Addresses Sam comments

* Updates README to use platinum dataset as default
* Removes project id flag
* Removes offending Optional.of debug spew
Fixes trio member print order

* replaces hashmaps wiht treemaps
Fixes #10 and normalizes output files

* Read caller output vanish fix
* File output path normalization
Removes enums Chromosomes cmdline

* Adds function to convert string chromosome to enum
* Adds tests