depristo c91712bd59 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. ... SAMFileWriterStub now supports BAQ writing as an internal feature. Several walkers have the @BAQMode applied to this, with parameters that I think are reasonable. Please look if you own these walkers, though git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4798 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-06 20:55:52 +00:00
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sting	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