depristo 1b6bec8e6b Trivial changes ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4803 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-07 20:06:54 +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	Trivial changes	2010-12-07 20:06:54 +00:00
test	BAQ calculation refactoring in the GATK. Single -baq argument can be NONE, CALCULATE_AS_NECESSARY, and RECALCULATE. Walkers can control bia the @BAQMode annotation how the BAQ calculation is applied. Can either be as a tag, by overwriting the qualities scores, or by only returning the baq-capped qualities scores. Additionally, walkers can be set up to have the BAQ applied to the incoming reads (ON_INPUT, the default), to output reads (ON_OUTPUT), or HANDLED_BY_WALKER, which means that calling into the BAQ system is the responsibility of the individual walker.	2010-12-06 20:55:52 +00:00