Filtering, bug fixes, and a few misc. changes

Can now filter samples by specifying a mapping file field and a list of acceptable values. Added ```--negate``` option to exclude (rather than include) the samples. This filtering functionality is pretty limited but it will cover all of the immediate use-cases (I verified this by going through the metadata fields of interest for the 8 datasets).

The command-line argument parsing code now handles flags (i.e., boolean options such as ```--negate```).

Fixed a file that had tabs instead of spaces for indentation. Fixed a bug in the code that prevented filtering (with or without my latest updates) from working. Added study 550 (Moving Pictures) to batch processing script. Updated fresco defaults to @rybern's latest suggestions.

Fixes #24 #25 #26.

@rybern can you please review?