/// <summary>
/// writes the prediction cache to disk
/// </summary>
public void Write(string cachePath)
{
using (var writer = new PredictionCacheWriter(cachePath, _header))
{
writer.Write(_lookupTable, _predictionsPerRef);
}
}
private void CombinePredictionsCaches()
{
Console.WriteLine("Writing combined Sift...");
var mergedSift = GetMergedPredictions(CacheConstants.SiftPath(_prefix1), CacheConstants.SiftPath(_prefix2));
using (var writer = new PredictionCacheWriter(CacheConstants.SiftPath(_outPrefix), PredictionCacheHeader.GetHeader(DateTime.Now.Ticks, _genomeAssembly, _numRefSeq)))
{
var lookupTableList = new List <Prediction.Entry>();
foreach (var predictionCach in mergedSift)
{
lookupTableList.AddRange(predictionCach.LookupTable);
}
writer.Write(lookupTableList.ToArray(), mergedSift.Select(cache => cache.Predictions).ToArray());
}
Console.WriteLine("Done.");
Console.WriteLine("writing combined polyphen");
var mergedPolyphen = GetMergedPredictions(CacheConstants.PolyPhenPath(_prefix1), CacheConstants.PolyPhenPath(_prefix2));
using (var writer = new PredictionCacheWriter(CacheConstants.PolyPhenPath(_outPrefix), PredictionCacheHeader.GetHeader(DateTime.Now.Ticks, _genomeAssembly, _numRefSeq)))
{
var lookupTableList = new List <Prediction.Entry>();
foreach (var predictionCach in mergedPolyphen)
{
lookupTableList.AddRange(predictionCach.LookupTable);
}
writer.Write(lookupTableList.ToArray(), mergedPolyphen.Select(cache => cache.Predictions).ToArray());
}
Console.WriteLine("Done");
}
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.");
}
}
private static void WritePredictions(ILogger logger, string description, string filePath,
PredictionHeader header, Prediction[][] predictionsPerRef)
{
logger.Write($"- writing {description} predictions... ");
using (var stream = new BlockStream(new Zstandard(), FileUtilities.GetCreateStream(filePath), CompressionMode.Compress))
using (var writer = new PredictionCacheWriter(stream, CloneHeader(header)))
{
writer.Write(header.LookupTable, predictionsPerRef);
}
logger.WriteLine("finished.");
}
