Add -lociFromFile argument to Common

 * Any caller that uses Common.Loci set of arguments now supports a -lociFromFile argument that accepts a path to a file giving loci to call at. Closes #232.
 * Loci parsing now ignores all whitespace (including newlines, etc.) instead of just spaces.
 * Add a test for parsing a file with containing loci
is this an args4j feature request? or is there a way to do this?