private void CreateDbsnpGaTsv(string fileName)
{
if (fileName == null)
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(fileName);
var dbsnpWriter = new SaTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(),
SaTsvCommon.DbSnpSchemaVersion, InterimSaCommon.DbsnpTag, null, true, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)));
var globalAlleleWriter = new SaTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(),
SaTsvCommon.DbSnpSchemaVersion, InterimSaCommon.GlobalAlleleTag, "GMAF", false, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)));
using (var tsvWriter = new DbsnpGaTsvWriter(dbsnpWriter, globalAlleleWriter))
{
var dbSnpReader = new DbSnpReader(GZipUtilities.GetAppropriateReadStream(fileName), _refNamesDictionary);
TsvWriterUtilities.WriteSortedItems(dbSnpReader.GetDbSnpItems(), tsvWriter);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("DbSNP", version.Version, timeSpan);
}
private void CreateMitoMapVarTsv(IReadOnlyList <string> mitoMapFileNames)
{
if (mitoMapFileNames.Count == 0 || mitoMapFileNames.Any(string.IsNullOrEmpty))
{
return;
}
var benchMark = new Benchmark();
var rootDirectory = new FileInfo(mitoMapFileNames[0]).Directory;
var version = DataSourceVersionReader.GetSourceVersion(Path.Combine(rootDirectory.ToString(), "mitoMapVar"));
var sequenceProvider =
new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath));
sequenceProvider.LoadChromosome(new Chromosome("chrM", "MT", 24));
var mitoMapVarReaders = new List <MitoMapVariantReader>();
foreach (var mitoMapFileName in mitoMapFileNames)
{
mitoMapVarReaders.Add(new MitoMapVariantReader(new FileInfo(mitoMapFileName), sequenceProvider));
}
var mergedMitoMapVarItems = MitoMapVariantReader.MergeAndSort(mitoMapVarReaders);
const string outputFilePrefix = InterimSaCommon.MitoMapTag;
using (var writer = new MitoMapVarTsvWriter(version, _outputDirectory, outputFilePrefix, sequenceProvider))
TsvWriterUtilities.WriteSortedItems(mergedMitoMapVarItems, writer);
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo(InterimSaCommon.MitoMapTag, version.Version, timeSpan);
}
public void CreateTsvs()
{
var benchMark = new Benchmark();
using (var writer = new TopMedTsvWriter(_version, _outputDirName, _refProvider.GenomeAssembly, _refProvider))
using (var reader = new TopMedReader(_streamReader, _refProvider.RefNameToChromosome))
{
TsvWriterUtilities.WriteSortedItems(reader.GetGnomadItems(), writer);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("TOPMed", _version.Version, timeSpan);
}
private void CreateOnekgTsv(string fileName)
{
if (fileName == null)
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(fileName);
using (var tsvWriter = new OnekgTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))))
{
var onekgReader = new OneKGenReader(new FileInfo(fileName), _refNamesDictionary);
TsvWriterUtilities.WriteSortedItems(onekgReader.GetOneKGenItems(), tsvWriter);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("OneKg", version.Version, timeSpan);
}
private void CreateEvsTsv(string fileName)
{
if (string.IsNullOrEmpty(fileName))
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(fileName);
using (var writer = new EvsTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))))
{
var evsReader = new EvsReader(GZipUtilities.GetAppropriateStreamReader(fileName), _refNamesDictionary);
TsvWriterUtilities.WriteSortedItems(evsReader.GetEvsItems(), writer);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("EVS", version.Version, timeSpan);
}
private void CreateCutomAnnoTsv(string fileName)
{
if (string.IsNullOrEmpty(fileName))
{
return;
}
Console.WriteLine($"Creating TSV from {fileName}");
var version = DataSourceVersionReader.GetSourceVersion(fileName);
var customReader = new CustomAnnotationReader(new FileInfo(fileName), _refNamesDictionary);
using (var writer = new CustomAnnoTsvWriter(version, _outputDirectory, _genomeAssembly, customReader.IsPositional, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))))
{
TsvWriterUtilities.WriteSortedItems(customReader.GetCustomItems(), writer);
}
Console.WriteLine($"Finished {fileName}");
}
public void CreateTsvs()
{
var benchMark = new Benchmark();
using (var writer = new GnomadTsvWriter(_version, _outputDirectory, _refProvider.GenomeAssembly, _refProvider, _sequencingDataType))
{
var count = 0;
foreach (var fileStreamReader in _streamReaders)
{
var reader = new GnomadReader(fileStreamReader, _refProvider.RefNameToChromosome);
TsvWriterUtilities.WriteSortedItems(reader.GetGnomadItems(), writer);
Console.WriteLine($"ingested {count++} file in " + benchMark.GetElapsedTime());
}
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("gnomAD", _version.Version, timeSpan);
}
private void CreateClinvarTsv(string fileName)
{
if (fileName == null)
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(fileName);
//clinvar items do not come in sorted order, hence we need to store them in an array, sort them and then flush them out
using (var writer = new ClinvarTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))))
{
var clinvarReader = new ClinVarXmlReader(new FileInfo(fileName), new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)));
TsvWriterUtilities.WriteSortedItems(clinvarReader.GetItems(), writer);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("ClinVar", version.Version, timeSpan);
}
private void CreateCosmicTsv(string vcfFile, string tsvFile)
{
if (string.IsNullOrEmpty(tsvFile) || string.IsNullOrEmpty(vcfFile))
{
return;
}
var benchMark = new Benchmark();
var version = DataSourceVersionReader.GetSourceVersion(vcfFile);
using (var writer = new CosmicTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))))
{
var tsvReader = GZipUtilities.GetAppropriateStreamReader(tsvFile);
var vcfReader = GZipUtilities.GetAppropriateStreamReader(vcfFile);
var reader = new MergedCosmicReader(vcfReader, tsvReader, _refNamesDictionary);
TsvWriterUtilities.WriteSortedItems(reader.GetCosmicItems(), writer);
}
var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime());
TsvWriterUtilities.WriteCompleteInfo("COSMIC", version.Version, timeSpan);
}
