Added --phenotype and --exclude-phenotype flags.
Added phenotype and exclude-phenotype flags to query.

These will filter variants based on ones that either are completely in
samples with a phenotype flag or not at all in samples with a given
phenotype, respectively.
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.