static void Main(string[] args)
{
if (args.Length < 4)
{
Console.WriteLine("EvaluateCNV {0}",
System.Reflection.Assembly.GetExecutingAssembly().GetName().Version);
Console.WriteLine("For more info see: http://confluence.illumina.com/display/BIOINFO/EvaluateCNV");
Console.WriteLine();
Console.WriteLine("Usage info:");
Console.WriteLine("EvaluateCNV $TruthSetPath $CNV.vcf $ExcludedRegionsBed $OutputPath [$RegionOfInterestBed]");
return;
}
CNVChecker checker = new CNVChecker();
string ROIBed = null;
double heterogeneityFraction = 1;
if (args.Length > 4)
{
ROIBed = args[4];
}
if (args.Length > 5)
{
heterogeneityFraction = double.Parse(args[5]);
}
checker.Evaluate(args[0], args[1], args[2], args[3], ROIBed, heterogeneityFraction);
}
private static int MainHelper(string[] args)
{
EvaluateCnvOptionsParser optionsParser = new EvaluateCnvOptionsParser();
if (args.Length < 4)
{
ShowHelp(optionsParser, Console.Error);
return(1);
}
var parsingResult = optionsParser.Parse(args.Skip(4));
if (!parsingResult.Success)
{
Console.Error.WriteLine(parsingResult.ErrorMessage);
ShowHelp(optionsParser, Console.Error);
return(1);
}
var options = parsingResult.Result;
if (options.Help)
{
ShowHelp(optionsParser, Console.Out);
return(0);
}
CNVChecker.Evaluate(args[0], args[1], args[2], args[3], options);
return(0);
}
static void Main(string[] args)
{
if (args.Length < 4)
{
Console.WriteLine("EvaluateCNV {0}",
System.Reflection.Assembly.GetExecutingAssembly().GetName().Version);
Console.WriteLine("For more info see: http://confluence.illumina.com/display/BIOINFO/EvaluateCNV");
Console.WriteLine();
Console.WriteLine("Usage info:");
Console.WriteLine("EvaluateCNV $TruthSetPath $CNV.vcf $ExcludedRegionsBed $OutputPath [$RegionOfInterestBed]");
return;
}
CNVChecker checker = new CNVChecker();
string ROIBed = null;
if (args.Length > 4) ROIBed = args[4];
checker.Evaluate(args[0], args[1], args[2], args[3], ROIBed);
}
private const int MaxCn = 5; // Currently the max copynum is 5
#endregion
public CnvEvaluator(CNVChecker cnvChecker)
{
_cnvChecker = cnvChecker;
}
public static void Evaluate(string truthSetPath, string cnvCallsPath, string excludedBed, string outputPath, EvaluateCnvOptions options)
{
double heterogeneityFraction = options.HeterogeneityFraction;
var knownCn = LoadKnownCn(truthSetPath, heterogeneityFraction);
knownCn = knownCn.SelectValues(
truthEntries => truthEntries.Where(truthEntry => truthEntry.Length >= options.MinEntrySize).ToList());
var calls = GetCnvCallsFromVcf(cnvCallsPath, options.DQscoreThreshold);
calls = calls.SelectValues(
chromosomeCalls => chromosomeCalls.Where(call => call.Length >= options.MinEntrySize).ToList());
// LoadRegionsOfInterest(options.RoiBed?.FullName);
var excludeIntervals = new Dictionary <string, List <CNInterval> >();
if (!string.IsNullOrEmpty(excludedBed))
{
var excludeIntervalsTmp = LoadIntervalsFromBed(excludedBed, false, 1.0);
List <string> keys = excludeIntervalsTmp.Keys.ToList();
foreach (string key in keys)
{
string chr = key;
if (!calls.ContainsKey(chr))
{
chr = key.Replace("chr", "");
}
if (!calls.ContainsKey(chr))
{
chr = "chr" + key;
}
if (!calls.ContainsKey(chr))
{
Console.WriteLine($"Error: Skipping exclude intervals for chromosome {key} with no truth data." +
$"Check that chromosome names are spelled correctly for exclude intervals");
continue;
}
excludeIntervals[chr] = excludeIntervalsTmp[key];
}
}
Console.WriteLine("TruthSet\t{0}", truthSetPath);
Console.WriteLine("CNVCalls\t{0}", cnvCallsPath);
bool includePassingOnly = Path.GetFileName(cnvCallsPath).ToLower().Contains("vcf");
var logger = new Logger(new[] { Console.Out }, new[] { Console.Error });
var settings = IsasConfigurationSettings.GetConfigSettings();
var output = new DirectoryLocation(outputPath);
var workerDirectory = new DirectoryLocation(Isas.Framework.Utilities.Utilities.GetAssemblyFolder(typeof(CNVChecker)));
var commandManager = new CommandManager(new ExecutableProcessor(settings, logger, workerDirectory));
WorkDoerFactory.RunWithWorkDoer(logger, settings, output, workDoer =>
{
var tabixWrapper = TabixWrapperFactory.GetTabixWrapper(logger, workDoer, commandManager);
var ploidyCorrector = new PloidyCorrector(logger, workDoer,
new PloidyEstimator(logger, workDoer, null, false, commandManager), tabixWrapper, false);
var checker = new CNVChecker(options.DQscoreThreshold, excludeIntervals, ploidyCorrector);
if (options.PloidyInfo.SexPloidyInfo != null)
{
Console.WriteLine($">>>Getting reference ploidy from provided ploidy information and PAR bed file '{options.PloidyInfo.ParBed}'");
var ploidy = checker.GetPloidy(options.PloidyInfo, output);
var referencePloidy = LoadReferencePloidy(options.PloidyInfo.SexPloidyInfo, options.PloidyInfo.ParBed);
knownCn = GetKnownCopyNumberWithReferencePloidy(referencePloidy, knownCn);
calls = GetCallsWithRefPloidy(calls, ploidy);
}
var cnvEvaluator = new CnvEvaluator(checker);
if (checker.DQscoreThreshold.HasValue && !Path.GetFileName(cnvCallsPath).ToLower().Contains("vcf"))
{
throw new ArgumentException("CNV.vcf must be in a vcf format when --dqscore option is used");
}
cnvEvaluator.ComputeAccuracy(knownCn, cnvCallsPath, outputPath, includePassingOnly, options, calls);
if (includePassingOnly)
{
cnvEvaluator.ComputeAccuracy(knownCn, cnvCallsPath, outputPath, false, options, calls);
}
ComputeCallability(logger, calls, options, output);
Console.WriteLine(">>>Done - results written to {0}", outputPath);
});
}