private void CreateCustIntervalTsv(string fileName)
{
if (string.IsNullOrEmpty(fileName))
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(fileName);
var reader = new CustomIntervalParser(new FileInfo(fileName), _refNamesDictionary);
using (var writer = new IntervalTsvWriter(_outputDirectory, version,
_genomeAssembly.ToString(), SaTsvCommon.CustIntervalSchemaVersion, reader.KeyName,
ReportFor.AllVariants))
{
foreach (var custInterval in reader.GetCustomIntervals())
{
writer.AddEntry(custInterval.Chromosome.EnsemblName, custInterval.Start, custInterval.End, custInterval.GetJsonString());
}
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("customInterval", fileName, timeSpan);
}
private static void CreateSvTsv(IEnumerable <SupplementaryDataItem> siItems, IntervalTsvWriter writer)
{
foreach (var siItem in siItems)
{
var interval = siItem.GetSupplementaryInterval();
writer.AddEntry(interval.Chromosome.EnsemblName, interval.Start, interval.End, interval.GetJsonString());
}
}
public void CreateTsv()
{
var benchMark = new Benchmark();
const string dataSource = "COSMIC";
if (_cnvStream != null)
{
using (var writer = new IntervalTsvWriter(_outputDirectory, _version,
_genomeAssembly.ToString(), SaTsvCommon.CosmicSvSchemaVersion, InterimSaCommon.CosmicCnvTag, ReportFor.StructuralVariants))
using (var cnvReader = new CosmicCnvReader(_cnvStream, _refNameToChorm, _genomeAssembly))
{
foreach (var cnvEntry in cnvReader.GetEntries())
{
writer.AddEntry(cnvEntry.Chromosome.EnsemblName, cnvEntry.Start, cnvEntry.End, cnvEntry.GetJsonString());
}
}
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo(dataSource, _version.Version, timeSpan);
}
