text: #!venv/bin/python
  """ExonCov CLI."""
  from flask_script import Manager
  from flask_migrate import Migrate, MigrateCommand
  
  from ExonCov import app, db, cli
  
  manager = Manager(app)
  migrate = Migrate(app, db)
  db_manager = Manager(usage='Database commands.')
  
  manager.add_command("db", db_manager)
  manager.add_command('import_bam', cli.ImportBam())
  manager.add_command('search_sample', cli.SearchSample())
  manager.add_command('sample_qc', cli.SampleQC())
  manager.add_command('remove_sample', cli.RemoveSample())
  manager.add_command('check_samples', cli.CheckSamples())
  manager.add_command('create_sample_set', cli.CreateSampleSet())
  
  db_manager.add_command('migrate', MigrateCommand)
  db_manager.add_command('stats', cli.PrintStats())
  db_manager.add_command('panel_genes', cli.PrintPanelGenesTable())
  db_manager.add_command('gene_transcripts', cli.PrintTranscripts())
  db_manager.add_command('import_alias_table', cli.ImportAliasTable())
  db_manager.add_command('export_panel_bed', cli.PrintPanelBed())
  # db_manager.add_command('load_design', cli.LoadDesign())  # Disabled, can be used to setup a new database from scratch
  
  if __name__ == "__main__":
      manager.run()
  