Package org.snpsift.caseControl

Class VariantCounter

java.lang.Object

org.snpsift.caseControl.VariantCounter

public class VariantCounter
extends java.lang.Object

A counnter for genotypes

Author:

pcingola

Constructor Summary

Constructors

Constructor	Description
VariantCounter(int size)

Method Summary

Modifier and Type	Method	Description
void	addEffect(java.lang.String effStr)
int	countNonZeroGenotypes()
int	getGenotype(int idx)
void	incGenotype(int idx)
void	incGenotype(int idx, int value)
void	parseGenotypes(org.snpeff.vcf.VcfEntry ve)	Update genotype counts
void	setGenotype(int idx, int value)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

VariantCounter

public VariantCounter(int size)

Method Detail

addEffect

public void addEffect(java.lang.String effStr)

countNonZeroGenotypes

public int countNonZeroGenotypes()

getGenotype

public int getGenotype(int idx)

incGenotype

public void incGenotype(int idx)

incGenotype

public void incGenotype(int idx,
                        int value)

parseGenotypes

public void parseGenotypes(org.snpeff.vcf.VcfEntry ve)

Update genotype counts

Parameters:

ve -

setGenotype

public void setGenotype(int idx,
                        int value)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object