TargetedCNVAnnotator

@groovy.util.logging.Log
class TargetedCNVAnnotator
extends java.lang.Object

Properties
Type	Name and description
`java.util.Map<java.lang.String, CNVDatabase>`	`cnvDatabases`
`double`	`mutualOverlapThreshold`
`java.lang.String`	`omimFile`
`Regions`	`target`
`boolean`	`verbose`

Constructors
Constructor and description
`TargetedCNVAnnotator (Regions targetRegions, RangedData dgv)`
`TargetedCNVAnnotator (Regions targetRegions, java.lang.String dgvFile)`
`TargetedCNVAnnotator (java.util.Map<java.lang.String, CNVDatabase> databases, Regions targetRegions)`

Methods
Type Params	Return Type	Name and description
	`void`	`annotate(java.lang.String vcfFile, java.io.Writer output)`
	`java.util.Map<java.lang.String, CNVFrequency>`	`annotate(IRegion v, java.lang.String type)` Compute the frequency of CNVs in databases that are compatible with a CNV identified in the given range, and matching the given type
	`CNVFrequency`	`annotateFromDatabase(CNVDatabase db, IRegion v, java.lang.String type)`
	`java.util.Map`	`annotateSize(IRegion cnv)`
	`gngs.Region`	`computeMaxRange(IRegion v)`
	`java.util.List<gngs.Region>`	`filterByType(java.lang.String type, java.util.List<gngs.Region> regions)`
	`java.util.List<gngs.Region>`	`findCompatibleRanges(CNVDatabase db, IRegion v)`
	`static void`	`main(java.lang.String[] args)`

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()`

Groovy Documentation

[Groovy] Class TargetedCNVAnnotator