/// <summary>
/// parses the database cache file and populates the specified lists and interval trees
/// </summary>
public TranscriptCacheData Read(IDictionary <ushort, IChromosome> refIndexToChromosome)
{
var genes = ReadItems(_reader, () => Gene.Read(_reader, refIndexToChromosome));
var transcriptRegions = ReadItems(_reader, () => TranscriptRegion.Read(_reader));
var mirnas = ReadItems(_reader, () => Interval.Read(_reader));
var peptideSeqs = ReadItems(_reader, () => _reader.ReadAsciiString());
var regulatoryRegions = ReadIntervals(_reader, () => RegulatoryRegion.Read(_reader, refIndexToChromosome));
var transcripts = ReadIntervals(_reader, () => Transcript.Read(_reader, refIndexToChromosome, genes, transcriptRegions, mirnas, peptideSeqs));
return(new TranscriptCacheData(Header, genes, transcriptRegions, mirnas, peptideSeqs, transcripts, regulatoryRegions));
}
public void TranscriptRegion_EndToEnd()
{
var expectedResults = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 13, 100, 200, 300, 400),
new TranscriptRegion(TranscriptRegionType.Gap, 0, 120, 230, 10, 20),
new TranscriptRegion(TranscriptRegionType.Intron, 14, 130, 230, 330, 430)
};
var observedResults = new ITranscriptRegion[expectedResults.Length];
using (var ms = new MemoryStream())
{
using (var writer = new ExtendedBinaryWriter(ms, Encoding.UTF8, true))
{
foreach (var region in expectedResults)
{
region.Write(writer);
}
}
ms.Position = 0;
using (var reader = new BufferedBinaryReader(ms))
{
for (int i = 0; i < expectedResults.Length; i++)
{
observedResults[i] = TranscriptRegion.Read(reader);
}
}
}
var comparer = new TranscriptRegionComparer();
Assert.Equal(expectedResults, observedResults, comparer);
}