private CanvasCallset GetCallset()
{
AnalysisDetails analysisDetails = new AnalysisDetails(CommonOptions.OutputDirectory, CommonOptions.WholeGenomeFasta, CommonOptions.KmerFasta, CommonOptions.FilterBed, SingleSampleCommonOptions.PloidyBed, null);
IFileLocation outputVcfPath = CommonOptions.OutputDirectory.GetFileLocation("CNV.vcf.gz");
CanvasCallset callSet = new CanvasCallset(
_tumorNormalOptions.TumorBam,
SingleSampleCommonOptions.SampleName,
SingleSampleCommonOptions.BAlleleSites,
SingleSampleCommonOptions.IsDbSnpVcf,
Enumerable.Empty <IFileLocation>(),
null,
_tumorNormalOptions.SomaticVcf,
outputVcfPath,
analysisDetails);
return(callSet);
}
private CanvasCallset GetCallset(ILogger logger)
{
AnalysisDetails analysisDetails = new AnalysisDetails(CommonOptions.OutputDirectory, CommonOptions.WholeGenomeFasta, CommonOptions.KmerFasta, CommonOptions.FilterBed, SingleSampleCommonOptions.PloidyVcf, null);
IFileLocation outputVcfPath = CommonOptions.OutputDirectory.GetFileLocation("CNV.vcf.gz");
var manifest = new NexteraManifest(_manifest.FullName, null, logger.Error);
CanvasCallset callSet = new CanvasCallset(
_tumorNormalOptions.TumorBam,
SingleSampleCommonOptions.SampleName,
SingleSampleCommonOptions.BAlleleSites,
SingleSampleCommonOptions.IsDbSnpVcf,
new[] { _normalBam },
manifest,
_tumorNormalOptions.SomaticVcf,
outputVcfPath,
analysisDetails);
return(callSet);
}
public CanvasCallset(
IFileLocation bam,
string sampleName,
IFileLocation normalVcfPath,
bool isDbSnpVcf,
IEnumerable <IFileLocation> normalBamPaths,
NexteraManifest manifest,
IFileLocation somaticVcfPath,
IFileLocation outputVcfPath,
AnalysisDetails analysisDetails)
{
SingleSampleCallset = new SingleSampleCallset(new Bam(bam), sampleName, normalVcfPath, isDbSnpVcf, analysisDetails.OutputFolder, outputVcfPath);
Manifest = manifest;
SomaticVcfPath = somaticVcfPath;
AnalysisDetails = analysisDetails;
NormalBamPaths = normalBamPaths.Select(file => new Bam(file));
}
public CanvasCallset(
SingleSampleCallset singleSampleCallset,
AnalysisDetails analysisDetails,
IEnumerable <IFileLocation> normalBamPaths,
NexteraManifest manifest,
IFileLocation somaticVcfPath)
{
SingleSampleCallset = singleSampleCallset;
Manifest = manifest;
if (somaticVcfPath != null)
{
SomaticVcfPath = somaticVcfPath;
}
AnalysisDetails = analysisDetails;
if (normalBamPaths != null)
{
NormalBamPaths = normalBamPaths.Select(file => new Bam(file));
}
}
private CanvasCallset GetCallset()
{
IFileLocation outputVcfPath = _input.CommonOptions.OutputDirectory.GetFileLocation("CNV.vcf.gz");
AnalysisDetails analysisDetails = new AnalysisDetails(
_input.CommonOptions.OutputDirectory,
_input.CommonOptions.WholeGenomeFasta,
_input.CommonOptions.KmerFasta,
_input.CommonOptions.FilterBed,
_input.SingleSampleCommonOptions.PloidyVcf,
null);
CanvasCallset callSet = new CanvasCallset(
_input.Bam,
_input.SingleSampleCommonOptions.SampleName,
_input.SingleSampleCommonOptions.BAlleleSites,
_input.SingleSampleCommonOptions.IsDbSnpVcf,
Enumerable.Empty <IFileLocation>(),
null,
null,
outputVcfPath,
analysisDetails);
return(callSet);
}
private CanvasCallset GetCallset(ILogger logger)
{
AnalysisDetails analysisDetails = new AnalysisDetails(CommonOptions.OutputDirectory, CommonOptions.WholeGenomeFasta,
CommonOptions.KmerFasta, CommonOptions.FilterBed, SingleSampleCommonOptions.PloidyVcf, null);
IFileLocation outputVcfPath = CommonOptions.OutputDirectory.GetFileLocation("CNV.vcf.gz");
var manifest = new NexteraManifest(_somaticEnrichmentOptions.Manifest.FullName, null, logger.Error);
// TODO: refactor and remove the following two lines
manifest.CanvasControlBinnedPath = _somaticEnrichmentOptions.ControlBinned?.FullName;
manifest.CanvasBinSize = _somaticEnrichmentOptions.ControlBinSize;
CanvasCallset callSet = new CanvasCallset(
_somaticEnrichmentOptions.Bam,
SingleSampleCommonOptions.SampleName,
SingleSampleCommonOptions.BAlleleSites,
SingleSampleCommonOptions.IsDbSnpVcf,
_somaticEnrichmentOptions.ControlBams,
manifest,
null,
outputVcfPath,
analysisDetails);
return(callSet);
}