Class Snp

  • All Implemented Interfaces:
    Comparable<Snp>

    public class Snp
    extends Object
    implements Comparable<Snp>
    Class to represent a SNP in context of a haplotype block that is used in fingerprinting.
    • Constructor Detail

      • Snp

        public Snp​(String name,
                   String chrom,
                   int pos,
                   byte allele1,
                   byte allele2,
                   double maf,
                   List<String> fingerprintPanels)
    • Method Detail

      • flip

        public Snp flip()
        Returns a new SNP object with the alleles swapped and MAF corrected.
      • getName

        public String getName()
      • getChrom

        public String getChrom()
      • getPos

        public int getPos()
      • getAllele1

        public byte getAllele1()
      • getAllele2

        public byte getAllele2()
      • getAlleles

        public List<htsjdk.variant.variantcontext.Allele> getAlleles()
      • getMaf

        public double getMaf()
      • getFingerprintPanels

        public List<String> getFingerprintPanels()
      • getHomozygousAllele1Genotype

        public DiploidGenotype getHomozygousAllele1Genotype()
      • getHeterogyzousGenotype

        public DiploidGenotype getHeterogyzousGenotype()
      • getHomozygousAllele2Genotype

        public DiploidGenotype getHomozygousAllele2Genotype()
      • getAlleleString

        public String getAlleleString()
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object