clinseq-converge-stats update

Add a new file to the converge stats command, this is the Stats.tsv from summarizing SNVIndelReports. To help accomplish this make base quality and mapping quality a parameter of Base.pm under Converge.
This and many of the other file accessors in this file may benefit from using [`File::Spec->join`](http://perldoc.perl.org/File/Spec.html#join).