Move give_me_readcounts.pl into a module.
Replace direct IO::File use with calls to Genome::Sys.
Clean up I/O operations.

*Don't run `cut` when we're going through the file anyway.
*Avoid repetition by using map and the "x" operator.
*Remove a few variables left over from GetOpt script version.
Incorporate miller-bam-readcount-to-stats into the readcount module.
Replace IO::File with Genome::Sys for the incorporated script.
Add _ to variable names for readability
Avoid repeatedly reading stats file and building the same hash.