Eric Banks 264cc9e78d Resolve protected->public dependencies for BQSR by wrapping the BQSR-specific arguments in a new class. ... Instead of the GATK Engine creating a new BaseRecalibrator (not clean), it just keeps track of the arguments (clean). There are still some dependency issues, but it looks like they are related to Ami's code. Need to look into it further.		2013-01-08 16:23:29 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Resolve protected->public dependencies for BQSR by wrapping the BQSR-specific arguments in a new class.	2013-01-08 16:23:29 -05:00
test	Moving integration tests to protected	2013-01-08 09:34:08 -05:00