Package picard.fingerprint

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