public VariantCaller(CopyNumberLikelihoodCalculator copyNumberLikelihoodCalculator, PedigreeCallerParameters callerParameters, int qualityFilterThreshold)
{
_copyNumberLikelihoodCalculator = copyNumberLikelihoodCalculator;
_callerParameters = callerParameters;
_qualityFilterThreshold = qualityFilterThreshold;
_genotypes = GenerateGenotypeCombinations(callerParameters.MaximumCopyNumber);
}
public CanvasPedigreeCaller(ILogger logger, int qualityFilterThreshold, int deNovoQualityFilterThreshold,
PedigreeCallerParameters callerParameters, CopyNumberLikelihoodCalculator copyNumberLikelihoodCalculator,
IVariantCaller variantCaller, ICoverageBigWigWriter coverageBigWigWriter,
ICopyNumberModelFactory copyNumberModelFactory, ICopyNumberBedGraphWriter copyNumberBedGraphWriter,
CoverageBedGraphWriter partitionCoverageBedGraphWriter)
{
_logger = logger;
_qualityFilterThreshold = qualityFilterThreshold;
_deNovoQualityFilterThreshold = deNovoQualityFilterThreshold;
_callerParameters = callerParameters;
_copyNumberLikelihoodCalculator = copyNumberLikelihoodCalculator;
_variantCaller = variantCaller;
_coverageBigWigWriter = coverageBigWigWriter;
_copyNumberModelFactory = copyNumberModelFactory;
_copyNumberBedGraphWriter = copyNumberBedGraphWriter;
_partitionCoverageBedGraphWriter = partitionCoverageBedGraphWriter;
}
private static int Run(string[] args)
{
Utilities.LogCommandLine(args);
string outDir = null;
var segmentFiles = new List <string>();
var variantFrequencyFiles = new List <string>();
var sampleTypesString = new List <string>();
string ploidyBedPath = null;
string referenceFolder = null;
var sampleNames = new List <string>();
bool needHelp = false;
int? qScoreThresholdOption = null;
int? dqScoreThresholdOption = null;
string commonCnvsBedPath = null;
string parameterconfigPath = Path.Combine(Isas.Framework.Utilities.Utilities.GetAssemblyFolder(typeof(Program)), "PedigreeCallerParameters.json");
var p = new OptionSet()
{
{ "i|infile=", "file containing bins, their counts, and assigned segments (obtained from CanvasPartition.exe)", v => segmentFiles.Add(v) },
{ "v|varfile=", "file containing variant frequencies (obtained from CanvasSNV.exe)", v => variantFrequencyFiles.Add(v) },
{ "t|sampleType=", "sample types", v => sampleTypesString.Add(v) },
{ "o|outdir=", "name of output directory", v => outDir = v },
{ "r|reference=", "reference genome folder that contains GenomeSize.xml", v => referenceFolder = v },
{ "n|sampleName=", "sample name for output VCF header (optional)", v => sampleNames.Add(v) },
{ "p|ploidyBed=", "bed file specifying reference ploidy (e.g. for sex chromosomes) (optional)", v => ploidyBedPath = v },
{ "h|help", "show this message and exit", v => needHelp = v != null },
{ "q|qscore=", $"quality filter threshold (default {CanvasPedigreeCaller.DefaultQualityFilterThreshold})", v => qScoreThresholdOption = int.Parse(v) },
{ "commoncnvs=", "bed file with common CNVs (always include these intervals into segmentation results)", v => commonCnvsBedPath = v },
{ "d|dqscore=", $"de novo quality filter threshold (default {CanvasPedigreeCaller.DefaultDeNovoQualityFilterThreshold})", v => dqScoreThresholdOption = int.Parse(v) },
{ "c|config=", $"parameter configuration path (default {parameterconfigPath})", v => parameterconfigPath = v }
};
var extraArgs = p.Parse(args);
if (extraArgs.Count > 0)
{
Console.WriteLine("* Error: I don't understand the argument '{0}'", extraArgs[0]);
needHelp = true;
}
if (needHelp)
{
ShowHelp(p);
return(0);
}
if (!segmentFiles.Any() || !variantFrequencyFiles.Any() || string.IsNullOrEmpty(referenceFolder) || string.IsNullOrEmpty(outDir))
{
ShowHelp(p);
return(0);
}
foreach (string segmentFile in segmentFiles)
{
if (File.Exists(segmentFile))
{
continue;
}
Console.WriteLine($"CanvasPedigreeCaller.exe: File {segmentFile} does not exist! Exiting.");
return(1);
}
foreach (string variantFrequencyFile in variantFrequencyFiles)
{
if (File.Exists(variantFrequencyFile))
{
continue;
}
Console.WriteLine($"CanvasPedigreeCaller.exe: File {variantFrequencyFile} does not exist! Exiting.");
return(1);
}
var sampleTypesEnum = sampleTypesString.Select(GetSampleType).ToList();
if (!File.Exists(Path.Combine(referenceFolder, "GenomeSize.xml")))
{
Console.WriteLine($"CanvasPedigreeCaller.exe: File {Path.Combine(referenceFolder, "GenomeSize.xml")} does not exist! Exiting.");
return(1);
}
if (!File.Exists(parameterconfigPath))
{
Console.WriteLine($"CanvasPedigreeCaller.exe: File {parameterconfigPath} does not exist! Exiting.");
return(1);
}
if (commonCnvsBedPath != null)
{
if (!File.Exists(commonCnvsBedPath))
{
Console.WriteLine($"CanvasPedigreeCaller.exe: File {commonCnvsBedPath} does not exist! Exiting.");
return(1);
}
}
var parameterconfigFile = new FileLocation(parameterconfigPath);
var callerParameters = Deserialize <PedigreeCallerParameters>(parameterconfigFile);
int qScoreThreshold = CanvasPedigreeCaller.DefaultQualityFilterThreshold;
if (qScoreThresholdOption != null)
{
qScoreThreshold = qScoreThresholdOption.Value;
Console.WriteLine($"CanvasPedigreeCaller.exe: Using user-supplied quality score threshold {qScoreThresholdOption}.");
}
if (qScoreThreshold < 0 || qScoreThreshold >= callerParameters.MaxQscore)
{
throw new IlluminaException($"Quality score threshold must be >= 0 and < {callerParameters.MaxQscore}");
}
int dqScoreThreshold = CanvasPedigreeCaller.DefaultDeNovoQualityFilterThreshold;
if (dqScoreThresholdOption != null)
{
dqScoreThreshold = dqScoreThresholdOption.Value;
Console.WriteLine($"CanvasPedigreeCaller.exe: Using user-supplied de novo quality score threshold {qScoreThresholdOption}.");
}
if (dqScoreThreshold < 0 || dqScoreThreshold >= callerParameters.MaxQscore)
{
throw new IlluminaException($"De novo quality score threshold must be >= 0 and < {callerParameters.MaxQscore}");
}
var logger = new Logger(new[] { Console.Out }, new[] { Console.Error });
var settings = IsasConfigurationSettings.GetConfigSettings();
var outputDirectory = new DirectoryLocation(outDir);
var workerDirectory = new DirectoryLocation(Isas.Framework.Utilities.Utilities.GetAssemblyFolder(typeof(CanvasPedigreeCaller)));
var commandManager = new CommandManager(new ExecutableProcessor(settings, logger, workerDirectory));
var result = -1;
var pedigreeCallerWorkDirectory = outputDirectory.GetDirectoryLocation("CanvasPedigreeCaller");
WorkDoerFactory.RunWithWorkDoer(logger, settings, pedigreeCallerWorkDirectory, workDoer =>
{
var copyNumberLikelihoodCalculator = new CopyNumberLikelihoodCalculator(callerParameters.MaximumCopyNumber);
var variantCaller = callerParameters.DefaultCaller == CallerType.VariantCaller ?
(IVariantCaller) new VariantCaller(copyNumberLikelihoodCalculator, callerParameters, qScoreThreshold) :
new HaplotypeVariantCaller(copyNumberLikelihoodCalculator, callerParameters, qScoreThreshold);
var copyNumberModelFactory = new HaplotypeCopyNumberModelFactory();
var referenceGenome = new ReferenceGenomeFactory().GetReferenceGenome(new DirectoryLocation(referenceFolder));
var genomeMetadata = referenceGenome.GenomeMetadata;
var coverageBigWigWriterFactory =
new CoverageVisualizationWriterFactory(logger, workDoer, commandManager, genomeMetadata);
var roundingBedGraphWriter = new RoundingBedGraphWriter(new BedGraphWriterFacade(), 4);
var coverageBigWigWriter = coverageBigWigWriterFactory.CreateBinCoverageBigWigWriter(roundingBedGraphWriter);
var segmentCoverageBedGraphWriter = coverageBigWigWriterFactory.CreateSegmentBedGraphWriter(roundingBedGraphWriter);
var tabixWrapper = TabixWrapperFactory.GetTabixWrapper(logger, workDoer, commandManager);
var bgzfBedGraphWriter = new BgzfBedGraphWriter(new BedGraphWriterFacade(), tabixWrapper);
var copyNumberBedGraphWriter = new CopyNumberBedGraphWriter(bgzfBedGraphWriter, new CopyNumberBedGraphCalculator());
var caller = new CanvasPedigreeCaller(logger, qScoreThreshold, dqScoreThreshold, callerParameters, copyNumberLikelihoodCalculator, variantCaller, coverageBigWigWriter, copyNumberModelFactory, copyNumberBedGraphWriter, segmentCoverageBedGraphWriter);
var outVcf = outputDirectory.GetFileLocation("CNV.vcf.gz");
result = caller.CallVariants(variantFrequencyFiles, segmentFiles, outVcf, ploidyBedPath, referenceFolder, sampleNames, commonCnvsBedPath, sampleTypesEnum);
});
return(result);
}
