Mauricio Carneiro 36600fd8e9 added MQ of low MQ/BQ to consensus RMS ... Bases that were excluded for MQ and BQ filters are now contributing to the MQ RMS (but not to consensus base counts and variant/not variant region triggers).		2011-11-01 17:46:12 -04:00
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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	added MQ of low MQ/BQ to consensus RMS	2011-11-01 17:46:12 -04:00