public RegionGenerator() { // NOTE // The following default column indexes must match the // GTF file type specifications. These specifications can // be obtained from various resources such as Ensembl: // https://uswest.ensembl.org/info/website/upload/gff.html Columns = new GtfColumns() { Chr = 0, Source = 1, Feature = 2, Left = 3, Right = 4, Score = 5, Strand = 6, Frame = 7, Attribute = 8 }; Source = "Source"; Feature = "Feature"; Chr = "chr1"; Left = 10; Right = 20; Score = 100.0; Strand = '*'; Frame = "Frame"; Attribute = "att1=1;att2=v2"; }
/// <summary> /// Parse General Transfer Format (GTF) format. /// </summary> /// <param name="sourceFilePath">Full path of source file name.</param> public GtfParser(GtfColumns columns, IGeneralFeatureConstructor <I> constructor) : base(columns) { _sourceColumn = columns.Source; _featureColumn = columns.Feature; _scoreColumn = columns.Score; _frameColumn = columns.Frame; _attributeColumn = columns.Attribute; _features = new Dictionary <string, int>(); _constructor = constructor; }
public GtfParser(GtfColumns columns) : base(columns, new GeneralFeatureConstructor()) { }