C# (CSharp) BgzfFile Examples

Example #1

File: IntermediateOutput.cs Project: zhang919/canvas

        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#pragma warning disable CS0618 // Type or member is obsolete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#pragma warning restore CS0618 // Type or member is obsolete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;
        }

Example #2

File: BgzfBedGraphWriter.cs Project: zhang919/canvas

 public void Write(IEnumerable <BedGraphEntry> bedGraphEntries, BgzfFile location, string header = null)
 {
     _bedGraphWriter.Write(bedGraphEntries, location.FileLocation, header);
     _tabixWrapper.BuildTabixIndex(location, TabixFileType.Bed);
 }

Example #3

File: CopyNumberBedGraphWriter.cs Project: zhang919/canvas

        public void Write(IReadOnlyList <CanvasSegment> segments, PloidyInfo ploidyInfo, BgzfFile location)
        {
            var entries = _calculator.Calculate(segments, ploidyInfo);

            _writer.Write(entries, location);
        }

Example #4

        public void Write(IFileLocation bafFile, BgzfFile bAllelesFile)
        {
            var bedGraphEntries = GetAlleleFrequencies(bafFile);

            _bedGraphWriter.Write(bedGraphEntries, bAllelesFile);
        }