public class Genotype extends Object
GenotypeCalls
. By convention, the
reference allele is represented by the integer 0
. -1
encodes no-call.Constructor and Description |
---|
Genotype(Collection<Integer> alleleNumbers)
Construct
Genotype with list of allele numbers |
Modifier and Type | Method and Description |
---|---|
boolean |
equals(Object obj) |
com.google.common.collect.ImmutableList<Integer> |
getAlleleNumbers() |
int |
getPloidy() |
int |
hashCode() |
boolean |
isDiploid() |
boolean |
isHet() |
boolean |
isHomAlt() |
boolean |
isHomRef() |
boolean |
isMonoploid() |
boolean |
isNotObserved() |
String |
toString() |
public static final int NO_CALL
public static final int REF_CALL
public Genotype(Collection<Integer> alleleNumbers)
Genotype
with list of allele numbersalleleNumbers
- The allele numbers to initialize withpublic com.google.common.collect.ImmutableList<Integer> getAlleleNumbers()
ImmutableList
of alleles in this genotypepublic int getPloidy()
public boolean isDiploid()
true
if the sample is diploid, false
otherwisepublic boolean isMonoploid()
true
if the sample is monoploid, false
otherwisepublic boolean isHet()
true
if the sample is heterozygous, false
otherwisepublic boolean isHomRef()
true
if the sample is homozygous ref, false
otherwisepublic boolean isHomAlt()
true
if the sample is homozygous alt, false
otherwisepublic boolean isNotObserved()
true
if the genotype is not observed in all allelesCopyright © 2016. All rights reserved.