private static void MarkCanonicalTranscripts(MutableTranscript[] transcripts)
{
var ccdsIdToEnsemblId = CcdsReader.GetCcdsIdToEnsemblId(ExternalFiles.CcdsFile.FilePath);
var lrgTranscriptIds = LrgReader.GetTranscriptIds(ExternalFiles.LrgFile.FilePath, ccdsIdToEnsemblId);
Logger.Write("- marking canonical transcripts... ");
var canonical = new CanonicalTranscriptMarker(lrgTranscriptIds);
int numCanonicalTranscripts = canonical.MarkTranscripts(transcripts);
Logger.WriteLine($"{numCanonicalTranscripts:N0} marked.");
}
public void MarkCanonicalTranscripts(string lrgPath)
{
// sanity check: make sure we're only doing this for RefSeq
if (_transcriptReader.Header.TranscriptSource != VD.TranscriptDataSource.RefSeq)
{
return;
}
Console.Write("- marking canonical transcripts... ");
var canonical = new CanonicalTranscriptMarker(lrgPath);
int numCanonicalFlagsChanged = canonical.MarkTranscripts(_transcripts);
Console.WriteLine($"{numCanonicalFlagsChanged} canonical transcripts marked.");
}