internal PredictionWriter(StreamWriter writer, IntermediateIoHeader header,
IntermediateIoCommon.FileType fileType)
{
_writer = writer;
_writer.NewLine = "\n";
header.Write(_writer, fileType);
}
// ReSharper disable once ParameterOnlyUsedForPreconditionCheck.Global
public static IntermediateIoHeader ReadHeader(StreamReader reader, FileType expectedType)
{
(string id, FileType type, IntermediateIoHeader header) = IntermediateIoHeader.Read(reader);
if (id != Header || type != expectedType)
{
throw new InvalidDataException("Could not verify the header tag or the file type in the header.");
}
return(header);
}
internal static (string Id, IntermediateIoCommon.FileType Type, IntermediateIoHeader Header) Read(StreamReader reader)
{
var cols = reader.ReadLine()?.Split('\t');
var cols2 = reader.ReadLine()?.Split('\t');
if (cols == null || cols2 == null)
{
throw new InvalidDataException("Found unexpected null lines when parsing the intermediate I/O file header");
}
var id = cols[0];
var type = (IntermediateIoCommon.FileType) byte.Parse(cols[1]);
var vepVersion = ushort.Parse(cols2[0]);
var vepReleaseTicks = long.Parse(cols2[1]);
var source = (Source)byte.Parse(cols2[2]);
var genomeAssembly = (GenomeAssembly)byte.Parse(cols2[3]);
var numRefSeqs = int.Parse(cols2[4]);
var header = new IntermediateIoHeader(vepVersion, vepReleaseTicks, source, genomeAssembly, numRefSeqs);
return(id, type, header);
}
internal MutableTranscriptWriter(StreamWriter writer, IntermediateIoHeader header)
{
_writer = writer;
_writer.NewLine = "\n";
header.Write(_writer, IntermediateIoCommon.FileType.Transcript);
}
internal RegulatoryRegionWriter(StreamWriter writer, IntermediateIoHeader header)
{
_writer = writer;
_writer.NewLine = "\n";
header.Write(_writer, IntermediateIoCommon.FileType.Regulatory);
}
internal GenbankWriter(StreamWriter writer, IntermediateIoHeader header)
{
_writer = writer;
_writer.NewLine = "\n";
header.Write(_writer, IntermediateIoCommon.FileType.Genbank);
}
internal MutableTranscriptReader(Stream stream, IDictionary <ushort, IChromosome> refIndexToChromosome)
{
_refIndexToChromosome = refIndexToChromosome;
_reader = FileUtilities.GetStreamReader(stream);
Header = IntermediateIoCommon.ReadHeader(_reader, IntermediateIoCommon.FileType.Transcript);
}