Canvas.SomaticEnrichmentRunner.GetCallset C# (CSharp) Method

        private CanvasCallset GetCallset(ILogger logger)
        {
            IFileLocation outputVcfPath = CommonOptions.OutputDirectory.GetFileLocation("CNV.vcf.gz");
            var manifest = new NexteraManifest(_somaticEnrichmentOptions.Manifest.FullName, null, logger.Error);
            CanvasCallset callSet = new CanvasCallset(
                    _somaticEnrichmentOptions.Bam,
                    CommonOptions.SampleName,
                    CommonOptions.WholeGenomeFasta,
                    CommonOptions.OutputDirectory,
                    CommonOptions.KmerFasta,
                    CommonOptions.FilterBed,
                    CommonOptions.PloidyBed,
                    CommonOptions.BAlleleSites,
                    CommonOptions.IsDbSnpVcf,
                    _somaticEnrichmentOptions.ControlBams,
                    manifest,
                    null,
                    outputVcfPath);
            return callSet;
        }