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())
{
}
