Mark DePristo dcc972a557 Usability cleanup for BQSR ... -- I'm seeing a lot of people trying to use BinaryTagCovariate in the community. They really shouldn't do this, so I moved it to private. -- Throw an exception if its required bintag argument is missing -- Check explicitly if user is requesting DinucCovariate and tell them that its been retired in favor of ContextCovariate -- Show the type (Required, Experimental, Standard) of the covariates when running --list		2012-08-25 14:53:00 -04:00
..
config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Usability cleanup for BQSR	2012-08-25 14:53:00 -04:00
test	WTF - why is support for whole-read insertions all messed up in LIBS? I've pushed a temporary patch for now (the right solution should certainly not be implemented in stable; LIBS needs to be better thought out). Added another unit test.	2012-08-22 00:24:01 -04:00