Remove code to read files from iRODS or local filesystem; instead take AssayResultSet objects as arguments
Modified for new input syntax
Include code to create AssayResultSet objects from iRODS or local filesystem (formerly in VCFConverter.pm)
Rename *_plex_dir to *_plex_coll
Rename arguments to converter and scripts
Rename plex_dir to plex_coll, additional sanity checking, update to help text