public static RoundedEntryPrediction[] GetRoundedEntryPredictions(this string[] predictionStrings)
{
var predictions = new RoundedEntryPrediction[predictionStrings.Length];
var currentIndex = 0;
foreach (string s in predictionStrings)
{
predictions[currentIndex++] = s.GetRoundedEntryPrediction();
}
return(predictions);
}
public (PredictionCacheStaging Sift, PredictionCacheStaging PolyPhen) CreatePredictionCaches(
Dictionary <ushort, List <MutableTranscript> > transcriptsByRefIndex, PredictionReader siftReader,
PredictionReader polyphenReader, int numRefSeqs)
{
_logger.Write("- converting prediction strings... ");
var siftRoundedPredictionsPerRef = new RoundedEntryPrediction[numRefSeqs][];
var polyPhenRoundedPredictionsPerRef = new RoundedEntryPrediction[numRefSeqs][];
for (ushort refIndex = 0; refIndex < numRefSeqs; refIndex++)
{
var sift = siftReader.GetPredictionData();
var polyphen = polyphenReader.GetPredictionData();
if (sift.Chromosome.Index != refIndex || polyphen.Chromosome.Index != refIndex)
{
throw new InvalidDataException(
$"Found mismatch between transcript chromosome index ({refIndex}) and prediction chromosome indices (SIFT: {sift.Chromosome.Index}, PolyPhen: {polyphen.Chromosome.Index}.");
}
if (!transcriptsByRefIndex.TryGetValue(refIndex, out var refTranscripts))
{
continue;
}
var(siftPredictions, polyPhenPredictions) = ProcessReference(refTranscripts,
sift.TranscriptToPredictionIndex, polyphen.TranscriptToPredictionIndex, sift.PredictionData,
polyphen.PredictionData);
siftRoundedPredictionsPerRef[refIndex] = siftPredictions;
polyPhenRoundedPredictionsPerRef[refIndex] = polyPhenPredictions;
}
_logger.WriteLine("finished.");
var siftStaging = BuildCacheStaging("SIFT", siftRoundedPredictionsPerRef, numRefSeqs);
var polyPhenStaging = BuildCacheStaging("PolyPhen", polyPhenRoundedPredictionsPerRef, numRefSeqs);
return(siftStaging, polyPhenStaging);
}
