Package picard.fingerprint

Class HaplotypeBlock

java.lang.Object
picard.fingerprint.HaplotypeBlock
All Implemented Interfaces:
Comparable<HaplotypeBlock>
public class HaplotypeBlock extends Object implements Comparable<HaplotypeBlock>
Represents information about a group of SNPs that form a haplotype in perfect LD with one another.

  • Constructor Details

    • HaplotypeBlock

      public HaplotypeBlock(double maf)
      Constructs a haplotype block with the provided minor allele frequency.

  • Method Details

    • getHaplotypeFrequencies

      public double[] getHaplotypeFrequencies()
      Gets the set of haplotype frequencies.

    • addSnp

      public void addSnp(Snp snp)
      Adds a SNP to the haplotype. Will throw an exception if the SNP is on the wrong chromosome.

    • getSnp

      public Snp getSnp(String name)
      Gets a SNP by name if it belongs to this haplotype.

    • getFirstSnp

      public Snp getFirstSnp()
      Gets the arbitrarily first SNP in the haplotype.

    • contains

      public boolean contains(Snp snp)
      Returns true if the SNP is contained within the haplotype block, false otherwise.

    • size

      public int size()
      Returns the number of SNPs within the haplotype block.

    • getSnps

      public Collection<Snp> getSnps()
      Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.

    • getHaplotypeFrequency

      public double getHaplotypeFrequency(int i)
      Gets the frequency of the i'th diploid haplotype where haplotypes are ordered accorinding to DiploidHaplotype.

    • getMaf

      public double getMaf()
      Returns the minor allele frequency of this haplotype.

    • getSnpGenotype

      public DiploidGenotype getSnpGenotype(Snp snp, DiploidHaplotype haplotype)
      Gets the expected genotype of the provided SNP given the provided haplotype of this haplotype block.

    • getDiploidHaplotype

      public DiploidHaplotype getDiploidHaplotype(Snp snp, DiploidGenotype gt)
      Gets the diploid haplotype for this haplotype block given the provided SNP and SNP genotype.

    • compareTo

      public int compareTo(HaplotypeBlock that)
      Specified by:
      compareTo in interface Comparable<HaplotypeBlock>

    • 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