Class Snp

java.lang.Object
picard.fingerprint.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 Details

    • Snp

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

    • 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()
    • compareTo

      public int compareTo(Snp that)
      Specified by:
      compareTo in interface Comparable<Snp>
    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object
    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object
    • toString

      public String toString()
      Overrides:
      toString in class Object