Add affected/unaffected to constants.
Add choices for phenotype filtering.
Add de_novo tests to master-test.sh
Add phenotype tests to test-query.
Look up phenotypes properly for --phenotype queries.
Added --region to gemini query.

This allows region-based queries to take advantage of all
of the options that can be applied to individual queries.
Handle adding to WHERE where WHERE already exists.
Update querying.rst

typo
[ENC] warn if parents are missing when looking for auto_* or de_novo variants
Merge branch 'master' of github.com:arq5x/gemini
[ENH] add ID field from VCF to database as vcf_id
[TST] update tests for new vcf_id column
Use set operations for speed.
Added family wise stratification of queries.
Merge branch 'master' of github.com:arq5x/gemini
Added documentation for family queries.
update docs
handle codon change vs distance
Merge pull request #219 from udp3f/master

Update docs, handle codon_change vs distance
--sample-filter added.

This allows for SQL-style queries on the sample table and
deprecates the --phenotype and --exclude-phenotype type
functionality.