private static void ComputeCallability(ILogger logger, Dictionary <string, List <CnvCall> > callsByContig,
EvaluateCnvOptions options, IDirectoryLocation output)
{
var kmerFasta = new FileLocation(options.KmerFa);
var canvasAnnotationDir = kmerFasta.Directory;
var filterBed = canvasAnnotationDir.GetFileLocation("filter13.bed");
if (!filterBed.Exists)
{
throw new ArgumentException($"Missing file at {filterBed}");
}
var annotationDir = canvasAnnotationDir.Parent;
var buildDir = annotationDir.Parent;
var genome = new ReferenceGenome(buildDir).GenomeMetadata;
var computer = CallabilityMetricsComputer.Create(logger, genome, filterBed, options.PloidyInfo.SexPloidyInfo.PloidyY == 0);
var callability = computer.CalculateMetric(callsByContig.SelectValues(calls => calls.Where(call => call.PassFilter).ToList()));
var callabilityFile = output.GetFileLocation($"{options.BaseFileName}_callability.txt");
File.WriteAllLines(callabilityFile.FullName, callability.GetMetrics().Select(metric => metric.ToCsv().Replace(",", "\t")));
logger.Info($"Callability: {callability.Callability}. Called bases: {callability.CalledBases}. Total bases: {callability.TotalBases}.");
}
public void ComputeAccuracy(Dictionary <string, List <CNInterval> > knownCN, string cnvCallsPath, string outputPath, bool includePassingOnly, EvaluateCnvOptions options, Dictionary <string, List <CnvCall> > calls)
{
// Make a note of how many bases in the truth set are not *actually* considered to be known bases, using
// the "cnaqc" exclusion set:
bool regionsOfInterest = !_cnvChecker.RegionsOfInterest.Empty();
var baseCounters = new List <BaseCounter> {
new BaseCounter(MaxCn, 0, Int32.MaxValue, regionsOfInterest)
};
if (options.SplitBySize)
{
baseCounters.Add(new BaseCounter(MaxCn, 0, 4999, regionsOfInterest));
baseCounters.Add(new BaseCounter(MaxCn, 5000, 9999, regionsOfInterest));
baseCounters.Add(new BaseCounter(MaxCn, 10000, 99999, regionsOfInterest));
baseCounters.Add(new BaseCounter(MaxCn, 100000, 499999, regionsOfInterest));
baseCounters.Add(new BaseCounter(MaxCn, 500000, int.MaxValue, regionsOfInterest));
}
// not parallel here as parallelism will be attained at the level of regression workflow
_cnvChecker.CountExcludedBasesInTruthSetIntervals(knownCN);
Dictionary <string, BitArray> referenceBases = null;
if (options.KmerFa != null)
{
referenceBases = new Dictionary <string, BitArray>();
foreach (var chr in knownCN.Keys)
{
string chromReferenceBases = FastaLoader.LoadFastaSequence(options.KmerFa, chr);
var bitArrayBases = new BitArray(chromReferenceBases.Length);
// Mark which k-mers in the fasta file are unique. These are indicated by upper-case letters.
for (var i = 0; i < chromReferenceBases.Length; i++)
{
if (char.IsUpper(chromReferenceBases[i]))
{
bitArrayBases[i] = true;
}
}
referenceBases[chr] = bitArrayBases;
}
}
foreach (var baseCounter in baseCounters)
{
_cnvChecker.InitializeIntervalMetrics(knownCN);
var metrics = CalculateMetrics(knownCN, calls, baseCounter, options.SkipDiploid, includePassingOnly, referenceBases);
string fileName = $"{options.BaseFileName}";
if (options.DQscoreThreshold.HasValue)
{
fileName += "_denovo";
}
if (baseCounter.MinSize != 0 || baseCounter.MaxSize != int.MaxValue)
{
fileName += $"_{Math.Round(baseCounter.MinSize / 1000.0)}kb";
fileName += baseCounter.MaxSize == int.MaxValue ? "+" : $"_{ Math.Round(baseCounter.MaxSize / 1000.0)}kb";
}
fileName += ".txt";
var outputDir = new DirectoryLocation(outputPath);
outputDir.Create();
var outputFile = outputDir.GetFileLocation(fileName);
using (FileStream stream = new FileStream(outputFile.FullName, includePassingOnly ?
FileMode.Create : FileMode.Append, FileAccess.Write))
using (StreamWriter outputWriter = new StreamWriter(stream))
{
outputWriter.NewLine = "\n";
WriteResults(cnvCallsPath, outputWriter, baseCounter, includePassingOnly, metrics);
}
}
}
public static void Evaluate(string truthSetPath, string cnvCallsPath, string excludedBed, string outputPath, EvaluateCnvOptions options)
{
double heterogeneityFraction = options.HeterogeneityFraction;
var knownCn = LoadKnownCn(truthSetPath, heterogeneityFraction);
knownCn = knownCn.SelectValues(
truthEntries => truthEntries.Where(truthEntry => truthEntry.Length >= options.MinEntrySize).ToList());
var calls = GetCnvCallsFromVcf(cnvCallsPath, options.DQscoreThreshold);
calls = calls.SelectValues(
chromosomeCalls => chromosomeCalls.Where(call => call.Length >= options.MinEntrySize).ToList());
// LoadRegionsOfInterest(options.RoiBed?.FullName);
var excludeIntervals = new Dictionary <string, List <CNInterval> >();
if (!string.IsNullOrEmpty(excludedBed))
{
var excludeIntervalsTmp = LoadIntervalsFromBed(excludedBed, false, 1.0);
List <string> keys = excludeIntervalsTmp.Keys.ToList();
foreach (string key in keys)
{
string chr = key;
if (!calls.ContainsKey(chr))
{
chr = key.Replace("chr", "");
}
if (!calls.ContainsKey(chr))
{
chr = "chr" + key;
}
if (!calls.ContainsKey(chr))
{
Console.WriteLine($"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);
});
}
