rpoplin 9b2733a54a Misc clean up in the recalibrator related to the nested hash map implementation. CountCovariates no longer creates the full flattened set of keys and iterates over them. The output csv file is in sorted order by default now but there is a new option -unsorted which can be used to save a little bit of run time. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2482 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-30 16:58:04 +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	Misc clean up in the recalibrator related to the nested hash map implementation. CountCovariates no longer creates the full flattened set of keys and iterates over them. The output csv file is in sorted order by default now but there is a new option -unsorted which can be used to save a little bit of run time.	2009-12-30 16:58:04 +00:00
test/org/broadinstitute/sting	Added: integration test for extended pileup (with indels included)	2009-12-29 23:02:23 +00:00