private static string GetOutputPrefix(string inputFilePath)
{
string fileName = CaUtilities.GetInputFileName(inputFilePath);
if (fileName.EndsWith(".tsv"))
{
return(fileName.Substring(0, fileName.Length - 4));
}
return(fileName.EndsWith(".tsv.gz") ? fileName.Substring(0, fileName.Length - 7) : fileName);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
List <CustomInterval> intervals;
SaJsonSchema intervalJsonSchema;
string jsonTag;
DataSourceVersion version;
string outputPrefix = GetOutputPrefix(_inputFile);
string nsaFileName = Path.Combine(_outputDirectory, outputPrefix + SaCommon.SaFileSuffix);
string nsaIndexFileName = nsaFileName + SaCommon.IndexSufix;
string nsaSchemaFileName = nsaFileName + SaCommon.JsonSchemaSuffix;
ReportFor reportFor;
var nsaItemCount = 0;
using (var parser = VariantAnnotationsParser.Create(GZipUtilities.GetAppropriateStreamReader(_inputFile), referenceProvider))
using (var nsaStream = FileUtilities.GetCreateStream(nsaFileName))
using (var indexStream = FileUtilities.GetCreateStream(nsaIndexFileName))
using (var nsaWriter = CaUtilities.GetNsaWriter(nsaStream, indexStream, parser, CaUtilities.GetInputFileName(_inputFile), referenceProvider, out version))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(nsaSchemaFileName))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
(jsonTag, nsaItemCount, intervalJsonSchema, intervals) = CaUtilities.WriteSmallVariants(parser, nsaWriter, schemaWriter);
reportFor = parser.ReportFor;
if (intervals == null)
{
return(ExitCodes.Success);
}
}
if (nsaItemCount == 0)
{
File.Delete(nsaFileName);
File.Delete(nsaIndexFileName);
File.Delete(nsaSchemaFileName);
}
using (var nsiStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outputPrefix + SaCommon.IntervalFileSuffix)))
using (var nsiWriter = CaUtilities.GetNsiWriter(nsiStream, version, referenceProvider.Assembly, jsonTag, reportFor))
using (var siJsonSchemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outputPrefix + SaCommon.IntervalFileSuffix + SaCommon.JsonSchemaSuffix)))
using (var schemaWriter = new StreamWriter(siJsonSchemaStream))
{
nsiWriter.Write(intervals);
schemaWriter.Write(intervalJsonSchema);
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = GeneUtilities.ParseUniversalGeneArchive(null, _universalGeneArchivePath);
string outputPrefix = GetOutputPrefix(_inputFile);
string ngaFilePath = Path.Combine(_outputDirectory, outputPrefix + SaCommon.NgaFileSuffix);
string ngaSchemaFilePath = ngaFilePath + SaCommon.JsonSchemaSuffix;
using (var parser = GeneAnnotationsParser.Create(GZipUtilities.GetAppropriateStreamReader(_inputFile), entrezGeneIdToSymbol, ensemblGeneIdToSymbol))
using (var ngaStream = FileUtilities.GetCreateStream(ngaFilePath))
using (var ngaWriter = CaUtilities.GetNgaWriter(ngaStream, parser, CaUtilities.GetInputFileName(_inputFile)))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(ngaSchemaFilePath))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
ngaWriter.Write(parser.GetItems());
schemaWriter.Write(parser.JsonSchema);
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var(entrezGeneIdToSymbol, ensemblGeneIdToSymbol) = GeneUtilities.ParseUniversalGeneArchive(null, _universalGeneArchivePath);
string outputPrefix = GetOutputPrefix(_inputFile);
string ngaFilePath = Path.Combine(_outputDirectory, outputPrefix + SaCommon.GeneFileSuffix);
string ngaSchemaFilePath = ngaFilePath + SaCommon.JsonSchemaSuffix;
using (var parser = GeneAnnotationsParser.Create(GZipUtilities.GetAppropriateStreamReader(_inputFile), entrezGeneIdToSymbol, ensemblGeneIdToSymbol))
using (var ngaStream = FileUtilities.GetCreateStream(ngaFilePath))
using (var ngaWriter = CaUtilities.GetNgaWriter(ngaStream, parser, CaUtilities.GetInputFileName(_inputFile)))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(ngaSchemaFilePath))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
ngaWriter.Write(parser.GetItems());
if (parser.GetUnknownGenes().Count > 0)
{
throw new UserErrorException($"The following gene IDs were not recognized in Nirvana: {string.Join(',',parser.GetUnknownGenes())}.");
}
schemaWriter.Write(parser.JsonSchema);
}
return(ExitCodes.Success);
}