public CanvasSmallPedigreeOutput Run(CanvasSmallPedigreeInput input, IDirectoryLocation sandbox, IFileMover fileMover)
{
var output = _wrapper.Run(input, sandbox);
_move(output, fileMover);
return(_load(input));
}
public CanvasSmallPedigreeOutput Run(CanvasSmallPedigreeInput input, IDirectoryLocation sampleSandbox)
{
if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
{
_logger.Info($"Skipping Canvas: unsupported reference genome '{input.GenomeMetadata.Name}'");
return(null);
}
if (!_annotationFileProvider.CustomDbSnpVcf(input.GenomeMetadata) && input.Vcf == null)
{
_logger.Info($"Skipping Canvas. A dbSNP VCF file was not provided and no small variant VCF file is available");
return(null);
}
var commandLine = new StringBuilder("SmallPedigree-WGS");
commandLine.Append(GetMultiSampleCommandLine(input.Samples, input.GenomeMetadata, input.Vcf, sampleSandbox));
// use sample vcf by default (performance could be similar with dbSNP vcf though)
var bAlleleVcf = input.Vcf.VcfFile;
var bAlleleVcfOptionName = SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName;
if (_annotationFileProvider.CustomDbSnpVcf(input.GenomeMetadata))
{
bAlleleVcf = _annotationFileProvider.GetDbSnpVcf(input.GenomeMetadata);
bAlleleVcfOptionName = SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName;
}
commandLine.Append($" --{bAlleleVcfOptionName} \"{bAlleleVcf}\"");
var ploidyInfos = input.Samples.SelectData(sample => sample.PloidyInfo);
var ploidyVcf = _canvasPloidyVcfCreator.CreatePloidyVcf(ploidyInfos, input.GenomeMetadata, sampleSandbox);
if (ploidyVcf != null)
{
commandLine.Append($" --{SmallPedigreeOptionsParser.PloidyVcfOptionName} \"{ploidyVcf.VcfFile}\"");
}
var moreCustomParameters = new Dictionary <string, string>();
// common cnv feature disabled by default due to CANV-397
// string canvasPedigreeCallerParam = $@"--commoncnvs {_annotationFileProvider.GetCanvasAnnotationFile(input.GenomeMetadata, "commoncnvs.bed")}";
// moreCustomParameters["CanvasPedigreeCaller"] = canvasPedigreeCallerParam;
commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters(moreCustomParameters));
commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
// use Proband or, when proband is not available, first sample as pedigree id
var pedigreeId = input.Samples.Where(x => x.Value.SampleType == SampleType.Proband).Select(x => x.Key.Id).FirstOrDefault();
if (pedigreeId.IsNullOrEmpty())
{
pedigreeId = input.Samples.First().Key.Id;
}
var job = new JobInfo(_runtimeExecutable.FullName, _canvasExe + " " + commandLine, "Canvas_" + pedigreeId);
return(_workDoer.DoWork(WorkResourceRequest.CreateExact(1, 8), job, GetCanvasOutput(input.Samples, sampleSandbox)).Await());
}
private CanvasSmallPedigreeOutput Load(CanvasSmallPedigreeInput input)
{
var intermediateOutputs = input.Samples.SelectData((info, sample) =>
{
var stub = GetStub(info.Id);
var coverageAndVariantFrequency = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(stub);
if (!_canvasWorkerFactory.IncludeIntermediateResults())
{
return(new IntermediateOutput(coverageAndVariantFrequency, null, null, null));
}
var partitioned = SingleSampleCallset.GetPartitionedPath(stub);
var variantFrequencies = SingleSampleCallset.GetVfSummaryPath(stub);
var variantFrequenciesBaf = SingleSampleCallset.GetVfSummaryPath(stub);
return(new IntermediateOutput(coverageAndVariantFrequency, variantFrequencies, variantFrequenciesBaf, partitioned));
});
return(new CanvasSmallPedigreeOutput(new Vcf(GetCnvVcf()), intermediateOutputs));
}
private CanvasSmallPedigreeOutput Load(CanvasSmallPedigreeInput input)
{
var intermediateOutputs = input.Samples.SelectData((info, sample) =>
{
var stub = GetSingleSampleOutputStub(info);
var coverageAndVariantFrequency = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(stub);
var singleSampleVcf = new Vcf(SingleSampleCallset.GetVcfOutput(stub));
var partitioned = SingleSampleCallset.GetPartitionedPath(stub);
var variantFrequencies = SingleSampleCallset.GetVfSummaryPath(stub);
var variantFrequenciesBaf = SingleSampleCallset.GetVfSummaryBafPath(stub);
var coverageBigwig = SingleSampleCallset.GetCoverageBigWig(stub);
var bAlleleBedgraph = SingleSampleCallset.GetBAlleleBedGraph(stub);
var copyNumberBedgraph = SingleSampleCallset.GetCopyNumberBedGraph(stub);
return(new IntermediateOutput(singleSampleVcf, coverageAndVariantFrequency, variantFrequencies, variantFrequenciesBaf, partitioned,
coverageBigwig, bAlleleBedgraph, copyNumberBedgraph));
});
return(new CanvasSmallPedigreeOutput(new Vcf(GetPedigreeVcf()), intermediateOutputs));
}
public CanvasSmallPedigreeOutput Run(CanvasSmallPedigreeInput input, IDirectoryLocation sampleSandbox)
{
if (!_annotationFileProvider.IsSupported(input.GenomeMetadata))
{
_logger.Info($"Skipping Canvas: unsupported reference genome '{input.GenomeMetadata.Name}'");
return(null);
}
if (!_annotationFileProvider.CustomDbSnpVcf(input.GenomeMetadata) && input.Vcf == null)
{
_logger.Info($"Skipping Canvas. A dbSNP VCF file was not provided and no small variant VCF file is available");
return(null);
}
var commandLine = new StringBuilder("SmallPedigree-WGS");
commandLine.Append(GetMultiSampleCommandLine(input.Samples, input.GenomeMetadata, input.Vcf, sampleSandbox));
// use sample vcf by default (performance could be similar with dbSNP vcf though)
var bAlleleVcf = input.Vcf.VcfFile;
var bAlleleVcfOptionName = SingleSampleCommonOptionsParser.SampleBAlleleVcfOptionName;
if (_annotationFileProvider.CustomDbSnpVcf(input.GenomeMetadata))
{
bAlleleVcf = _annotationFileProvider.GetDbSnpVcf(input.GenomeMetadata);
bAlleleVcfOptionName = SingleSampleCommonOptionsParser.PopulationBAlleleVcfOptionName;
}
commandLine.Append($" --{bAlleleVcfOptionName} \"{bAlleleVcf}\"");
var ploidyInfos = input.Samples.SelectData(sample => sample.PloidyInfo);
var ploidyVcf = _canvasPloidyVcfCreator.CreatePloidyVcf(ploidyInfos, input.GenomeMetadata, sampleSandbox);
if (ploidyVcf != null)
{
commandLine.Append($" --{SmallPedigreeOptionsParser.PloidyVcfOptionName} \"{ploidyVcf.VcfFile}\"");
}
var canvasPartitionParam = $@"--commoncnvs {_annotationFileProvider.GetCanvasAnnotationFile(input.GenomeMetadata, "commoncnvs.bed")}";
var moreCustomParameters = new Dictionary <string, string> {
["CanvasPartition"] = canvasPartitionParam
};
commandLine.Append(_singleSampleInputCommandLineBuilder.GetCustomParameters(moreCustomParameters));
commandLine = _singleSampleInputCommandLineBuilder.MergeCustomCanvasParameters(commandLine);
// use Proband or, when proband is not available, first sample as pedigree id
var pedigreeId = input.Samples.Where(x => x.Value.SampleType == SampleType.Proband).Select(x => x.Key.Id).FirstOrDefault();
if (pedigreeId.IsNullOrEmpty())
{
pedigreeId = input.Samples.First().Key.Id;
}
var singleSampleJob = new UnitOfWork()
{
ExecutablePath = CrossPlatform.IsThisLinux() ? _runtimeExecutable.FullName : _canvasExe.FullName,
CommandLine = CrossPlatform.IsThisLinux() ? _canvasExe + " " + commandLine : commandLine.ToString(),
LoggingFolder = _workManager.LoggingFolder.FullName,
LoggingStub = "Canvas_" + pedigreeId,
};
_workManager.DoWorkSingleThread(singleSampleJob);
var sampleBams = input.Samples.SelectData(sample => sample.Bam);
return(GetCanvasOutput(sampleBams, sampleSandbox));
}
public CanvasSmallPedigreeOutput Run(CanvasSmallPedigreeInput input, IDirectoryLocation sandbox, IFileMover fileMover)
{
_logger.Info("Canvas is disabled.");
return(null);
}
