New CLP to collect coverage information according to Illumina-defined filters.

New CLP to collect coverage information according to Illumina-defined filters.

Reads must have passed PF, and not be marked as duplicates, secondary or supplemental, and they must be mapped.
Overlapping bases are only counted once.
Tool assumes that all reads in the same file are of same length.

Moved from private to public.
Responded to reviewer comments.
Added tests.