Region (groovy-ngs-utils API)

gngs.Region

All Implemented Interfaces and Traits:

IRegion, java.io.Serializable
```
class Region
extends groovy.util.Expando
```
Region of a genome
Among all the different region-based objects this is the highest level and most heavy weight representation of a region. The Region is a Groovy groovy.util.Expando object, so arbitrary properties can be set on it dynamically.
Regions can be created from common string representations of regions:
```
 Region r = new Region("chr1:20000-300000")
 
```
Alternatively they can be created directly:
```
 Region r = new Region("chr1", 20000, 300000)
 
```
Authors:
simon.sadedin@mcri.edu.au

Field Summary

Fields
Modifiers	Name	Description
`static long`	`serialVersionUID`

Properties Summary

Properties
Type	Name and description
`static Region`	`EMPTY_REGION`
`java.lang.String`	`chr`
`groovy.lang.IntRange`	`range`

Constructor Summary

Constructors
Constructor and description
`Region ()`
`Region (IRegion other)`
`Region (Map props = null, java.lang.String region)`
`Region (Map props = null, java.lang.String chr, groovy.lang.Range range)`
`Region (Map props = null, java.lang.String chr, int from, int to)`
`Region (htsjdk.samtools.SAMRecord read)`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`java.lang.Object`	`asType(java.lang.Class clazz)`
	`Region`	`copy()`
	`java.lang.String`	`endString()`
	`java.lang.Object`	`getExtra()`
	`java.lang.Integer`	`getFrom()`
	`int`	`getMidpoint()`
	`java.lang.Integer`	`getTo()`
	`java.lang.String`	`igv()`
	`Region`	`intersect(IRegion other)`
	`boolean`	`isCase(IRegion other)` Return true of this region overlaps the other.
	`boolean`	`isEmpty()` There is a design flaw in that because the range is inclusive of both start and end, we cannot represent an empty region.
	`boolean`	`isMinorContig()`
	`static boolean`	`isMinorContig(java.lang.String chr)` A hueristic that returns true if this the given contig represents a non-primary assembly contig or alternate haplotype in commonly used human genome assemblies.
	`double`	`mutualOverlap(IRegion other)` Compute the fraction of mutual overlap of this region with the other.
	`boolean`	`overlaps(java.lang.String chr, int from, int to)` @return true iff the specified region partially or fully overlaps this one
	`boolean`	`overlaps(Regions regions)` @return true if any region within the given Regions partially or fully overlaps this one
	`boolean`	`overlaps(IRegion other)` @return true iff the specified region partially or fully overlaps this one
	`static boolean`	`overlaps(IRegion r1, IRegion r2)` @return true iff the specified region partially or fully overlaps this one
	`void`	`parseRegion(java.lang.String region)`
	`void`	`setProps(Map props)`
	`long`	`size()` @return the number of positions spanned by this region
	`boolean`	`spans(IRegion r)` @return true iff this region fully encompasses the given region
	`java.lang.String`	`startString()`
	`Region`	`stripContigPrefix()`
	`java.lang.String`	`toString()`
	`Region`	`union(IRegion other)`
	`static Region`	`union(IRegion r1, IRegion r2)`
	`Region`	`widen(int bp)`
	`Region`	`widen(int leftBp, int rightBp)` @param bp number of base pairs to widen by

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class groovy.util.Expando`	groovy.util.Expando#setProperty(java.lang.String, java.lang.Object), groovy.util.Expando#getProperty(java.lang.String), groovy.util.Expando#equals(java.lang.Object), groovy.util.Expando#toString(), groovy.util.Expando#hashCode(), groovy.util.Expando#getProperties(), groovy.util.Expando#getMetaPropertyValues(), groovy.util.Expando#invokeMethod(java.lang.String, java.lang.Object), groovy.util.Expando#getMetaClass(), groovy.util.Expando#setMetaClass(groovy.lang.MetaClass), groovy.util.Expando#wait(long, int), groovy.util.Expando#wait(long), groovy.util.Expando#wait(), groovy.util.Expando#getClass(), groovy.util.Expando#notify(), groovy.util.Expando#notifyAll()
`class groovy.lang.GroovyObjectSupport`	groovy.lang.GroovyObjectSupport#setProperty(java.lang.String, java.lang.Object), groovy.lang.GroovyObjectSupport#getProperty(java.lang.String), groovy.lang.GroovyObjectSupport#getMetaClass(), groovy.lang.GroovyObjectSupport#setMetaClass(groovy.lang.MetaClass), groovy.lang.GroovyObjectSupport#invokeMethod(java.lang.String, java.lang.Object), groovy.lang.GroovyObjectSupport#wait(long, int), groovy.lang.GroovyObjectSupport#wait(long), groovy.lang.GroovyObjectSupport#wait(), groovy.lang.GroovyObjectSupport#equals(java.lang.Object), groovy.lang.GroovyObjectSupport#toString(), groovy.lang.GroovyObjectSupport#hashCode(), groovy.lang.GroovyObjectSupport#getClass(), groovy.lang.GroovyObjectSupport#notify(), groovy.lang.GroovyObjectSupport#notifyAll()

- Field Detail
  - public static final long serialVersionUID
- Property Detail
  - static final Region EMPTY_REGION
  - java.lang.String chr
  - groovy.lang.IntRange range
- Constructor Detail
  - Region()
  - Region(IRegion other)
  - Region(Map props = null, java.lang.String region)
  - Region(Map props = null, java.lang.String chr, groovy.lang.Range range)
  - Region(Map props = null, java.lang.String chr, int from, int to)
  - Region(htsjdk.samtools.SAMRecord read)
- Method Detail
  - @groovy.transform.CompileStatic java.lang.Object asType(java.lang.Class clazz)
  - Region copy()
  - java.lang.String endString()
  - @groovy.transform.CompileStatic java.lang.Object getExtra()
  - @groovy.transform.CompileStatic java.lang.Integer getFrom()
  - @groovy.transform.CompileStatic int getMidpoint()
  - @groovy.transform.CompileStatic java.lang.Integer getTo()
  - java.lang.String igv()
  - @groovy.transform.CompileStatic Region intersect(IRegion other)
  - @groovy.transform.CompileStatic boolean isCase(IRegion other)
    
    Return true of this region overlaps the other.
    Supports the groovy syntax:
```
 Region r1 = new Region("chr1:1-10")
 Region r2 = new Region("chr1:5-10")
 
 assert r1 in r2
 
```
    Note however that any overlap will return true, the region does not have to be contained entirely.
    Parameters:
    other
    Returns:
    true iff this region overlaps the other
  - boolean isEmpty()
    
    There is a design flaw in that because the range is inclusive of both start and end, we cannot represent an empty region. Some functions therefore return a special designated reigon that signifies "empty".
    Returns:
  - @groovy.transform.CompileStatic boolean isMinorContig()
  - @groovy.transform.CompileStatic static boolean isMinorContig(java.lang.String chr)
    
    A hueristic that returns true if this the given contig represents a non-primary assembly contig or alternate haplotype in commonly used human genome assemblies.
  - @groovy.transform.CompileStatic double mutualOverlap(IRegion other)
    
    Compute the fraction of mutual overlap of this region with the other.
    This is defined as, the minimum fraction of either region's overlap with the other. | 20 | |----------------------| 60 |------------------------------| 80 mutual overlap = min(20/60, 20/80) = 0.25
    Parameters:
    other
    Returns:
  - @groovy.transform.CompileStatic boolean overlaps(java.lang.String chr, int from, int to)
    
    Returns:
    true iff the specified region partially or fully overlaps this one
  - @groovy.transform.CompileStatic boolean overlaps(Regions regions)
    
    Returns:
    true if any region within the given Regions partially or fully overlaps this one
  - @groovy.transform.CompileStatic boolean overlaps(IRegion other)
    
    Returns:
    true iff the specified region partially or fully overlaps this one
  - @groovy.transform.CompileStatic static boolean overlaps(IRegion r1, IRegion r2)
    
    Returns:
    true iff the specified region partially or fully overlaps this one
  - @groovy.transform.CompileStatic void parseRegion(java.lang.String region)
  - @groovy.transform.CompileStatic void setProps(Map props)
  - @groovy.transform.CompileStatic long size()
    
    Returns:
    the number of positions spanned by this region
  - @groovy.transform.CompileStatic boolean spans(IRegion r)
    
    Returns:
    true iff this region fully encompasses the given region
  - java.lang.String startString()
  - @groovy.transform.CompileStatic Region stripContigPrefix()
  - java.lang.String toString()
  - @groovy.transform.CompileStatic Region union(IRegion other)
  - @groovy.transform.CompileStatic static Region union(IRegion r1, IRegion r2)
  - @groovy.transform.CompileStatic Region widen(int bp)
  - @groovy.transform.CompileStatic Region widen(int leftBp, int rightBp)
    
    Parameters:
    bp - number of base pairs to widen by
    Returns:
    a new Region object representing an interval bp wider than this one, with the lower boundary being limited to zero

Summary:
Field
Property
Constructor
Method

Groovy Documentation

[Groovy] Class Region

Field Summary

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Field Detail

public static final long serialVersionUID

Property Detail

static final Region EMPTY_REGION

java.lang.String chr

groovy.lang.IntRange range

Constructor Detail

Region()

Region(IRegion other)

Region(Map props = null, java.lang.String region)

Region(Map props = null, java.lang.String chr, groovy.lang.Range range)

Region(Map props = null, java.lang.String chr, int from, int to)

Region(htsjdk.samtools.SAMRecord read)

Method Detail

@groovy.transform.CompileStatic java.lang.Object asType(java.lang.Class clazz)

Region copy()

java.lang.String endString()

@groovy.transform.CompileStatic java.lang.Object getExtra()

@groovy.transform.CompileStatic java.lang.Integer getFrom()

@groovy.transform.CompileStatic int getMidpoint()

@groovy.transform.CompileStatic java.lang.Integer getTo()

java.lang.String igv()

@groovy.transform.CompileStatic Region intersect(IRegion other)

@groovy.transform.CompileStatic boolean isCase(IRegion other)

boolean isEmpty()

@groovy.transform.CompileStatic boolean isMinorContig()

@groovy.transform.CompileStatic static boolean isMinorContig(java.lang.String chr)

@groovy.transform.CompileStatic double mutualOverlap(IRegion other)

@groovy.transform.CompileStatic boolean overlaps(java.lang.String chr, int from, int to)

@groovy.transform.CompileStatic boolean overlaps(Regions regions)

@groovy.transform.CompileStatic boolean overlaps(IRegion other)

@groovy.transform.CompileStatic static boolean overlaps(IRegion r1, IRegion r2)

@groovy.transform.CompileStatic void parseRegion(java.lang.String region)

@groovy.transform.CompileStatic void setProps(Map props)

@groovy.transform.CompileStatic long size()

@groovy.transform.CompileStatic boolean spans(IRegion r)

java.lang.String startString()

@groovy.transform.CompileStatic Region stripContigPrefix()

java.lang.String toString()

@groovy.transform.CompileStatic Region union(IRegion other)

@groovy.transform.CompileStatic static Region union(IRegion r1, IRegion r2)

@groovy.transform.CompileStatic Region widen(int bp)

@groovy.transform.CompileStatic Region widen(int leftBp, int rightBp)