private SmallPedigreeCallset GetCallset()
{
var callSets = new List <PedigreeSample>();
var outputVcf = CommonOptions.OutputDirectory.GetFileLocation("CNV.vcf.gz");
foreach (var sample in SmallPedigreeOptions.Samples)
{
string sampleName = sample.SampleName;
SingleSampleCallset callSet = new SingleSampleCallset(
new Bam(sample.Bam),
sampleName,
SmallPedigreeOptions.BAlleleSites,
SmallPedigreeOptions.IsPopulationBAlleleSites,
CommonOptions.OutputDirectory,
outputVcf);
callSet.SampleOutputFolder.Create();
callSets.Add(new PedigreeSample(callSet, sample.SampleType));
}
AnalysisDetails analysisDetails = new AnalysisDetails(
CommonOptions.OutputDirectory,
CommonOptions.WholeGenomeFasta,
CommonOptions.KmerFasta,
CommonOptions.FilterBed,
SmallPedigreeOptions.MultiSamplePloidyVcf,
SmallPedigreeOptions.CommonCnvsBed);
return(new SmallPedigreeCallset(callSets, analysisDetails));
}
public SmallPedigreeCallset(List <PedigreeSample> pedigreeSample, AnalysisDetails analysisDetails)
{
PedigreeSample = pedigreeSample;
AnalysisDetails = analysisDetails;
}
