private AssemblyDataStore(string description, EnsemblGtf ensemblGtf, RefSeqGff refSeqGff, GlobalCache globalCache) { _description = description; EnsemblGtf = ensemblGtf; RefSeqGff = refSeqGff; _globalCache = globalCache; }
public static AssemblyDataStore Create(string description, FilePaths.AssemblySpecificPaths paths, IDictionary <string, IChromosome> refNameToChromosome, bool useGrch37) { string ensemblGtfPath = useGrch37 ? ExternalFiles.EnsemblGtfFile37.FilePath : ExternalFiles.EnsemblGtfFile38.FilePath; string refseqGffPath = useGrch37 ? ExternalFiles.RefSeqGffFile37.FilePath : ExternalFiles.RefSeqGffFile38.FilePath; string refseqGenomeGffPath = useGrch37 ? ExternalFiles.RefSeqGenomeGffFile37.FilePath : ExternalFiles.RefSeqGenomeGffFile38.FilePath; var ensemblGtf = EnsemblGtf.Create(ensemblGtfPath, refNameToChromosome); var refSeqGff = RefSeqGff.Create(refseqGffPath, refseqGenomeGffPath, refNameToChromosome); var(refIndexToChromosome, _, _) = SequenceHelper.GetDictionaries(paths.ReferencePath); var globalCache = GlobalCache.Create(paths.RefSeqCachePath, paths.EnsemblCachePath, refIndexToChromosome, refNameToChromosome); return(new AssemblyDataStore(description, ensemblGtf, refSeqGff, globalCache)); }