picard.fingerprint

Class Snp

java.lang.Object

picard.fingerprint.Snp

All Implemented Interfaces:

java.lang.Comparable<Snp>

public class Snp
extends java.lang.Object
implements java.lang.Comparable<Snp>

Class to represent a SNP in context of a haplotype block that is used in fingerprinting.

Constructor Summary

Constructors

Constructor and Description
Snp(java.lang.String name, java.lang.String chrom, int pos, byte allele1, byte allele2, double maf, java.util.List<java.lang.String> fingerprintPanels)

Method Summary

Modifier and Type	Method and Description
int	compareTo(Snp that)
boolean	equals(java.lang.Object o)
Snp	flip() Returns a new SNP object with the alleles swapped and MAF corrected.
byte	getAllele1()
byte	getAllele2()
java.util.List<htsjdk.variant.variantcontext.Allele>	getAlleles()
java.lang.String	getAlleleString()
java.lang.String	getChrom()
java.util.List<java.lang.String>	getFingerprintPanels()
DiploidGenotype	getHeterogyzousGenotype()
DiploidGenotype	getHomozygousAllele1Genotype()
DiploidGenotype	getHomozygousAllele2Genotype()
double	getMaf()
java.lang.String	getName()
int	getPos()
int	hashCode()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Snp

public Snp(java.lang.String name,
           java.lang.String chrom,
           int pos,
           byte allele1,
           byte allele2,
           double maf,
           java.util.List<java.lang.String> fingerprintPanels)

Method Detail

flip

public Snp flip()

Returns a new SNP object with the alleles swapped and MAF corrected.

getName

public java.lang.String getName()

getChrom

public java.lang.String getChrom()

getPos

public int getPos()

getAllele1

public byte getAllele1()

getAllele2

public byte getAllele2()

getAlleles

public java.util.List<htsjdk.variant.variantcontext.Allele> getAlleles()

getMaf

public double getMaf()

getFingerprintPanels

public java.util.List<java.lang.String> getFingerprintPanels()

getHomozygousAllele1Genotype

public DiploidGenotype getHomozygousAllele1Genotype()

getHeterogyzousGenotype

public DiploidGenotype getHeterogyzousGenotype()

getHomozygousAllele2Genotype

public DiploidGenotype getHomozygousAllele2Genotype()

getAlleleString

public java.lang.String getAlleleString()

compareTo

public int compareTo(Snp that)

Specified by:

compareTo in interface java.lang.Comparable<Snp>

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object