[CommandLineOptions] Add command line option to manage DB

[antonylebechec]

Additional command line options could help to manage DB without interface:

• [x] Import a VCF into an database
• [ ] Import a pedigree file
• [ ] Import a tags file
• [x] Query a database (VQL/SQL), with export in JSON
• [ ] Export queries in VCF
• [ ] Generate reports (sample, variant...) in json/html/pdf

[antonylebechec]

branch "option_comman_line_import_vcf" push for importing VCF in command line

Options:
  -h, --help                               Displays help on commandline
                                           options.
  --help-all                               Displays help including Qt specific
                                           options.
  --version                                Display the version of Cutevariant
                                           and exit.
  -c, --config <config>                    Set the config path
  -v, --verbose <notset|debug|info|error>  Modify verbosity.
  -i, --import_vcf <import_vcf>            Import VCF file
  -a, --vcf_annotations <vcf_annotations>  VCF annotations type
  -p, --project_db <project_db>            Connexion to a project DB

[antonylebechec]

New options to query project DB:

Usage: /Users/lebechea/BIOINFO/git/cutevariant/cutevariant/__main__.py [options]

Options:
  -h, --help                                Displays help on commandline
                                            options.
  --help-all                                Displays help including Qt specific
                                            options.
  --version                                 Display the version of Cutevariant
                                            and exit.
  -c, --config <config>                     Set the config path
  -v, --verbose <notset|debug|info|error>   Modify verbosity.
  -p, --project_db <project.db>             Connexion to a project DB
                                            (e.g. import VCF, query in VQL or
                                            SQL...)
  -i, --import_vcf <file.vcf>               Import VCF file
                                            VCF file will be imported to the
                                            project DB (mandatory)
                                            (NB: Choose annotations type)
  -a, --vcf_annotations <annotations_type>  VCF annotations type
                                            Choose annotation type provided by
                                            the VCF file
                                            (either 'snpeff' or 'vep')
                                            (default '')
  -q, --query_vql <vql>                     Query in VQL format
                                            Query a project DB in VQL format
                                            Multiple queries allowed
                                            See CuteVariant VQL query format
                                            Examples:
                                            - 'SELECT favorite, classification,
                                            chr, pos, ref, alt FROM variants'-
                                            'SELECT favorite, classification,
                                            chr, pos, ref, alt, ann.gene,
                                            ann.hgvs_p FROM variants WHERE
                                            samples['ANY'].gt>=1'
  -s, --query_sql <sql>                     Query a project DB in SQL format
                                            See SQL query format
                                            Examples:
                                            - 'SELECT favorite, classification,
                                            chr, pos, ref, alt FROM variants'
                                            - SELECT * FROM samples
  -r, --query_results <results.json>        Query results in JSON format file
                                            Standard output by default