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);
}
public static IWittyerSettings Parse(string[] args) => WittyerParameters.ParsePrivate(args);
