public RegionGenerator()
{
// NOTE
// The following default column indexes must match the
// VCF file type specifications. These specifications can
// be obtained from various resources such as the following:
// http://www.internationalgenome.org/wiki/Analysis/vcf4.0
Columns = new VcfColumns()
{
Chr = 0,
Left = 1,
Right = -1,
ID = 2,
RefBase = 3,
AltBase = 4,
Quality = 5,
Filter = 6,
Info = 7,
Strand = 8
};
Chr = "chr1";
Position = 10;
Id = "id_001";
RefBase = new Base[] { Base.A, Base.C, Base.G };
AltBase = new Base[] { Base.U, Base.T, Base.N };
Quality = 654.321;
Filter = "filter_001";
Info = "info_001";
Strand = '*';
}
public VcfParser(VcfColumns columns, IVariantConstructor <I> constructor) : base(columns)
{
_idColumn = columns.ID;;
_refbColumn = columns.RefBase;
_altbColumn = columns.AltBase;
_qualityColumn = columns.Quality;
_filterColumn = columns.Filter;
_infoColumn = columns.Info;
_constructor = constructor;
}
public VcfParser(VcfColumns columns) : base(columns, new VariantConstructor())
{
}
