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);
}