public IntermediateOutput(Vcf cnvVcf, IFileLocation coverageAndVariantFrequencies, IFileLocation variantFrequencies, IFileLocation variantFrequenciesBaf,
IFileLocation partitioned, IFileLocation coverageBigwig, BgzfFile bAlleleBedgraph, BgzfFile copyNumberBedgraph)
{
CnvVcf = cnvVcf;
#pragma warning disable CS0618 // Type or member is obsolete
CoverageAndVariantFrequencies = coverageAndVariantFrequencies;
VariantFrequencies = variantFrequencies;
VariantFrequenciesBaf = variantFrequenciesBaf;
Partitioned = partitioned;
#pragma warning restore CS0618 // Type or member is obsolete
CoverageBigwig = coverageBigwig;
BAlleleBedgraph = bAlleleBedgraph;
CopyNumberBedgraph = copyNumberBedgraph;
}
public void Write(IEnumerable <BedGraphEntry> bedGraphEntries, BgzfFile location, string header = null)
{
_bedGraphWriter.Write(bedGraphEntries, location.FileLocation, header);
_tabixWrapper.BuildTabixIndex(location, TabixFileType.Bed);
}
public void Write(IReadOnlyList <CanvasSegment> segments, PloidyInfo ploidyInfo, BgzfFile location)
{
var entries = _calculator.Calculate(segments, ploidyInfo);
_writer.Write(entries, location);
}
public void Write(IFileLocation bafFile, BgzfFile bAllelesFile)
{
var bedGraphEntries = GetAlleleFrequencies(bafFile);
_bedGraphWriter.Write(bedGraphEntries, bAllelesFile);
}