public ExitCodes Create()
{
var mimIdToEntry = new Dictionary <int, OmimImportEntry>();
AddOmimEntries(mimIdToEntry, _geneMap2Path);
AddOmimEntries(mimIdToEntry, _mim2GenePath);
UpdateGeneSymbols(mimIdToEntry);
var geneToOmimEntries = GetGeneToOmimEntries(mimIdToEntry);
var dataSourceVersion = DataSourceVersionReader.GetSourceVersion(_geneMap2Path + ".version");
using (var omimWriter = new GeneAnnotationTsvWriter(_outputDirectory, dataSourceVersion, null, 0, JsonKeyName, true))
{
foreach (var kvp in geneToOmimEntries.OrderBy(x => x.Key))
{
omimWriter.AddEntry(kvp.Key,
kvp.Value.OrderBy(x => x.MimNumber).Select(x => x.ToString()).ToList());
}
}
_geneSymbolUpdater.DisplayStatistics();
WriteUpdatedGeneSymbols();
return(ExitCodes.Success);
}
private ExitCodes ProgramExecution()
{
if (!_supportedSequencingDataType.Contains(_sequencingDataType))
{
throw new ArgumentException($"Only the following sequencing data types are supported: {string.Join(_supportedSequencingDataType.ToString(), ", ")}");
}
var inputStreamReaders = Directory.GetFiles(_inputDirectory, "*.vcf.bgz").Select(fileName => GZipUtilities.GetAppropriateStreamReader(Path.Combine(_inputDirectory, fileName))).ToArray();
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
if (inputStreamReaders.Length == 0)
{
throw new UserErrorException("input directory does not conatin any .vcf.bgz files");
}
var versionFiles = Directory.GetFiles(_inputDirectory, "*.version");
if (versionFiles.Length != 1)
{
throw new InvalidDataException("more than one .version file found in input directory");
}
Console.WriteLine($"Creating gnomAD TSV file from {inputStreamReaders.Length} input files");
var version = DataSourceVersionReader.GetSourceVersion(versionFiles[0]);
var gnomadTsvCreator = new GnomadTsvCreator(inputStreamReaders, referenceProvider, version, _outputDirectory, _sequencingDataType);
gnomadTsvCreator.CreateTsvs();
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
TranscriptCacheData transcriptData;
using (var transcriptCacheReader = new TranscriptCacheReader(FileUtilities.GetReadStream(CacheConstants.TranscriptPath(_transcriptCachePrefix))))
{
transcriptData = transcriptCacheReader.Read(referenceProvider.RefIndexToChromosome);
}
var(entrezToHgnc, ensemblToHgnc) = PrimateAiUtilities.GetIdToSymbols(transcriptData);
using (var primateAiParser = new PrimateAiParser(GZipUtilities.GetAppropriateReadStream(_inputFile), referenceProvider, entrezToHgnc, ensemblToHgnc))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.PrimateAiTag, true, true, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(primateAiParser.GetItems());
}
return(ExitCodes.Success);
}
private static DataSourceVersion GetVersion()
{
var genomeVersionFiles = Directory.GetFiles(_genomeDirectory, "*.version");
if (genomeVersionFiles.Length != 1)
{
throw new InvalidDataException($"Only one .version file should exist in: {_genomeDirectory}");
}
var genomeVersion = DataSourceVersionReader.GetSourceVersion(genomeVersionFiles[0]);
if (string.IsNullOrEmpty(_exomeDirectory))
{
return(genomeVersion);
}
var exomeVersionFiles = Directory.GetFiles(_exomeDirectory, "*.version");
if (exomeVersionFiles.Length != 1)
{
throw new InvalidDataException($"Only one .version file should exist in: {_exomeDirectory}");
}
var exomeVersion = DataSourceVersionReader.GetSourceVersion(genomeVersionFiles[0]);
if (genomeVersion.Version != exomeVersion.Version)
{
throw new DataMisalignedException(
$"Version mismatch! Genome version: {genomeVersion.Version}, Exome Version: {exomeVersion.Version}.");
}
return(genomeVersion);
}
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 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 static ExitCodes ProgramExecution()
{
var rootDirectory = new FileInfo(MitoMapFileNames[0]).Directory;
if (rootDirectory == null)
{
return(ExitCodes.PathNotFound);
}
var version = DataSourceVersionReader.GetSourceVersion(Path.Combine(rootDirectory.ToString(), "mitoMapVar"));
var sequenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var chrom = sequenceProvider.RefNameToChromosome["chrM"];
sequenceProvider.LoadChromosome(chrom);
MitoMapInputDb mitoMapInputDb = MitoMapDatabaseUtilities.Create(_mitoMapDatabase);
var mitoMapVarReaders = MitoMapFileNames.Select(mitoMapFileName => new MitoMapVariantReader(new FileInfo(mitoMapFileName), mitoMapInputDb, sequenceProvider)).ToList();
var mergedMitoMapVarItems = MitoMapVariantReader.GetMergeAndSortedItems(mitoMapVarReaders);
string outFileName = $"{version.Name}_{version.Version}";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, sequenceProvider, SaCommon.MitoMapTag, false, true, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(mergedMitoMapVarItems);
}
return(ExitCodes.Success);
}
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 ExitCodes ProgramExecution()
{
var rootDirectory = new FileInfo(MitoMapFileNames[0]).Directory;
if (rootDirectory == null)
{
return(ExitCodes.PathNotFound);
}
var version = DataSourceVersionReader.GetSourceVersion(Path.Combine(rootDirectory.ToString(), "mitoMapSv"));
var sequenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var chrom = sequenceProvider.RefNameToChromosome["chrM"];
sequenceProvider.LoadChromosome(chrom);
var mitoMapSvReaders = MitoMapFileNames.Select(mitoMapFileName => new MitoMapSvReader(new FileInfo(mitoMapFileName), sequenceProvider)).ToList();
var mergedMitoMapVarItems = MitoMapSvReader.MergeAndSort(mitoMapSvReaders);
string outFileName = $"{version.Name}_{version.Version}";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SiFileSuffix)))
{
var nsiWriter = new NsiWriter(new ExtendedBinaryWriter(nsaStream), version, GenomeAssembly.rCRS, SaCommon.MitoMapTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion);
nsiWriter.Write(mergedMitoMapVarItems);
}
return(ExitCodes.Success);
}
private void CreateSvTsv(string sourceName, string fileName)
{
if (string.IsNullOrEmpty(fileName))
{
return;
}
var benchMark = new Benchmark();
//Console.WriteLine($"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);
}
private void AddSourceVersion(string dataFileName)
{
var versionFileName = dataFileName + ".version";
var version = DataSourceVersionReader.GetSourceVersion(versionFileName);
Console.WriteLine(version.ToString());
_dataSources.Add(version);
}
public void GetSourceVersionTest()
{
var versionPath = Resources.TopPath("dbSNP.version");
var version = DataSourceVersionReader.GetSourceVersion(versionPath);
Assert.Equal("dbSNP", version.Name);
Assert.Equal("147", version.Version);
Assert.Equal(DateTime.Parse("2016-04-08").Ticks, version.ReleaseDateTicks);
}
private ExitCodes ProgramExecution()
{
var reader = GZipUtilities.GetAppropriateStreamReader(_inputFileArg);
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferenceArg));
var version = DataSourceVersionReader.GetSourceVersion(_inputFileArg + ".version");
var topMedTsvCreator = new TopMedTsvCreator(reader, referenceProvider, version, _outputDirArg);
topMedTsvCreator.CreateTsvs();
return(ExitCodes.Success);
}
private static DataSourceVersion GetDataVersion()
{
var versionFileName = ConfigurationSettings.InputWigFixFile + ".version";
if (!File.Exists(versionFileName))
{
throw new FileNotFoundException(versionFileName);
}
var versionReader = new DataSourceVersionReader(versionFileName);
var version = versionReader.GetVersion();
return(version);
}
private static ExitCodes ProgramExecution()
{
var dosageSensitivityVersion = DataSourceVersionReader.GetSourceVersion(_dosageSensitivityFile + ".version");
string outFileName = $"{dosageSensitivityVersion.Name.Replace(' ','_')}_{dosageSensitivityVersion.Version}";
using (var dosageSensitivityParser = new DosageSensitivityParser(GZipUtilities.GetAppropriateReadStream(_dosageSensitivityFile)))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.NgaFileSuffix)))
using (var ngaWriter = new NgaWriter(stream, dosageSensitivityVersion, SaCommon.DosageSensitivityTag, SaCommon.SchemaVersion, false))
{
ngaWriter.Write(dosageSensitivityParser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFileName + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var clinGenReader = new ClinGenReader(GZipUtilities.GetAppropriateStreamReader(_inputFileName), referenceProvider.RefNameToChromosome))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SiFileSuffix)))
using (var nsiWriter = new NsiWriter(new ExtendedBinaryWriter(nsaStream), version, referenceProvider.Assembly, SaCommon.ClinGenTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(clinGenReader.GetItems());
}
return(ExitCodes.Success);
}
private static DataSourceVersion AddSourceVersion(string dataFileName)
{
var versionFileName = dataFileName + ".version";
if (!File.Exists(versionFileName))
{
throw new FileNotFoundException(versionFileName);
}
var versionReader = new DataSourceVersionReader(versionFileName);
var version = versionReader.GetVersion();
Console.WriteLine(version.ToString());
return(version);
}
private static ExitCodes ProgramExecution()
{
var dosageMapRegionVersion = DataSourceVersionReader.GetSourceVersion(_dosageMapRegionFile + ".version");
string outFileName = $"{dosageMapRegionVersion.Name.Replace(' ', '_')}_{dosageMapRegionVersion.Version}";
var referenceProvider = new ReferenceSequenceProvider(GZipUtilities.GetAppropriateReadStream(_inputReferencePath));
using (var dosageSensitivityParser = new DosageMapRegionParser(GZipUtilities.GetAppropriateReadStream(_dosageMapRegionFile), referenceProvider.RefNameToChromosome))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SiFileSuffix)))
using (var nsiWriter = new NsiWriter(stream, dosageMapRegionVersion, referenceProvider.Assembly, SaCommon.DosageSensitivityTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(dosageSensitivityParser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var refProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_referenceSequencePath));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
var outFileName = $"{version.Name}_{version.Version}";
using (var parser = new LcrRegionParser(GZipUtilities.GetAppropriateStreamReader(_inputFile), refProvider))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.LcrFileSuffix)))
using (var writer = new NsiWriter(stream, version, refProvider.Assembly, SaCommon.LowComplexityRegionTag, ReportFor.AllVariants, SaCommon.NsiSchemaVersion))
{
writer.Write(parser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
using (var indexStream = FileUtilities.GetReadStream(_inputIndexFile))
using (var outStream = FileUtilities.GetCreateStream(_outputIndexFile))
using (var extWriter = new ExtendedBinaryWriter(outStream))
{
var version = DataSourceVersionReader.GetSourceVersion(_versionFile);
var oldIndex = new NsaIndex(indexStream);
var newIndex = new NsaIndex(extWriter, oldIndex.Assembly, version, oldIndex.JsonKey, oldIndex.MatchByAllele, oldIndex.IsArray, oldIndex.SchemaVersion, oldIndex.IsPositional);
newIndex.Write(oldIndex.GetBlocks());
}
return(ExitCodes.Success);
}
private ExitCodes ProgramExecution()
{
var version = DataSourceVersionReader.GetSourceVersion(_cnvTsv + ".version");
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var cnvStream = _cnvTsv == null? null: GZipUtilities.GetAppropriateReadStream(_cnvTsv);
var breakendStream = _breakendTsv == null ? null : GZipUtilities.GetAppropriateReadStream(_breakendTsv);
using (var cosmicSvExtractor = new CosmicSvReader(cnvStream, breakendStream, version, _outputDir,
referenceProvider.GenomeAssembly, referenceProvider.RefNameToChromosome))
{
cosmicSvExtractor.CreateTsv();
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}_{SaCommon.RefMinorTag}".Replace(' ', '_');
using (var refMinorReader = new RefMinorReader(GZipUtilities.GetAppropriateStreamReader(_inputFile), referenceProvider))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.RefMinorFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.RefMinorFileSuffix + SaCommon.IndexSufix)))
using (var writer = new RefMinorDbWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, referenceProvider, SaCommon.SchemaVersion))
{
writer.Write(refMinorReader.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var primateAiParser = new MitoHeteroplasmyParser(GZipUtilities.GetAppropriateReadStream(_inputFile), referenceProvider))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.MitoHeteroplasmyTag, true, false, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(primateAiParser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var dosageSensitivityVersion = DataSourceVersionReader.GetSourceVersion(_diseaseValidityFile + ".version");
string outFileName = $"{dosageSensitivityVersion.Name.Replace(' ', '_')}_{dosageSensitivityVersion.Version}";
// read uga file to get hgnc id to gene symbols dictionary
using (var diseaseValidityParser = new GeneDiseaseValidityParser(GZipUtilities.GetAppropriateReadStream(_diseaseValidityFile), GetHgncIdToGeneSymbols()))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.GeneFileSuffix)))
using (var ngaWriter = new NgaWriter(stream, dosageSensitivityVersion, SaCommon.DiseaseValidityTag, SaCommon.SchemaVersion, true))
{
ngaWriter.Write(diseaseValidityParser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
//create universal gene archive
using (var exacParser = new ExacScoresParser(GZipUtilities.GetAppropriateStreamReader(_inputFile)))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.NgaFileSuffix)))
using (var ngaWriter = new NgaWriter(stream, version, SaCommon.ExacScoreTag, SaCommon.SchemaVersion, false))
{
ngaWriter.Write(exacParser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var cosmicReader = new MergedCosmicReader(_vcfFile, _tsvFile, referenceProvider);
var version = DataSourceVersionReader.GetSourceVersion(_vcfFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, referenceProvider, SaCommon.CosmicTag, false, true, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(cosmicReader.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var phylopParser = new PhylopParser(GZipUtilities.GetAppropriateReadStream(_inputFile), referenceProvider.Assembly, referenceProvider.RefNameToChromosome))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.PhylopFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.PhylopFileSuffix + SaCommon.IndexSufix)))
using (var writer = new NpdWriter(nsaStream, indexStream, version, referenceProvider.Assembly, SaCommon.PhylopTag, SaCommon.SchemaVersion))
{
writer.Write(phylopParser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var globalMinorReader = new GlobalMinorReader(GZipUtilities.GetAppropriateReadStream(_inputFile), referenceProvider.RefNameToChromosome);
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}_globalMinor";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.GlobalAlleleTag, true, false, SaCommon.SchemaVersion, true))
{
nsaWriter.Write(globalMinorReader.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFileName + ".version");
string outFileName = $"{version.Name}_{version.Version}".Replace(' ', '_');
using (var reader = GZipUtilities.GetAppropriateStreamReader(_inputFileName))
using (var oneKGenSvReader = new OneKGenSvReader(reader, referenceProvider.RefNameToChromosome))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.IntervalFileSuffix)))
using (var nsiWriter = new NsiWriter(nsaStream, version, referenceProvider.Assembly,
SaCommon.OnekSvTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(oneKGenSvReader.GetItems());
}
return(ExitCodes.Success);
}
