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);
}
private static FilePaths GetFilePaths(string jsonPath)
{
var builder = new ConfigurationBuilder();
builder.AddJsonFile(jsonPath);
var configuration = builder.Build();
var filePaths = new FilePaths();
configuration.Bind(filePaths);
UpdatePaths(filePaths.GRCh37);
UpdatePaths(filePaths.GRCh38);
CheckPaths(filePaths.GRCh37);
CheckPaths(filePaths.GRCh38);
return(filePaths);
}