private List <PredictionCache> GetMergedPredictions(string path1, string path2)
{
var mergedPredictions = new List <PredictionCache>();
using (var reader1 = new PredictionCacheReader(FileUtilities.GetReadStream(path1)))
using (var reader2 = new PredictionCacheReader(FileUtilities.GetReadStream(path2)))
{
_genomeAssembly = reader1.FileHeader.GenomeAssembly;
_numRefSeq = reader1.FileHeader.Index.Size;
if (_genomeAssembly != reader2.FileHeader.GenomeAssembly)
{
throw new UserErrorException($"Observed different genome assemblies: {reader1.FileHeader.GenomeAssembly}, {reader2.FileHeader.GenomeAssembly}");
}
for (ushort i = 0; i < _numRefSeq; i++)
{
var cache1 = reader1.Read(i);
var cache2 = reader2.Read(i);
if (cache1 == PredictionCache.Empty ^ cache2 == PredictionCache.Empty)
{
throw new DataMisalignedException("one of the cache ran out before the other");
}
mergedPredictions.Add(cache1.GetMergedCache(cache2));
}
//todo: take care of ref sequences unique to one cache
}
return(mergedPredictions);
}
public void Load(ushort refIndex)
{
if (refIndex == CurrentRefIndex)
{
return;
}
SequenceReader.GetCompressedSequence(Sequence.Renamer.EnsemblReferenceNames[refIndex]);
SiftCache = SiftReader.Read(refIndex);
PolyPhenCache = PolyPhenReader.Read(refIndex);
CurrentRefIndex = refIndex;
}
private void LoadPredictionCaches(ushort refIndex)
{
if (refIndex == _currentRefIndex)
{
return;
}
if (refIndex == ushort.MaxValue)
{
ClearCache();
return;
}
_siftCache = _siftReader.Read(refIndex);
_polyphenCache = _polyphenReader.Read(refIndex);
_currentRefIndex = refIndex;
}
private Dictionary <ushort, int> GetPredictionMatrixCount(string path)
{
var countPerRefSeq = new Dictionary <ushort, int>();
using (var reader1 = new PredictionCacheReader(FileUtilities.GetReadStream(path)))
{
_numRefSeq = reader1.FileHeader.Index.Size;
for (ushort i = 0; i < _numRefSeq; i++)
{
var cache1 = reader1.Read(i);
countPerRefSeq[i] = cache1.PredictionCount;
}
}
return(countPerRefSeq);
}