public void TestAllChromsInBedAreInBam() { CanvasBinParameters parameters = new CanvasBinParameters(); string assemblyFolder = Isas.Shared.Utilities.GetAssemblyFolder(typeof(TestCanvasBin)); string dataFolder = Path.Combine(assemblyFolder, "Data"); parameters.predefinedBinsFile = Path.Combine(dataFolder, "bins_chrU.bed"); parameters.bamFile = Path.Combine(dataFolder, "single-end.bam"); parameters.isPairedEnd = true; FragmentBinner fragmentBinner = new FragmentBinner(parameters); bool exceptionCaught = false; try { fragmentBinner.Bin(); } catch (ApplicationException e) { if (e.Message.Contains(String.Format("Not all chromosomes in {0} are found in {1}.", parameters.predefinedBinsFile, parameters.bamFile))) exceptionCaught = true; } Assert.IsTrue(exceptionCaught); }