All Implemented Interfaces:


public class HaplotypeNode.VariantInfo

These will be instantiated only when requested.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description
`public final boolean`	`isVariant`
`public final static String`	`Ref`
`public final static String`	`NonRef`
`public final static String`	`missing`

Constructor Summary

Constructors
Constructor	Description
`HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, long varLong)`
`HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, long varLong, String asmChr, int asmStart, int asmEnd, String asmStrand)`
`HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, Array<int> alleleDepths)`
`HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, Array<int> alleleDepths, String asmChr, int asmStart, int asmEnd, String asmStrand)`
`HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, Array<int> alleleDepths, long varLong, String asmChr, int asmStart, int asmEnd, String asmStrand)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`boolean`	`isVariant()`
`String`	`chromosome()`
`int`	`start()`
`int`	`end()`
`String`	`genotypeString()`
`String`	`refAlleleString()`
`String`	`altAlleleString()`
`boolean`	`isIndel()`
`boolean`	`isSymbolic()`
`int`	`length()`
`Array<int>`	`depth()`
`long`	`toLong()`
`String`	`asmChr()`
`int`	`asmStart()`
`int`	`asmEnd()`
`String`	`asmStrand()`

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

Constructor Detail

HaplotypeNode.VariantInfo

HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, long varLong)

HaplotypeNode.VariantInfo

HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, long varLong, String asmChr, int asmStart, int asmEnd, String asmStrand)

HaplotypeNode.VariantInfo

HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, Array<int> alleleDepths)

HaplotypeNode.VariantInfo

HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, Array<int> alleleDepths, String asmChr, int asmStart, int asmEnd, String asmStrand)

HaplotypeNode.VariantInfo

HaplotypeNode.VariantInfo(String chr, int startPos, int endPos, String genotype, String refAllele, String altAllele, boolean isVariant, Array<int> alleleDepths, long varLong, String asmChr, int asmStart, int asmEnd, String asmStrand)

Method Detail

isVariant
```
 boolean isVariant()
```

chromosome
```
 String chromosome()
```

start
```
 int start()
```

end
```
 int end()
```

genotypeString
```
 String genotypeString()
```

refAlleleString
```
 String refAlleleString()
```

altAlleleString
```
 String altAlleleString()
```

isIndel
```
 boolean isIndel()
```

isSymbolic
```
 boolean isSymbolic()
```

length
```
 int length()
```

depth
```
 Array<int> depth()
```

toLong
```
 long toLong()
```

asmChr
```
 String asmChr()
```

asmStart
```
 int asmStart()
```

asmEnd
```
 int asmEnd()
```

asmStrand
```
 String asmStrand()
```

Class HaplotypeNode.VariantInfo

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

HaplotypeNode.VariantInfo

HaplotypeNode.VariantInfo

HaplotypeNode.VariantInfo

HaplotypeNode.VariantInfo

HaplotypeNode.VariantInfo

Method Detail

isVariant

chromosome

start

end

genotypeString

refAlleleString

altAlleleString

isIndel

isSymbolic

length

depth

toLong

asmChr

asmStart

asmEnd

asmStrand