public void ParseLine_AsExpected(string line, string fileName, string expectedJsonString)
{
var reader = new MitoMapSvReader(new FileInfo(fileName), _sequenceProvider);
var jsonString = reader.ParseLine(line).FirstOrDefault().GetJsonString();
Assert.Equal(expectedJsonString, jsonString);
}
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);
}