SnpEffInfo

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

gngs.SnpEffInfo

```
class SnpEffInfo
extends java.lang.Object
```
Support for parsing annotations from SnpEff
Authors:
simon.sadedin@mcri.edu.au

Properties Summary

Properties
Type	Name and description
`static java.lang.Object`	`EFFECTS_RANKED` Valid values of SnpEFF impacts
`static java.lang.Object`	`EFFECT_TO_VEP`
`java.lang.String`	`gene` The gene impacted (if any) by the variant
`java.lang.String`	`impact` The severity of the impact - HIGH, MODIFIER, MODERATE, LOW
`java.lang.String`	`info` The original subclause within the info line from which
`java.lang.String`	`transcript` The transcript impacted (if any) by the variant
`java.lang.String`	`type` The kind of impact.

Constructor Summary

Constructors
Constructor and description
`SnpEffInfo ()`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`java.lang.String`	`getConsequence()` This is an alias for the SNPEFF 'type' which is useful when trying to make code use both SNPEFF and VEP annotations
	`boolean`	`isTruncating()`
	`java.lang.String`	`toString()`

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
  - static java.lang.Object EFFECTS_RANKED
    
    Valid values of SnpEFF impacts
  - static java.lang.Object EFFECT_TO_VEP
  - java.lang.String gene
    
    The gene impacted (if any) by the variant
  - java.lang.String impact
    
    The severity of the impact - HIGH, MODIFIER, MODERATE, LOW
  - java.lang.String info
    
    The original subclause within the info line from which
  - java.lang.String transcript
    
    The transcript impacted (if any) by the variant
  - java.lang.String type
    
    The kind of impact. One of the values from SnpEffInfo.EFFECTS_RANKED
- Constructor Detail
  - SnpEffInfo()
- Method Detail
  - java.lang.String getConsequence()
    
    This is an alias for the SNPEFF 'type' which is useful when trying to make code use both SNPEFF and VEP annotations
    Returns:
    the type of SNPEFF effect
  - boolean isTruncating()
  - java.lang.String toString()

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation