/// <summary>
/// Tells us that the resulting VariantContext should have the specified location </summary>
/// <param name="contig"> </param>
/// <param name="start"> </param>
/// <param name="stop">
/// @return </param>
public virtual VariantContextBuilder loc(string contig, long start, long stop)
{
this.Contig = contig;
this.start_Renamed = start;
this.stop_Renamed = stop;
toValidate = toValidate | VariantContext.Validation.ALLELES;
return(this);
}
/// <summary>
/// Tells this builder that the resulting VariantContext should use this genotypes GenotypeContext
///
/// Note that genotypes can be null -> meaning there are no genotypes
/// </summary>
/// <param name="genotypes"> </param>
public void SetGenotypes(GenotypesContext genotypes, bool requireValidation = true)
{
this.genotypes_Renamed = genotypes;
if (genotypes != null && requireValidation)
{
toValidate = toValidate | VariantContext.Validation.GENOTYPES;
}
//TODO: Perhaps if the genotypes are reset we should remove the validation flag if it was not required but was already present?
}
/// <summary>
/// Create an empty VariantContextBuilder where all values adopt their default values, but the bare min.
/// of info (source, chr, start, stop, and alleles) have been provided to start.
/// </summary>
public VariantContextBuilder(string source, string contig, long start, long stop, ICollection <Allele> alleles) : this()
{
this.Source = source;
this.Contig = contig;
this.start_Renamed = start;
this.stop_Renamed = stop;
this.alleles_Renamed = alleles;
this.attributes_Renamed = new Dictionary <string, object> (); // Collections.emptyMap(); // immutable
toValidate = toValidate | VariantContext.Validation.ALLELES; //using as bit flags
}
/// <summary>
/// Tells this builder to use this collection of alleles for the resulting VariantContext
/// </summary>
/// <param name="alleles"> </param>
/// <returns> this builder </returns>
public void SetAlleles(ICollection <Allele> alleles)
{
this.alleles_Renamed = alleles;
toValidate = toValidate | VariantContext.Validation.ALLELES;
}
/// <summary>
/// Create an empty VariantContextBuilder where all values adopt their default values, but the bare min.
/// of info (source, chr, start, stop, and alleles) have been provided to start.
/// </summary>
public VariantContextBuilder (string source, string contig, long start, long stop, ICollection<Allele> alleles) : this ()
{
this.Source = source;
this.Contig = contig;
this.start_Renamed = start;
this.stop_Renamed = stop;
this.alleles_Renamed = alleles;
this.attributes_Renamed = new Dictionary<string, object> ();// Collections.emptyMap(); // immutable
toValidate = toValidate | VariantContext.Validation.ALLELES;//using as bit flags
}
/// <summary>
/// Tells us that the resulting VariantContext should have the specified location </summary>
/// <param name="contig"> </param>
/// <param name="start"> </param>
/// <param name="stop">
/// @return </param>
public virtual VariantContextBuilder loc (string contig, long start, long stop)
{
this.Contig = contig;
this.start_Renamed = start;
this.stop_Renamed = stop;
toValidate = toValidate | VariantContext.Validation.ALLELES;
return this;
}
/// <summary>
/// Tells this builder that the resulting VariantContext should use this genotypes GenotypeContext
///
/// Note that genotypes can be null -> meaning there are no genotypes
/// </summary>
/// <param name="genotypes"> </param>
public void SetGenotypes (GenotypesContext genotypes, bool requireValidation = true)
{
this.genotypes_Renamed = genotypes;
if (genotypes != null && requireValidation) {
toValidate = toValidate | VariantContext.Validation.GENOTYPES;
}
//TODO: Perhaps if the genotypes are reset we should remove the validation flag if it was not required but was already present?
}
/// <summary>
/// Tells this builder to use this collection of alleles for the resulting VariantContext
/// </summary>
/// <param name="alleles"> </param>
/// <returns> this builder </returns>
public void SetAlleles (ICollection<Allele> alleles)
{
this.alleles_Renamed = alleles;
toValidate = toValidate | VariantContext.Validation.ALLELES;
}
