Bugfix for BQSR: Offset into qualityScore list was wrong

The wrong offset was being used to retrieve the quality score for a read.  The original code filtered the BaseCovar iterator to only process high quality bases and all of the "offset" value was to the first high quality base, but then was used to look up the qualityScore in the full quality score sequence.  This change

1) Renames and uses proper indices
2) Tests for ReadCovariates
3) Removed RDD arguments to covar classes as they were unsused