private static (PredictionCacheStaging Staging, Prediction[] Predictions) GetPredictionStaging(ILogger logger,
string description, IEnumerable <ITranscript> transcripts, IChromosome chromosome, IReadOnlyList <Prediction> oldPredictions,
PredictionCacheReader reader, Func <ITranscript, int> indexFunc, int numRefSeqs)
{
logger.Write($"- retrieving {description} predictions... ");
var indexSet = GetUniqueIndices(transcripts, indexFunc);
var predictionsPerRef = GetPredictions(indexSet, chromosome, numRefSeqs, oldPredictions);
var staging = new PredictionCacheStaging(reader.Header, predictionsPerRef);
logger.WriteLine($"found {indexSet.Count} predictions.");
return(staging, predictionsPerRef[chromosome.Index]);
public static void WritePredictionCaches(PredictionCacheStaging sift, PredictionCacheStaging polyPhen,
string outputStub, List <string> outputFiles)
{
var siftPath = outputStub + ".sift" + TempCacheExt;
var polyphenPath = outputStub + ".polyphen" + TempCacheExt;
outputFiles.Add(siftPath);
outputFiles.Add(polyphenPath);
sift?.Write(siftPath);
polyPhen?.Write(polyphenPath);
}
