public void Preload()
{
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks, "description");
using (var saStream = new MemoryStream())
using (var indexStream = new MemoryStream())
{
using (var extWriter = new ExtendedBinaryWriter(saStream, Encoding.UTF8, true))
using (var indexExtWriter = new ExtendedBinaryWriter(indexStream, Encoding.UTF8, true))
{
var saWriter = new NsaWriter(extWriter, indexExtWriter, version, GetAllASequenceProvider(), "dbsnp", true, true, SaCommon.SchemaVersion, false, true, false, 1024);
saWriter.Write(GetDbsnpItems(1000));
}
saStream.Position = 0;
indexStream.Position = 0;
using (var saReader = new NsaReader(saStream, indexStream, 1024))
{
saReader.PreLoad(_chrom1, GetPositions(50, 1000));
Assert.Null(saReader.GetAnnotation(90)); //before any SA existed
Assert.NotNull(saReader.GetAnnotation(100)); //first entry of first block
Assert.NotNull(saReader.GetAnnotation(480)); //last query of first block
Assert.Null(saReader.GetAnnotation(488)); //between first and second block
Assert.NotNull(saReader.GetAnnotation(490)); //first entry of second block
}
}
}
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 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);
var mitoMapVarReaders = MitoMapFileNames.Select(mitoMapFileName => new MitoMapVariantReader(new FileInfo(mitoMapFileName), sequenceProvider)).ToList();
var mergedMitoMapVarItems = MitoMapVariantReader.MergeAndSort(mitoMapVarReaders);
string outFileName = $"{version.Name}_{version.Version}";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
{
var nsaWriter = new NsaWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, sequenceProvider, SaCommon.MitoMapTag, false, true, SaCommon.SchemaVersion, false);
nsaWriter.Write(mergedMitoMapVarItems);
}
return(ExitCodes.Success);
}
public static void ConcatenateNsaFiles(IEnumerable <string> filePaths, string outFilePrefix)
{
if (filePaths == null || !filePaths.Any())
{
return;
}
var nsaReaders = new List <NsaReader>();
foreach (var fileName in filePaths)
{
nsaReaders.Add(new NsaReader(FileUtilities.GetReadStream(fileName), FileUtilities.GetReadStream(fileName + SaCommon.IndexSufix)));
}
Console.WriteLine($"Merging {nsaReaders.Count} NSA files...");
var(version, jsonKey, matchByAllele, isArray, isPositional, assembly) = GetIndexFields(nsaReaders);
using (var nsaStream = FileUtilities.GetCreateStream(outFilePrefix + SaCommon.SaFileSuffix))
using (var indexStream = FileUtilities.GetCreateStream(outFilePrefix + SaCommon.SaFileSuffix + SaCommon.IndexSufix))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, null, jsonKey, matchByAllele, isArray, SaCommon.SchemaVersion, isPositional, true, false, SaCommon.DefaultBlockSize, assembly))
{
var chromIndices = GetChromIndices(nsaReaders);
foreach (var chromIndex in chromIndices)
{
Console.WriteLine($"Working on chromosome index: {chromIndex}");
nsaWriter.Write(chromIndex, GetNsaReader(chromIndex, nsaReaders));
}
}
}
public void RemoveConflictinItems()
{
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks, "description");
using (var saStream = new MemoryStream())
using (var indexStream = new MemoryStream())
using (var saWriter = new NsaWriter(saStream, indexStream, version, GetAllASequenceProvider(), "gnomad",
true, true, SaCommon.SchemaVersion, false, true, false, 1024))
{
Assert.Equal(0, saWriter.Write(GetConflictingGnomadItems()));
}
}
private void WriteCustomSaItem(CustomItem customItem)
{
using (var saStream = new MemoryStream())
using (var indexStream = new MemoryStream())
using (var saWriter = new NsaWriter(
new ExtendedBinaryWriter(saStream),
new ExtendedBinaryWriter(indexStream),
new DataSourceVersion("customeSa", "test", DateTime.Now.Ticks),
GetSequenceProvider(),
"customeSa", false, true, SaCommon.SchemaVersion, false, false))
{
saWriter.Write(new[] { customItem });
}
}
public void Write_clinvar_basic()
{
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks, "description");
using (var saStream = new MemoryStream())
using (var indexStream = new MemoryStream())
{
using (var saWriter = new NsaWriter(saStream, indexStream, version, GetSequenceProvider(), "clinvar",
false, true, SaCommon.SchemaVersion, false, true, false, 1024, GenomeAssembly.GRCh37, true))
{
saWriter.Write(GetClinvarItems());
}
saStream.Position = 0;
indexStream.Position = 0;
using (var saReader = new NsaReader(saStream, indexStream, 1024))
{
Assert.Equal(GenomeAssembly.GRCh37, saReader.Assembly);
Assert.Equal(version.ToString(), saReader.Version.ToString());
saReader.PreLoad(ChromosomeUtilities.Chr1, new List <int> {
100, 101, 106
});
var annotations = saReader.GetAnnotation(100).ToList();
Assert.Equal("T", annotations[0].refAllele);
Assert.Equal("A", annotations[0].altAllele);
Assert.Equal(
"\"id\":\"RCV0001\",\"reviewStatus\":\"no assertion provided\",\"alleleOrigins\":[\"origin1\"],\"refAllele\":\"T\",\"altAllele\":\"A\",\"phenotypes\":[\"phenotype1\"],\"medGenIds\":[\"medgen1\"],\"omimIds\":[\"omim1\"],\"orphanetIds\":[\"orpha1\"],\"significance\":[\"significance\"],\"lastUpdatedDate\":\"0001-01-01\",\"pubMedIds\":[\"10024875684920\"]",
annotations[0].annotation);
annotations = saReader.GetAnnotation(101).ToList();
Assert.Equal("A", annotations[0].refAllele);
Assert.Equal("", annotations[0].altAllele);
Assert.Equal(
"\"id\":\"RCV00011\",\"variationId\":101,\"reviewStatus\":\"no assertion provided\",\"alleleOrigins\":[\"origin1\"],\"refAllele\":\"A\",\"altAllele\":\"-\",\"phenotypes\":[\"phenotype1\"],\"medGenIds\":[\"medgen1\"],\"omimIds\":[\"omim1\"],\"orphanetIds\":[\"orpha1\"],\"significance\":[\"significance\"],\"lastUpdatedDate\":\"0001-01-01\",\"pubMedIds\":[\"10024875684920\"]",
annotations[0].annotation);
saReader.PreLoad(ChromosomeUtilities.Chr2, new List <int> {
200, 205
});
var(refAllele, altAllele, annotation) = saReader.GetAnnotation(200).First();
Assert.Equal("G", refAllele);
Assert.Equal("A", altAllele);
Assert.NotNull(annotation);
}
}
}
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 referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}_ancestralAlleles".Replace(' ', '_');
using (var ancestralAlleleReader = new AncestralAlleleReader(GZipUtilities.GetAppropriateStreamReader(_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 writer = new NsaWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, referenceProvider, SaCommon.AncestralAlleleTag, true, false, SaCommon.SchemaVersion, true))
{
writer.Write(ancestralAlleleReader.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 = $"{version.Name}_{version.Version}";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, referenceProvider, SaCommon.CosmicTag, false, true, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(cosmicReader.GetItems());
}
return(ExitCodes.Success);
}
private static void CreateNsa(string[] exomeFiles, string genomeFile, DataSourceVersion version)
{
Console.WriteLine($"Processing file: {genomeFile}");
var outName = Path.GetFileNameWithoutExtension(genomeFile);
using (var exomeReader = GetExomeReader(exomeFiles, genomeFile))
using (var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference)))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_tempDirectory, outName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_tempDirectory, outName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.GnomadTag, true, false, SaCommon.SchemaVersion, false))
using (var reader = GZipUtilities.GetAppropriateStreamReader(genomeFile))
{
var gnomadReader = new GnomadSnvReader(reader, exomeReader, referenceProvider);
var count = nsaWriter.Write(gnomadReader.GetCombinedItems());
Console.WriteLine($"Wrote {count} items to NSA file.");
}
}
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 version = DataSourceVersionReader.GetSourceVersion(_rcvFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference)))
using (var clinvarReader = new ClinVarReader(GZipUtilities.GetAppropriateReadStream(_rcvFile), GZipUtilities.GetAppropriateReadStream(_vcvFile), referenceProvider))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.ClinvarTag, false, true, SaCommon.SchemaVersion, false))
using (var schemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.JsonSchemaSuffix)))
using (var schemaWriter = new StreamWriter(schemaStream))
{
nsaWriter.Write(clinvarReader.GetItems());
schemaWriter.Write(clinvarReader.JsonSchema);
}
return(ExitCodes.Success);
}
private ExitCodes ProgramExecution()
{
if (!_supportedSequencingDataType.Contains(_sequencingDataType))
{
throw new ArgumentException($"Only the following sequencing data types are supported: {string.Join(_supportedSequencingDataType.ToString(), ", ")}");
}
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var inputFiles = Directory.GetFiles(_inputDirectory, "*.vcf.bgz");
if (inputFiles.Length == 0)
{
inputFiles = Directory.GetFiles(_inputDirectory, "*.vcf.gz");
}
if (inputFiles.Length == 0)
{
throw new UserErrorException("input directory does not contain 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");
}
var version = DataSourceVersionReader.GetSourceVersion(versionFiles[0]);
Console.WriteLine($"Creating gnomAD TSV file from {inputFiles.Length} input files");
string outFileName = $"{version.Name}_{version.Version}";
var jsonTag = _sequencingDataType == "genome" ? SaCommon.GnomadTag : SaCommon.GnomadExomeTag;
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, referenceProvider, jsonTag, true, false, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(GetItems(inputFiles, referenceProvider));
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
TranscriptCacheData transcriptData;
using (var transcriptCacheReader = new TranscriptCacheReader(FileUtilities.GetReadStream(CacheConstants.TranscriptPath(_transcriptCachePrefix))))
{
transcriptData = transcriptCacheReader.Read(referenceProvider.RefIndexToChromosome);
}
var spliceIntervals = SpliceUtilities.GetSpliceIntervals(referenceProvider, transcriptData);
var nirEnstToGeneSymbols = SpliceUtilities.GetEnstToGeneSymbols(referenceProvider, transcriptData);
Dictionary <string, string> spliceAiEnstToGeneSymbols;
using (var reader = new StreamReader(GZipUtilities.GetAppropriateReadStream(_geneInfoFile)))
{
spliceAiEnstToGeneSymbols = SpliceUtilities.GetSpliceAiGeneSymbols(reader);
}
var spliceAiToNirvanaGeneSymbols =
SpliceUtilities.GetSymbolMapping(spliceAiEnstToGeneSymbols, nirEnstToGeneSymbols);
Console.WriteLine($"Mapped {spliceAiToNirvanaGeneSymbols.Count} spliceAI gene symbols to Nirvana gene symbols (out of {spliceAiEnstToGeneSymbols.Count})");
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var spliceAiParser = new SpliceAiParser(
GZipUtilities.GetAppropriateReadStream(_inputFile),
referenceProvider, spliceIntervals, spliceAiToNirvanaGeneSymbols))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.SpliceAiTag, true, true, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(spliceAiParser.GetItems());
}
Console.WriteLine($"Total number of entries from Splice AI: {SpliceAiParser.Count}");
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
TranscriptCacheData transcriptData;
using (var transcriptCacheReader = new TranscriptCacheReader(FileUtilities.GetReadStream(CacheConstants.TranscriptPath(_transcriptCachePrefix))))
{
transcriptData = transcriptCacheReader.Read(referenceProvider.RefIndexToChromosome);
}
var spliceIntervals = SpliceUtilities.GetSpliceIntervals(referenceProvider, transcriptData);
var nirvanaGeneForest = SpliceUtilities.GetGeneForest(transcriptData);
Console.WriteLine("Loaded transcripts and generated splice intervals.");
Dictionary <string, List <string> > geneSymbolSynonyms;
using (var geneInfoParser = new GeneInfoParser(GZipUtilities.GetAppropriateStreamReader(_geneInfoFile)))
{
geneSymbolSynonyms = geneInfoParser.GetGeneSymbolSynonyms();
}
Console.WriteLine("Loaded gene symbol synonyms");
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var spliceAiParser = new SpliceAiParser(
GZipUtilities.GetAppropriateReadStream(_inputFile),
referenceProvider, spliceIntervals, nirvanaGeneForest, geneSymbolSynonyms))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
{
var nsaWriter = new NsaWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, referenceProvider, SaCommon.SpliceAiTag, true, true, SaCommon.SchemaVersion, false);
nsaWriter.Write(spliceAiParser.GetItems());
}
Console.WriteLine($"Total number of entries from Splice AI: {SpliceAiParser.Count}");
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
List <CustomInterval> intervals;
SaJsonSchema intervalJsonSchema;
string jsonTag;
DataSourceVersion version;
string outputPrefix = GetOutputPrefix(_inputFile);
var nsaFileName = Path.Combine(_outputDirectory, outputPrefix + SaCommon.SaFileSuffix);
var nsaIndexFileName = Path.Combine(_outputDirectory, outputPrefix + SaCommon.SaFileSuffix + SaCommon.IndexSufix);
var nsaSchemaFileName = Path.Combine(_outputDirectory, outputPrefix + SaCommon.SaFileSuffix + SaCommon.JsonSchemaSuffix);
var nsaItemsCount = 0;
using (var customReader = CustomAnnotationsParser.Create(GZipUtilities.GetAppropriateStreamReader(_inputFile), referenceProvider))
using (var nsaStream = FileUtilities.GetCreateStream(nsaFileName))
using (var indexStream = FileUtilities.GetCreateStream(nsaIndexFileName))
using (var nsaWriter = new NsaWriter(
new ExtendedBinaryWriter(nsaStream),
new ExtendedBinaryWriter(indexStream),
version = new DataSourceVersion(customReader.JsonTag, GetInputFileName(_inputFile), DateTime.Now.Ticks),
referenceProvider,
customReader.JsonTag,
customReader.MatchByAllele, // match by allele
customReader.IsArray, // is array
SaCommon.SchemaVersion,
false, // is positional
false, // skip incorrect ref base
true // throw error on conflicting entries
))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(nsaSchemaFileName))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
jsonTag = customReader.JsonTag;
nsaItemsCount = nsaWriter.Write(customReader.GetItems());
schemaWriter.Write(customReader.JsonSchema);
intervalJsonSchema = customReader.IntervalJsonSchema;
intervals = customReader.GetCustomIntervals();
}
if (nsaItemsCount == 0)
{
if (File.Exists(nsaFileName))
{
File.Delete(nsaFileName);
}
if (File.Exists(nsaIndexFileName))
{
File.Delete(nsaIndexFileName);
}
if (File.Exists(nsaSchemaFileName))
{
File.Delete(nsaSchemaFileName);
}
}
if (nsaItemsCount == 0 && intervals == null)
{
throw new UserErrorException("The provided TSV has no valid custom annotation entries.");
}
if (intervals == null)
{
return(ExitCodes.Success);
}
using (var nsiStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outputPrefix + SaCommon.SiFileSuffix)))
using (var nsiWriter = new NsiWriter(new ExtendedBinaryWriter(nsiStream), version, referenceProvider.Assembly, jsonTag, ReportFor.AllVariants, SaCommon.SchemaVersion))
using (var siJsonSchemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outputPrefix + SaCommon.SiFileSuffix + SaCommon.JsonSchemaSuffix)))
using (var schemaWriter = new StreamWriter(siJsonSchemaStream))
{
nsiWriter.Write(intervals);
schemaWriter.Write(intervalJsonSchema);
}
return(ExitCodes.Success);
}
public static (string JsonTag, int NsaItemsCount, SaJsonSchema IntervalJsonSchema, List <CustomInterval> Intervals) WriteSmallVariants(VariantAnnotationsParser parser, NsaWriter nsaWriter, StreamWriter schemaWriter)
{
int nsaItemsCount = nsaWriter.Write(parser.GetItems());
schemaWriter.Write(parser.JsonSchema);
var intervals = parser.GetCustomIntervals();
if (nsaItemsCount == 0 & intervals == null)
{
throw new UserErrorException("The provided TSV has no valid custom annotation entries.");
}
return(parser.JsonTag, nsaItemsCount, parser.IntervalJsonSchema, intervals);
}
