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 void CreateMitoMapSvTsv(IReadOnlyList <string> mitoMapSvFileNames)
{
if (mitoMapSvFileNames.Count == 0 || mitoMapSvFileNames.Any(string.IsNullOrEmpty))
{
return;
}
var benchMark = new Benchmark();
var rootDirectory = new FileInfo(mitoMapSvFileNames[0]).Directory;
var version = DataSourceVersionReader.GetSourceVersion(Path.Combine(rootDirectory.ToString(), "mitoMapSV"));
var sequenceProvider =
new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath));
sequenceProvider.LoadChromosome(new Chromosome("chrM", "MT", 24));
var mitoMapSvReaders = new List <MitoMapSvReader>();
foreach (var mitoMapFileName in mitoMapSvFileNames)
{
mitoMapSvReaders.Add(new MitoMapSvReader(new FileInfo(mitoMapFileName), sequenceProvider));
}
var mergedMitoMapItems = MitoMapSvReader.MergeAndSort(mitoMapSvReaders);
using (var writer = new IntervalTsvWriter(_outputDirectory, version,
GenomeAssembly.rCRS.ToString(), SaTsvCommon.MitoMapSchemaVersion, InterimSaCommon.MitoMapTag,
ReportFor.StructuralVariants))
CreateSvTsv(mergedMitoMapItems, writer);
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo(InterimSaCommon.MitoMapTag, version.Version, 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());
}
}
private void CreateSvTsv(string sourceName, string fileName)
{
if (string.IsNullOrEmpty(fileName))
{
return;
}
var benchMark = new Benchmark();
//Console.WriteLine($"Creating TSV from {fileName}");
var dataSource = "";
var version = DataSourceVersionReader.GetSourceVersion(fileName);
switch (sourceName)
{
case InterimSaCommon.DgvTag:
dataSource = "DGV";
using (var writer = new IntervalTsvWriter(_outputDirectory, version,
_genomeAssembly.ToString(), SaTsvCommon.DgvSchemaVersion, InterimSaCommon.DgvTag, ReportFor.StructuralVariants))
{
var reader = new DgvReader(new FileInfo(fileName), _refNamesDictionary);
CreateSvTsv(reader.GetDgvItems(), writer);
}
break;
case InterimSaCommon.ClinGenTag:
dataSource = "ClinGen";
using (var writer = new IntervalTsvWriter(_outputDirectory, version,
_genomeAssembly.ToString(), SaTsvCommon.ClinGenSchemaVersion, InterimSaCommon.ClinGenTag,
ReportFor.StructuralVariants))
{
var reader = new ClinGenReader(new FileInfo(fileName), _refNamesDictionary);
CreateSvTsv(reader.GetClinGenItems(), writer);
}
break;
case InterimSaCommon.OnekSvTag:
dataSource = "OnekSv";
using (var writer = new IntervalTsvWriter(_outputDirectory, version,
_genomeAssembly.ToString(), SaTsvCommon.OneKgenSchemaVersion, InterimSaCommon.OnekSvTag,
ReportFor.StructuralVariants))
{
var reader = new OneKGenSvReader(new FileInfo(fileName), _refNamesDictionary);
CreateSvTsv(reader.GetOneKGenSvItems(), writer);
}
break;
default:
Console.WriteLine("invalid source name");
break;
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo(dataSource, version.Version, timeSpan);
}
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);
}
