ebanks 8901e63879 Cheap optimization: don't keep calculating the log of a constant. (How did I not catch this before?) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4791 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-05 04:36:21 +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	Cheap optimization: don't keep calculating the log of a constant. (How did I not catch this before?)	2010-12-05 04:36:21 +00:00
test	Engine-level BAQ calculation now available in the GATK [totally experimental right now]. -baq argument to disable (NONE), to only use the tags in the BAM (USE_TAG_ONLY), use the tag when present but calculate on the fly as necessary (CALCULATE_AS_NECESSARY), and to always recalculate (RECALCULATE_ALWAYS). BAQ.java contains the complete implementation, for those interested. ValidateBAQWalker is a useful QC tool for verifying the BAQ is correct. BAQSamIterator applies BAQ to reads, as needed, in the engine. Let me know if you encounter any problems. Before prime-time, needs a caching implementation of IndexedFastaReader to avoid loading *lots* of reference data all of the time	2010-12-04 20:23:06 +00:00