wednesday. Some cleanup still needed.	2011-01-26 13:45:40 +00:00