Package org.gorpipe.gor.haplotype

Class GBasicRulesCalculator

java.lang.Object

org.gorpipe.gor.haplotype.GBasicRulesCalculator

public class GBasicRulesCalculator
extends java.lang.Object

Checks the correctness of phase of haplotypes/genotypes using basic rules.

Field Summary

Fields

Modifier and Type	Field	Description
static byte	INCOMPATIBLE_GENOTYPES	Indicates that the genotypes of the trio are incompatible in some way.
protected byte	unknown

Constructor Summary

Constructors

Constructor	Description
GBasicRulesCalculator()

Method Summary

Modifier and Type	Method	Description
byte	checkBasicRules(byte[] child, byte[] father, byte[] mother)	Check basic rules (inhertance error and phase) at an single autosomal locus for a child in a triad.
void	setUnknownAllele(byte unknown)	Set the value for an unknown allele (default is Byte.MIN_VALUE) .

Methods inherited from class java.lang.Object

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

Field Detail

INCOMPATIBLE_GENOTYPES

public static final byte INCOMPATIBLE_GENOTYPES

Indicates that the genotypes of the trio are incompatible in some way.

See Also:

Constant Field Values

unknown

protected byte unknown

Constructor Detail

GBasicRulesCalculator

public GBasicRulesCalculator()

Method Detail

setUnknownAllele

public void setUnknownAllele(byte unknown)

Set the value for an unknown allele (default is Byte.MIN_VALUE) .

Parameters:

unknown - the unknonw value

checkBasicRules

public byte checkBasicRules(byte[] child,
                            byte[] father,
                            byte[] mother)

Check basic rules (inhertance error and phase) at an single autosomal locus for a child in a triad.

Parameters:

child - the child genotypes

father - the father genotypes

mother - the mother genotypes

Returns:

A byte value indicating the phase UNDETERMINED_PHASE, CORRECT_PHASE, INCORRECT_PHASE, DOUBLE_CONGRUENCY, TRIPLE_CONGRUENCY, INCOMPATIBLE_GENOTYPES.