/// <summary>
/// constructor
/// </summary>
public PredictionCacheStaging(PredictionCacheHeader header, Prediction.Entry[] lut,
Prediction[][] predictionsPerRef)
{
_header = header;
_lookupTable = lut;
_predictionsPerRef = predictionsPerRef;
}
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 PredictionCacheStaging GetStagingWithPredictionIndices(PredictionCache cache, bool useSift,
List <TranscriptPacket> packets, int numRefSeqs)
{
var predictionsPerRef = new Prediction[numRefSeqs][];
for (ushort refIndex = 0; refIndex < numRefSeqs; refIndex++)
{
predictionsPerRef[refIndex] = GetPredictions(packets, useSift, refIndex);
}
var header = PredictionCacheHeader.GetHeader(cache.Header.CreationTimeTicks, cache.Header.GenomeAssembly,
numRefSeqs);
return(new PredictionCacheStaging(header, cache.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");
}
