Initial work towards fixing VarScan's VCF output

This covers most of the use cases, although VarScan also produces
invalid REF records (e.g. CAA/A) which aren't handled yet.

Most of the contribution is by Sean Davis, who graciously agreed to
provide it under a MIT license.

This is needed to handle issue #134.
Merge pull request #137 from lbeltrame/fix-varscan-output

Initial work towards fixing VarScan's VCF output