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));
}
