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);
}
public static NsaWriter GetNsaWriter(Stream nsaStream, Stream indexStream, VariantAnnotationsParser parser, string dataVersion, ISequenceProvider referenceProvider, out DataSourceVersion version)
{
return(new NsaWriter(
nsaStream,
indexStream,
version = new DataSourceVersion(parser.JsonTag, dataVersion, DateTime.Now.Ticks),
referenceProvider,
parser.JsonTag,
parser.MatchByAllele, // match by allele
parser.IsArray, // is array
SaCommon.SchemaVersion,
false, // is positional
false, // skip incorrect ref base
true // throw error on conflicting entries
));
}
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);
}