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);
}
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 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 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);
}
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);
}
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);
}
