Added VariantFunction output field, various bug fixes
 * TranscriptEffect now reports the VariantFunction, which uses
SequenceOntology terms to describe the impact of the variant on the
transcript (ie stop_gained or intron_variant).  This annotation is in
the default OutputGroup.
 * BugFix: No longer writes invalid characters to VCF INFO fields. 
This means that "p.(=)" is now written to the VCF as "p.(&eq;)"
 * BugFix: Intergenic variants no longer crash due to a null
Transcript
 * BugFix: "track" and "browser" lines of a BED file are now skipped
rather than causing an error
 * BugFix: intronic deletions that remove part of a splice
acceptor/donor site are now correctly called