net.maizegenetics.dna.snp.genotypecall

Class BasicGenotypeMergeRule

java.lang.Object

net.maizegenetics.dna.snp.genotypecall.BasicGenotypeMergeRule

All Implemented Interfaces:

GenotypeMergeRule

public class BasicGenotypeMergeRule
extends Object
implements GenotypeMergeRule

Defines the methods for merging the calls from two taxa. The merge rules need to be defined at the level of genotypic calls and for read depth. In general if depth is available, it will be used to merge.

Author:

Ed Buckler, Jeff Glaubitz

Constructor Summary

Constructors

Constructor and Description
BasicGenotypeMergeRule(double errorRate)

Method Summary

Modifier and Type	Method and Description
byte	callBasedOnDepth(byte[] genoDepths) Makes a genotypic call based on allele depths
byte	callBasedOnDepth(int[] genoDepths) Makes a genotypic call based on allele depths
boolean	isMergePossible() Whether merge is even possible
byte	mergeCalls(byte geno1, byte geno2) Merges diploid genotypic calls into one
byte[]	mergeWithDepth(byte[] geno1depths, byte[] geno2depths) Merges sequencing depths of two taxa

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicGenotypeMergeRule

public BasicGenotypeMergeRule(double errorRate)

Method Detail

isMergePossible

public boolean isMergePossible()

Description copied from interface: GenotypeMergeRule

Whether merge is even possible

Specified by:

isMergePossible in interface GenotypeMergeRule

Returns:

whether merging is allowed.

mergeCalls

public byte mergeCalls(byte geno1,
                       byte geno2)

Description copied from interface: GenotypeMergeRule

Merges diploid genotypic calls into one

Specified by:

mergeCalls in interface GenotypeMergeRule

Parameters:

geno1 - genotype call of taxa 1

geno2 - genotype call of taxa 2

Returns:

merged genotype call

mergeWithDepth

public byte[] mergeWithDepth(byte[] geno1depths,
                             byte[] geno2depths)

Description copied from interface: GenotypeMergeRule

Merges sequencing depths of two taxa

Specified by:

mergeWithDepth in interface GenotypeMergeRule

Parameters:

geno1depths - allele depth of taxa 1

geno2depths - allele depths of taxa 2

Returns:

merged depths

callBasedOnDepth

public byte callBasedOnDepth(byte[] genoDepths)

Description copied from interface: GenotypeMergeRule

Makes a genotypic call based on allele depths

Specified by:

callBasedOnDepth in interface GenotypeMergeRule

Parameters:

genoDepths - allele depth of taxa

Returns:

genotype call

callBasedOnDepth

public byte callBasedOnDepth(int[] genoDepths)

Description copied from interface: GenotypeMergeRule

Makes a genotypic call based on allele depths

Specified by:

callBasedOnDepth in interface GenotypeMergeRule

Parameters:

genoDepths - allele depth of taxa

Returns:

genotype call