Added code to process VCF files in batches, cleaning temporary files as it goes.  We still create way too many temporary files, but for now these changes will help.
(Untested, testing should happen before final commit)
Added "alt number" to database schema.
Reworked variant import/annotation to use views and avoid dumping and reloading of tables in certain places.  This particular implementation should be faster for large databases (>1e6 variants).
Changed variant subset table so that it either tracks the main variant view (if num variants < 1e6) or is a random sampling of approximately 1e6 variants of the main view otherwise.
Tidied up some code and stale comments.