public void ExecuteTest(string inputBamFile, string outputBamFile, int expectedNumRealignedReads, int maxShift = 250) { if (File.Exists(outputBamFile)) { File.Delete(outputBamFile); } var options = new HygeaOptions(); options.SkipAndRemoveDuplicates = false; //(old default/simple behavior for regression testing basic execution) options.MaxRealignShift = maxShift; var factory = new Factory(options); var chrRef = GetGenomeSnippet(); var writer = new RemapBamWriter(inputBamFile, outputBamFile); writer.Initialize(); var realigner = (ChrRealigner)factory.CreateRealigner(chrRef, inputBamFile, writer); realigner.Execute(); writer.FinishAll(); Assert.True(File.Exists(outputBamFile)); Assert.Equal(expectedNumRealignedReads, realigner.TotalRealignedReads); }
public void HappyPath() { if (!Directory.Exists(_outputDirectory)) { Directory.CreateDirectory(_outputDirectory); } if (File.Exists(_outputFile)) { File.Delete(_outputFile); } if (File.Exists(_outputFile + ".bai")) { File.Delete(_outputFile + ".bai"); } var happyBamWriter = new RemapBamWriter(_bamFilePath, _outputFile, 10); happyBamWriter.Initialize(); BamAlignment bam = CreateAlignment(10, 20, "Test"); happyBamWriter.WriteRead(ref bam, false); happyBamWriter.FinishAll(); happyBamWriter.FlushAllBufferedRecords(); Assert.True(File.Exists(_outputFile)); Assert.True(File.Exists(_outputFile + ".bai")); }