public TranscriptCacheStaging CreateTranscriptCache(MutableTranscript[] mutableTranscripts,
IEnumerable <IRegulatoryRegion> regulatoryRegions, IIntervalForest <UgaGene> geneForest, int numRefSeqs)
{
Logger.Write("- assigning UGA genes to transcripts... ");
AssignUgaGenesToTranscripts(mutableTranscripts, geneForest);
Logger.WriteLine("finished.");
var transcriptIntervalArrays = mutableTranscripts.ToTranscripts().ToIntervalArrays(numRefSeqs);
var regulatoryRegionIntervalArrays = regulatoryRegions.ToIntervalArrays(numRefSeqs);
var customHeader = new TranscriptCacheCustomHeader(_vepVersion, _vepReleaseTicks);
var header = new CacheHeader(HeaderUtilities.GetHeader(_source, _genomeAssembly), customHeader);
return(TranscriptCacheStaging.GetStaging(header, transcriptIntervalArrays, regulatoryRegionIntervalArrays));
}
private PredictionHeader CreateHeader(int numReferenceSeqs, Prediction.Entry[] lut)
{
var customHeader = new PredictionCacheCustomHeader(new IndexEntry[numReferenceSeqs]);
return(new PredictionHeader(HeaderUtilities.GetHeader(Source.None, _genomeAssembly), customHeader, lut));
}