public void NoChangeAfterDeserializeReserializeDeserialize()
{
var defaultConfigFilePath = Path.Combine(Environment.CurrentDirectory, "Config-default.json");
var text = File.ReadAllText(defaultConfigFilePath);
var deserializedWittyerConfigObject =
JsonConvert.DeserializeObject <IEnumerable <InputSpec> >(text,
InputSpecConverter.Create());
var reserialized = JsonConvert.SerializeObject(deserializedWittyerConfigObject, Formatting.Indented);
var deserializeReserializeDeserializedWittyerConfigObject =
JsonConvert.DeserializeObject <IEnumerable <InputSpec> >(reserialized,
InputSpecConverter.Create());
Assert.True(deserializedWittyerConfigObject.IsScrambledEquals(deserializeReserializeDeserializedWittyerConfigObject));
}
public void CanSuccessfullyParseSkippedBins()
{
var skippedBinsConfig = Path.Combine(ConfigsFolder, "Config-just-cng-skipped-bins.json");
var text = File.ReadAllText(skippedBinsConfig);
var deserializedWittyerConfigObject =
JsonConvert.DeserializeObject <IEnumerable <InputSpec> >(text,
InputSpecConverter.Create());
var copyNumberGainInputSpec =
deserializedWittyerConfigObject.First(inputSpec => inputSpec.VariantType == WittyerType.CopyNumberGain);
var bins = copyNumberGainInputSpec.BinSizes;
var expectedBins = ImmutableList <(uint size, bool skip)> .Empty
.Add((1, true))
.Add((1000, false))
.Add((5000, true))
.Add((10000, false))
.Add((20000, true));
Assert.Equal(bins, expectedBins);
}
public void ParsingIsCaseSensitive()
{
Assert.Throws <JsonSerializationException>(() => JsonConvert.DeserializeObject <IEnumerable <InputSpec> >(
File.ReadAllText(Path.Combine(ConfigsFolder, "Config-just-deletion-weirdcase.json")),
InputSpecConverter.Create()));
}
public void UsingDefaultConfigFileProducesSameInputSpecsAsCommandLineDefaults()
{
var defaultConfigFilePath = Path.Combine(Environment.CurrentDirectory, "Config-default.json");
var defaultInputSpecsCommandLine = InputSpec
.GenerateDefaultInputSpecs(true, WittyerType.AllTypes.OrderBy(s => s.Name))
.ToImmutableDictionary(x => x.VariantType, x => x);
var defaultInputSpecsConfig = JsonConvert
.DeserializeObject <IEnumerable <InputSpec> >(File.ReadAllText(defaultConfigFilePath),
InputSpecConverter.Create()).OrderBy(x => x.VariantType.Name)
.ToImmutableDictionary(x => x.VariantType, x => x);
foreach (var(key, value) in defaultInputSpecsConfig)
{
if (!defaultInputSpecsCommandLine.TryGetValue(key, out var value2))
{
MultiAssert.Equal(string.Empty, key.ToString());
}
if (!value.Equals(value2))
{
MultiAssert.Equal(value, value2);
}
}
MultiAssert.AssertAll();
}
public void ConfigFileDuplicateThrowsException()
{
Assert.Throws <JsonReaderException>(() =>
JsonConvert.DeserializeObject <IEnumerable <InputSpec> >(File.ReadAllText(Path.Combine(ConfigsFolder, "Config-duplicate-field.txt")),
InputSpecConverter.Create()));
}
public void InvalidConfigFileThrowsException(string configFileName, string expectedExceptionMessage)
{
var exception = Assert.Throws <JsonSerializationException>(() =>
JsonConvert.DeserializeObject <IEnumerable <InputSpec> >(File.ReadAllText(Path.Combine(ConfigsFolder, configFileName)),
InputSpecConverter.Create()));
Assert.Equal(expectedExceptionMessage, exception.Message.Replace("\r\n", "\n"));
}
internal static IWittyerSettings ParsePrivate(string[] args)
{
var parameters = new WittyerParameters();
var ndeskParser = new NdeskOptionParser(parameters, args);
var unparsed = ndeskParser.UnparsedArgs;
if (unparsed.Count > 0)
{
Console.WriteLine("Warning: Unparsed args: " + string.Join(" ", unparsed));
}
if (parameters._isDisplayVersion.Argument)
{
Console.WriteLine($"witty.er {CurrentVersion}");
Console.WriteLine(parameters.AdditionalHelpHeader);
Environment.Exit(0);
}
if (parameters._configFile.IsArgumentAssigned)
{
if (parameters._configOptions.Any(x => x.IsArgumentAssigned))
{
Console.Error.WriteLine(
"Config file argument cannot be used in combination with arguments for bin sizes, basepair distance, " +
"percent distance, included filters, excluded filters, variant types, or include bed. Exiting.");
Environment.Exit(1);
}
var fi = parameters._configFile.Argument;
if (!fi.ExistsNow())
{
Console.WriteLine(
$"Config file {fi.FullName} did not exist! Generating default config file in its place. Rerun with exactly same command line and it will work this time.");
File.WriteAllText(fi.FullName, InputSpec.GenerateDefaultInputSpecs(
parameters.Mode == EvaluationMode.CrossTypeAndSimpleCounting).SerializeToString());
Environment.Exit(0);
}
var configText = File.ReadAllText(parameters._configFile.Argument.FullName);
if (string.IsNullOrWhiteSpace(configText))
{
Console.Error.WriteLine("Bad Config file passed in at " + fi.FullName);
Environment.Exit(1);
}
parameters.InputSpecs = JsonConvert
.DeserializeObject <IEnumerable <InputSpec> >(configText, InputSpecConverter.Create())
.ToImmutableDictionary(x => x.VariantType, x => x);
}
else
{
var generatedSpecs = InputSpec.GenerateCustomInputSpecs(
parameters.Mode != EvaluationMode.CrossTypeAndSimpleCounting,
parameters._variantTypes.Argument, parameters._binSizes.Argument,
parameters._basepairDistance.Argument, parameters._percentDistance.Argument,
parameters._excludedFilters.Argument,
parameters._includedFilters.Argument, parameters._bedFile.Argument);
if (!parameters._basepairDistance.IsArgumentAssigned) // keep default
{
generatedSpecs = generatedSpecs.Select(i =>
i.VariantType == WittyerType.Insertion
? InputSpec.Create(i.VariantType, i.BinSizes, DefaultInsertionSpec.BasepairDistance,
i.PercentDistance, i.ExcludedFilters, i.IncludedFilters, i.IncludedRegions)
: i);
}
parameters.InputSpecs = generatedSpecs.ToImmutableDictionary(s => s.VariantType, s => s);
}
if (parameters.Mode == EvaluationMode.CrossTypeAndSimpleCounting &&
parameters.InputSpecs.Keys.Any(s => s.IsCopyNumberVariant))
{
Console.WriteLine(
$"Warning: {WittyerType.CopyNumberGain} and/or {WittyerType.CopyNumberLoss}" +
$" setting given when using {EvaluationMode.CrossTypeAndSimpleCounting}" +
" mode! This setting will be ignored.");
}
ValidateRequiredParameters(parameters._inputVcf);
ValidateRequiredParameters(parameters._truthVcf);
return(parameters);
}