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);
}
public void ParseLine_AsExpected(string line, string fileName, string expectedJsonString)
{
string jsonString = MitoMapVariantReader.ParseLine(line, fileName, SequenceProvider, VariantAligner, ChromosomeUtilities.ChrM, MitoMapInputDb)
.FirstOrDefault()
?.GetJsonString();
Assert.Equal(expectedJsonString, jsonString);
}
public void GetAltAllelesTests()
{
const string altAlleleString1 = "ACT";
const string altAlleleString2 = "ACT;AGT";
const string altAlleleString3 = "AKY";
const string altAlleleString4 = "ACT;AKY";
const string altAlleleString5 = "CNT;AKY";
Assert.Equal(new[] { "ACT" }, MitoMapVariantReader.GetAltAlleles(altAlleleString1));
Assert.Equal(new[] { "ACT", "AGT" }, MitoMapVariantReader.GetAltAlleles(altAlleleString2));
Assert.Equal(new[] { "AGC", "AGT", "ATC", "ATT" }, MitoMapVariantReader.GetAltAlleles(altAlleleString3));
Assert.Equal(new[] { "ACT", "AGC", "AGT", "ATC", "ATT" }, MitoMapVariantReader.GetAltAlleles(altAlleleString4));
Assert.Equal(new[] { "CNT", "AGC", "AGT", "ATC", "ATT" }, MitoMapVariantReader.GetAltAlleles(altAlleleString5));
}
public void GetNumFullLengthSequences_AsExpected(string field, string dataType, int numFullLengthSequences)
{
Assert.Equal(numFullLengthSequences, MitoMapVariantReader.GetNumFullLengthSequences(field, dataType));
}
