Package picard.fingerprint

Class Snp

java.lang.Object
picard.fingerprint.Snp
All Implemented Interfaces:
htsjdk.samtools.util.Locatable, Comparable<Snp>
public class Snp extends Object implements Comparable<Snp>, htsjdk.samtools.util.Locatable
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

    • getContig

      public String getContig()
      Specified by:
      getContig in interface htsjdk.samtools.util.Locatable

    • getStart

      public int getStart()
      Specified by:
      getStart in interface htsjdk.samtools.util.Locatable

    • getEnd

      public int getEnd()
      Specified by:
      getEnd in interface htsjdk.samtools.util.Locatable