Remove some unnecessary catches, add null checks when closing streams
Fix bug in default output file name for sort command

Was splitting on first period, which meant folders with periods in the name were handled improperly. Now splitting on last (we require files have an extension for sorting so this should be alright). Add headed test for same
Refactor IgvToolsGui to use an enum for tools, rather than String

Make IgvToolsGuiTest headless (we are just testing the output file naming logic right now), some refactoring of IgvToolsGui was necessary for this.
Remove unused SequenceArray class
Add conversion from motif ambiguity codes to regex, some tests for it.