/// <summary>
/// Constructor used to get the codec and map from these things
/// </summary>
/// <param name="baseCodec">The base codec, necessary to get the string cache from</param>
public ListAndSetHash(AbstractVCFCodec baseCodec)
{
this.parentCodec = baseCodec;
ListAndHash passList = new ListAndHash() { List = new List<string>().AsReadOnly(), Hash = new ImmutableHashSet<string>() };
_strToListAndHash[VCFConstants.PASSES_FILTERS_v3] = passList;
_strToListAndHash[VCFConstants.PASSES_FILTERS_v4] = passList;
}
/// <summary>
/// Constructor used to get the codec and map from these things
/// </summary>
/// <param name="baseCodec">The base codec, necessary to get the string cache from</param>
public ListAndSetHash(AbstractVCFCodec baseCodec)
{
this.parentCodec = baseCodec;
ListAndHash passList = new ListAndHash()
{
List = new List <string>().AsReadOnly(), Hash = new ImmutableHashSet <string>()
};
_strToListAndHash[VCFConstants.PASSES_FILTERS_v3] = passList;
_strToListAndHash[VCFConstants.PASSES_FILTERS_v4] = passList;
}
/// <summary>
/// Creates a new lazy loading genotypes context using the LazyParser to create
/// genotypes data on demand.
/// </summary>
/// <param name="parser"> the parser to be used to load on-demand genotypes data </param>
/// <param name="unparsedGenotypeData"> the encoded genotypes data that we will decode if necessary </param>
/// <param name="nUnparsedGenotypes"> the number of genotypes that will be produced if / when we actually decode the genotypes data </param>
public LazyGenotypesContext (AbstractVCFCodec codec, IList<Allele> alleles, string contig, int start, string unparsedGenotypeData, int nUnparsedGenotypes)
: base (EMPTY)
{
this.codec = codec;
this.alleles = alleles;
this.contig = contig;
this.start = start;
//Note: This formally kept a reference to a parser interface, decided that was too much overhead though so skipped it.
//this.parser = parser;
this.UnparsedGenotypeData = unparsedGenotypeData;
this.nUnparsedGenotypes = nUnparsedGenotypes;
}
/// <summary>
/// Creates a new lazy loading genotypes context using the LazyParser to create
/// genotypes data on demand.
/// </summary>
/// <param name="parser"> the parser to be used to load on-demand genotypes data </param>
/// <param name="unparsedGenotypeData"> the encoded genotypes data that we will decode if necessary </param>
/// <param name="nUnparsedGenotypes"> the number of genotypes that will be produced if / when we actually decode the genotypes data </param>
public LazyGenotypesContext(AbstractVCFCodec codec, IList <Allele> alleles, string contig, int start, string unparsedGenotypeData, int nUnparsedGenotypes)
: base(EMPTY)
{
this.codec = codec;
this.alleles = alleles;
this.contig = contig;
this.start = start;
//Note: This formally kept a reference to a parser interface, decided that was too much overhead though so skipped it.
//this.parser = parser;
this.UnparsedGenotypeData = unparsedGenotypeData;
this.nUnparsedGenotypes = nUnparsedGenotypes;
}
