public ParallelSaTsvReader(string fileName)
{
_fileName = fileName;
using (var tsvIndex = new TsvIndex(new BinaryReader(FileUtilities.GetReadStream(_fileName + TsvIndex.FileExtension))))
{
_refNameOffsets = tsvIndex.TagPositions;
}
}
public IntervalTsvWriter(string outputPath, DataSourceVersion dataSourceVersion, string assembly, int dataVersion, string keyName,
ReportFor reportingFor)
{
var fileName = keyName + "_" + dataSourceVersion.Version.Replace(" ", "_") + ".interval.tsv.gz";
_bgzipTextWriter = new BgzipTextWriter(Path.Combine(outputPath, fileName));
_bgzipTextWriter.Write(GetHeader(dataSourceVersion, dataVersion, assembly, keyName, reportingFor));
_tsvIndex = new TsvIndex(Path.Combine(outputPath, fileName) + ".tvi");
}
public SaMiscTsvWriter(string outputPath, DataSourceVersion dataSourceVersion, string assembly, string keyName, ISequenceProvider sequenceProvider)
{
var fileName = keyName + "_" + dataSourceVersion.Version.Replace(" ", "_") + ".misc.tsv.gz";
_bgzipTextWriter = new BgzipTextWriter(Path.Combine(outputPath, fileName));
_bgzipTextWriter.Write(GetHeader(dataSourceVersion, assembly));
_tsvIndex = new TsvIndex(Path.Combine(outputPath, fileName + ".tvi"));
_sequenceProvider = sequenceProvider;
}
private SaTsvWriter(string outputDir, DataSourceVersion dataSourceVersion, string assembly, int schemaVersion,
string jsonKey, string vcfKeys,
bool isAlleleSpecific, bool isArray = false)
{
var fileName = jsonKey + "_" + dataSourceVersion.Version.Replace(" ", "_") + ".tsv.gz";
_bgzipTextWriter = new BgzipTextWriter(Path.Combine(outputDir, fileName));
_bgzipTextWriter.Write(GetHeader(dataSourceVersion, schemaVersion, assembly, jsonKey, vcfKeys, isAlleleSpecific, isArray));
_tsvIndex = new TsvIndex(Path.Combine(outputDir, fileName + ".tvi"));
}
