public void TestBinSingleEndBam() { string assemblyFolder = Isas.Shared.Utilities.GetAssemblyFolder(typeof(TestCanvasBin)); string dataFolder = Path.Combine(assemblyFolder, "Data"); string bedPath = Path.Combine(dataFolder, "bins_chrM.bed"); string bamPath = Path.Combine(dataFolder, "single-end.bam"); Dictionary<string, List<GenomicBin>> bins = CanvasCommon.Utilities.LoadBedFile(bedPath, gcIndex: 3); string chrom = "chrM"; FragmentBinner.BinTask binTask = new FragmentBinner.BinTask(null, chrom, bamPath, bins[chrom]); bool exceptionCaught = false; try { binTask.DoIt(); } catch (ApplicationException e) { if (e.Message.Contains("No paired alignments found")) exceptionCaught = true; } Assert.IsTrue(exceptionCaught); }