VariantInjector

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

gngs.VariantInjector

```
@groovy.util.logging.Log
class VariantInjector
extends java.lang.Object
```
Injects a variant into a FASTQ read based on recognising the sequence corresponding to the reference sequence for the location of the variant within the read.
Authors:
Simon Sadedin

Properties Summary

Properties
Type	Name and description
`double`	`alleleFraction`
`boolean`	`debugMode`
`int`	`nReplaced`
`int`	`padding`
`gngs.FASTA`	`reference`
`java.lang.String`	`referenceBases`
`java.lang.String`	`referenceBasesRC`
`java.lang.String`	`replacementBases`
`java.lang.String`	`replacementBasesRC`
`int`	`total`
`gngs.Variant`	`variant`
`int`	`variantOffset`

Constructor Summary

Constructors
Constructor and description
`VariantInjector (gngs.FASTA reference, gngs.Variant variant, int variantOffset)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`void`	`computeReplacementBases()` Computes the corresponding sequence after a reference sequence is mutated by a variant which must be a SNV, insertion or deletion
	`void`	`inject(gngs.FASTQRead r1, gngs.FASTQRead r2)` Injects the variant for this VariantInjector into the given reads, and adjusts the base quality string accordingly.
	`boolean`	`inject(gngs.FASTQRead r, java.lang.String refBases, java.lang.String repBases, boolean random)`
	`void`	`renameRead(gngs.FASTQRead r1, gngs.FASTQRead r2)`

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll()`

- Property Detail
  - double alleleFraction
  - boolean debugMode
  - int nReplaced
  - int padding
  - gngs.FASTA reference
  - java.lang.String referenceBases
  - java.lang.String referenceBasesRC
  - java.lang.String replacementBases
  - java.lang.String replacementBasesRC
  - int total
  - gngs.Variant variant
  - int variantOffset
- Constructor Detail
  - VariantInjector(gngs.FASTA reference, gngs.Variant variant, int variantOffset)
- Method Detail
  - @groovy.transform.CompileStatic void computeReplacementBases()
    
    Computes the corresponding sequence after a reference sequence is mutated by a variant which must be a SNV, insertion or deletion
  - @groovy.transform.CompileStatic void inject(gngs.FASTQRead r1, gngs.FASTQRead r2)
    
    Injects the variant for this VariantInjector into the given reads, and adjusts the base quality string accordingly.
    Parameters:
    r1 - read 1
    r2 - read 2
  - @groovy.transform.CompileStatic boolean inject(gngs.FASTQRead r, java.lang.String refBases, java.lang.String repBases, boolean random)
  - @groovy.transform.CompileStatic void renameRead(gngs.FASTQRead r1, gngs.FASTQRead r2)

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation