def load_singlecore(args): # create a new gemini loader and populate # the gemini db and files from the VCF l = GeminiLoader(args) l.populate_from_vcf() if not args.no_genotypes and not args.no_load_genotypes: l.store_sample_gt_counts() return l
def finish(args, loader=None): """ all things that are performed by single core, multi, ipython should be done here """ if loader is None: loader = GeminiLoader(args, prepare_db=False) print("storing version, header, etc.") loader.store_resources() loader.store_version() loader.store_vcf_header() if not args.skip_gene_tables: print("storing gene-detailed") loader._get_gene_detailed() print("storing gene-summary") loader._get_gene_summary() if not args.test_mode: print("updating gene-table") loader.update_gene_table() if not args.test_mode: print("building indices") loader.build_indices_and_disconnect() else: from gemini import database database.close_and_commit(loader.c)