public void Convert(string outputPath, string description, GlobalImportCommon.FileType fileType)
{
var inputPath = outputPath.Replace(".dat", ".dat.tmp");
using (var reader = new TempPredictionReader(inputPath, description, fileType))
{
Console.Write($"- loading {description}... ");
var tempPredictions = Load(reader);
Console.WriteLine("finished.");
Console.Write($"- creating {description} LUT... ");
var oldLut = TempPrediction.CreateLookupTable(tempPredictions);
var newLut = TempPrediction.ConvertLookupTable(oldLut);
Console.WriteLine("finished.");
Console.Write($"- converting {description} matrices... ");
var predictionsPerRef = TempPrediction.ConvertMatrices(tempPredictions, oldLut, newLut, _numReferenceSeqs);
Console.WriteLine("finished.");
tempPredictions.Clear();
var header = PredictionCacheHeader.GetHeader(CurrentTimeTicks, reader.Header.GenomeAssembly, _numReferenceSeqs);
Console.Write($"- writing to {Path.GetFileName(outputPath)}... ");
using (var writer = new PredictionCacheWriter(outputPath, header))
{
writer.Write(newLut, predictionsPerRef);
}
Console.WriteLine("finished.");
}
}
/// <summary>
/// loads the items from the VEP reader
/// </summary>
private static List <TempPrediction> Load(TempPredictionReader reader)
{
var values = new List <TempPrediction>();
while (true)
{
var value = reader.Next();
if (value == null)
{
break;
}
values.Add(value);
}
return(values);
}
