GenomeInfo

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

gngs.GenomeInfo

```
@groovy.transform.CompileStatic
class GenomeInfo
extends java.lang.Object
```
Static constant information about various genomes used to enable auto-sniffing etc
Authors:
simon.sadedin

Properties Summary

Properties
Type	Name and description
`static java.util.Map`	`grcMap`
`static java.util.Map`	`hgMap`
`static java.util.Map`	`mouseMap`

Constructor Summary

Constructors
Constructor and description
`GenomeInfo ()`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`static java.lang.Integer`	`humanGenomeCoordinateVersion(java.util.Map<java.lang.String, java.lang.Integer> contigSizes)` Parameters: contigSizes
	`static java.lang.String`	`sniffGenomeBuild(java.util.Map<java.lang.String, java.lang.Integer> contigSizes)` Infers the identity of the genome build used based on given contig sizes.

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.util.Map grcMap
  - static java.util.Map hgMap
  - static java.util.Map mouseMap
- Constructor Detail
  - GenomeInfo()
- Method Detail
  - static java.lang.Integer humanGenomeCoordinateVersion(java.util.Map<java.lang.String, java.lang.Integer> contigSizes)
    
    Parameters:
    contigSizes
    Returns:
    38, 37 or 18 indicating the coordinate system of the genome version for the given contig sizes
  - static java.lang.String sniffGenomeBuild(java.util.Map<java.lang.String, java.lang.Integer> contigSizes)
    
    Infers the identity of the genome build used based on given contig sizes.
    Parameters:
    contigSizes
    Returns:
    String identifier for genome build

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation