Package picard.fingerprint
Class Snp
- java.lang.Object
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- picard.fingerprint.Snp
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- 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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
compareTo(Snp that)
boolean
equals(Object o)
Snp
flip()
Returns a new SNP object with the alleles swapped and MAF corrected.byte
getAllele1()
byte
getAllele2()
String
getAlleleString()
String
getChrom()
List<String>
getFingerprintPanels()
DiploidGenotype
getHeterogyzousGenotype()
DiploidGenotype
getHomozygousAllele1Genotype()
DiploidGenotype
getHomozygousAllele2Genotype()
double
getMaf()
String
getName()
int
getPos()
int
hashCode()
String
toString()
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Method Detail
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flip
public Snp flip()
Returns a new SNP object with the alleles swapped and MAF corrected.
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getName
public String getName()
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getChrom
public String getChrom()
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getPos
public int getPos()
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getAllele1
public byte getAllele1()
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getAllele2
public byte getAllele2()
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getMaf
public double getMaf()
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getHomozygousAllele1Genotype
public DiploidGenotype getHomozygousAllele1Genotype()
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getHeterogyzousGenotype
public DiploidGenotype getHeterogyzousGenotype()
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getHomozygousAllele2Genotype
public DiploidGenotype getHomozygousAllele2Genotype()
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getAlleleString
public String getAlleleString()
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compareTo
public int compareTo(Snp that)
- Specified by:
compareTo
in interfaceComparable<Snp>
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