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 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 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);
}