Reorganize files, make modular, and correct

Now displays truly concordant calls--no more displaying concordance of
rejected calls. Does this by only passing calls through that have
the PASS filter on the; may need to verify that this is a valid
assumption by looking at output of other callers.
Merge pull request #4 from ihodes/reorganize_files_fix_passing_variants

Reorganize files, make modular, and correct