depristo 16e1bbd380 Hidden command line option to control BAQ gap open penalty for testing by me and eric. ValidateBAQWalker has misc. useful improvements. PrintReads now adds BAQ tags on output, if requested. ... BAQ has generally useful improvements. Refactor code to make it easier for BAQUnitTest to run. minBaseQuality enforced on output, as well as input now. Added BAQUnitTest that checks that the BAQ calculation is performing as expected. Still needs to be expanded significantly. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4804 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-08 01:01:39 +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	Hidden command line option to control BAQ gap open penalty for testing by me and eric. ValidateBAQWalker has misc. useful improvements. PrintReads now adds BAQ tags on output, if requested.	2010-12-08 01:01:39 +00:00
test	Hidden command line option to control BAQ gap open penalty for testing by me and eric. ValidateBAQWalker has misc. useful improvements. PrintReads now adds BAQ tags on output, if requested.	2010-12-08 01:01:39 +00:00