LoadDataStores(ILogger logger, FilePaths filePaths) { logger.Write("- loading datastores... "); var loadBenchmark = new Benchmark(); var dicts = GetSequenceDictionaries(filePaths.GRCh38.ReferencePath, ExternalFiles.AssemblyFile37.FilePath, ExternalFiles.AssemblyFile38.FilePath); var geneInfoData = GeneInfoData.Create(ExternalFiles.GeneInfoFile.FilePath); var dataStore37 = AssemblyDataStore.Create("GRCh37", logger, filePaths.GRCh37, dicts.RefNameToChromosome, dicts.Accession37, true); var dataStore38 = AssemblyDataStore.Create("GRCh38", logger, filePaths.GRCh38, dicts.RefNameToChromosome, dicts.Accession38, false); var hgnc = Hgnc.Create(ExternalFiles.HgncFile.FilePath, dicts.RefNameToChromosome); logger.WriteLine($"{Benchmark.ToHumanReadable(loadBenchmark.GetElapsedTime())}"); return(geneInfoData, dataStore37, dataStore38, hgnc); }
LoadDataStores(FilePaths filePaths) { Logger.Write("- loading datastores... "); var loadBenchmark = new Benchmark(); var(_, refNameToChromosome, _) = SequenceHelper.GetDictionaries(filePaths.GRCh38.ReferencePath); var geneInfoData = GeneInfoData.Create(ExternalFiles.GeneInfoFile.FilePath); var dataStore37 = AssemblyDataStore.Create("GRCh37", filePaths.GRCh37, refNameToChromosome, true); var dataStore38 = AssemblyDataStore.Create("GRCh38", filePaths.GRCh38, refNameToChromosome, false); var hgnc = Hgnc.Create(ExternalFiles.HgncFile.FilePath, refNameToChromosome); Logger.WriteLine($"{Benchmark.ToHumanReadable(loadBenchmark.GetElapsedTime())}"); return(geneInfoData, dataStore37, dataStore38, hgnc); }