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
Updates README
Cleans up full pipeline run mode
Replaces print statements with logging
fixes readme space
Fixes missing inferMethod
Adds periodic INFO logging
Updates README build gif
Updates README build gif
Updates README
Replaces AtomicCounter with AtomicInteger
Logger fixes

* Renames Logger frequency constants
* Removes Thread locking for logger statements
Merge pull request #13 from smoitra87/master

Addresses Sam comments.