GenotypeVector (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.genotypes.GenotypeVector

All Implemented Interfaces:

java.io.Serializable
```
public class GenotypeVector
extends java.lang.Object
implements java.io.Serializable
```
A vector of genotypes in a 'compact' structure Note: Genotypes 0/0, 0/1, 1/0, 1/1 are stored in 2 bits. WARNIGN: Other genotypes are ignored or silently converted to 0/0

Author:

pcingola

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field Description

static byte[] mask

static byte[] reverseMask

Constructor Summary

Constructors
Constructor Description

GenotypeVector(int size)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`get(int sampleNum)`
`void`	`set(int sampleNum, int code)`	Set genotype code Codes {0, 1, 2, 3} => Genotypes { 0/0, 0/1, 1/0, 1/1 }
`void`	`set(int sampleNum, VcfGenotype vg)`	Set genotype
`int`	`size()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mask
```
public static final byte[] mask
```

reverseMask
```
public static final byte[] reverseMask
```

Constructor Detail
- GenotypeVector
```
public GenotypeVector(int size)
```

Method Detail

get
```
public int get(int sampleNum)
```

set
```
public void set(int sampleNum,
                int code)
```
Set genotype code Codes {0, 1, 2, 3} => Genotypes { 0/0, 0/1, 1/0, 1/1 }

Parameters:

sampleNum -

code -

set

public void set(int sampleNum,
                VcfGenotype vg)

Set genotype

Parameters:: sampleNum -; vg -

size
```
public int size()
```