public void ReadItems_EndToEnd()
{
var expectedStrings = new[] { "Huey", "Duey", "Louie" };
string[] observedStrings;
using (var ms = new MemoryStream())
{
// ReSharper disable AccessToDisposedClosure
using (var writer = new ExtendedBinaryWriter(ms, Encoding.UTF8, true))
{
TranscriptCacheWriter.WriteItems(writer, expectedStrings, x => writer.WriteOptAscii(x));
}
ms.Position = 0;
using (var reader = new BufferedBinaryReader(ms))
{
observedStrings = TranscriptCacheReader.ReadItems(reader, () => reader.ReadAsciiString());
}
// ReSharper restore AccessToDisposedClosure
}
Assert.NotNull(observedStrings);
Assert.Equal(expectedStrings, observedStrings);
}
public static IRnaEdit Read(BufferedBinaryReader reader)
{
int start = reader.ReadOptInt32();
int end = reader.ReadOptInt32();
string bases = reader.ReadAsciiString();
return(new RnaEdit(start, end, bases));
}
/// <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, () => IntervalExtensions.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));
}