Regions

gngs.Regions

All Implemented Interfaces and Traits:

java.lang.Iterable<gngs.Region>
```
class Regions
extends java.lang.Object
implements java.lang.Iterable<gngs.Region>
```
A set of genomic regions, each indexed by chromosome, start and end position.
The Regions class provides operations for working on Ranges but adds awareness of chromosomes (or contigs) to RangeIndex. It offers most of the same functions as exist for a RangeIndex but transparently handles multiple chromosomes.
The internal representation for each genomic range stored in a Regions object is a Groovy groovy.lang.IntRange. For efficiency, many of the methods return these underlying IntRange objects directly, whenever a method is clearly appliciable only to a single chromosome. When functionality spans chromosomes, the groovy.lang.IntRange objects will be converted to gngs.Region objects which carries an extra field for the chromosome. This adds a small amount of overhead, but enables the class to support various useful functions such as implementing Groovy's enhanced support for java.lang.Iterable objects.
Often Regions will be loaded from a BED file. In that case, see the BED class which extends Regions, but provides extensive support for parsing, loading and filtering BED files. To create a purely in-memory set of regions, use the constructor:
```
 Regions regions = new Regions()
 regions.addRegion("chr1",100,200)
 regions.addRegion("chr1",150,300)
 
```
When added this way, Regions follows the BED file convention that the start of the range is considered inclusive, but the end value is considered exclusive of the range added. Once loaded, various operations can be performed on the ranges. Since the Iterable interface is implemented, you can use any of the Groovy special operations that work on iterables:
```
 int bases = regions.grep { it.chr == "chrX" || it.chr == "chrY" }*.size().sum()
 println "There were $bases bases from sex chromosomes"
 
```
The Regions class offers many operations for convenient querying of and logical operations on intervals: Finding overlaps:
```
 Region r = new Region("chr1",120,130)
 regions.getOverlaps(r).size()==1
 
```
Many operations are possible using built in Groovy iterator methods. for example, to find the indexes of overlapping regions:
```
 assert regions.findIndexValues { r.overlaps(it) } == [ 0 ]
 
```
Authors:
simon.sadedin@mcri.edu.au

Properties Summary

Properties
Type	Name and description
`java.util.Map<java.lang.String, java.util.List<groovy.lang.IntRange>>`	`allRanges` A list of ranges in the order they were loaded
`java.util.Map<java.lang.String, RangeIndex>`	`index` Index for looking up overlaps

Constructor Summary

Constructors
Constructor and description
`Regions (java.util.Map attributes)` Create new empty set of regions
`Regions (java.util.Map attributes, java.lang.String chr, java.lang.Iterable<groovy.lang.Range> ranges)` Create a Regions from a list of Ranges
`Regions (java.util.Map attributes, java.lang.Iterable<IRegion> regions)` Create a Regions from a list of regions

Methods Summary

Methods
Type Params	Return Type	Name and description
	`Regions`	`addRegion(java.lang.String chr, int start, int end, java.lang.Object extra)` Add the specified range to this Regions file.
	`Regions`	`addRegion(gngs.Region r)` Adds the region to this Regions object in such a way that the same Region object is returned in iteration, preserving any expando properties set on the region.
	`groovy.lang.IntRange`	`backward(java.lang.String chr, int pos, int count)` Returns the region that is count regions backwards from the given position
	`java.util.List<Regions>`	`balancedSplit()` Divide these regions into two regions objects with approximately the same total bp in each half
	`java.util.List<java.util.Map>`	`bkr()`
	`boolean`	`contains(java.lang.String chr, int position)` Return true iff the given chromosome and position fall into a range covered by this BED file
	`Regions`	`coverage()` Return a new regions object that has each distinct region of this object with a "coverage" value assigned.
	`int`	`distanceTo(java.lang.String chr, int pos)` Returns: the distance to the nearest region in this Regions object, or -1 if there is no region in the same contig, if a region onverlaps, returns 0
	`int`	`distanceTo(gngs.Region r)` Returns: the distance to the nearest region in this Regions object, or -1 if there is no region in the same contig, if a region onverlaps, returns 0
	`void`	`eachOverlap(java.lang.String chr, int pos, groovy.lang.Closure c)` Call closure c for each range that overlaps the given position
	`void`	`eachRange(groovy.lang.Closure c)`
	`void`	`eachRange(java.util.Map options, groovy.lang.Closure c)`
	`java.util.List<groovy.lang.Range>`	`endingAt(java.lang.String chr, int pos)` Return a list of ranges that end exactly at the specified position.
	`Regions`	`enhance()`
	`groovy.lang.IntRange`	`forward(java.lang.String chr, int pos, int count)` Returns the region that is count regions forward of the given position
	`java.lang.Object`	`getAt(java.lang.Object obj)`
	`java.lang.Object`	`getAtIndex(java.lang.Object obj)`
	`Regions`	`getContigRegions(java.lang.String chr)`
	`java.util.List<java.lang.Object>`	`getExtrasAtPosition(java.lang.String chr, int position)`
	`int`	`getNumberOfRanges()`
	`java.util.List<gngs.Region>`	`getOverlapRegions(IRegion r)` Returns the overlaps with with the given region as region objects.
	`java.util.List<groovy.lang.IntRange>`	`getOverlaps(IRegion r)` Find the ranges that have at least 1bp overlap with the given region
	`java.util.List<groovy.lang.IntRange>`	`getOverlaps(java.lang.String chr, int start, int end)` Return a list of ranges that overlap the specified range.
	`gngs.Region`	`getSpan(java.lang.String contig)` Returns the total span from the beginning of the first region to the end of the last region on the given contig (chromosome).
	`java.util.List<groovy.lang.IntRange>`	`intersect(IRegion region)`
	`java.util.List<groovy.lang.IntRange>`	`intersect(java.lang.String chr, int start, int end)`
	`Regions`	`intersect(BED other)`
	`Regions`	`intersect(Regions other)`
	`Regions`	`intersectImpl(Regions other)` Returns a set of regions representing each region in this Regions intersected with the Regions in the other regions.
	`Regions`	`intersectRegion(gngs.Region other)`
	`Regions`	`intersectRegions(Regions other)`
	`boolean`	`isEmpty()`
	`java.util.Iterator<gngs.Region>`	`iterator()`
	`groovy.lang.IntRange`	`nearest(java.lang.String chr, int pos)` Returns the range that is "closest" to the given position.
	`groovy.lang.IntRange`	`nextRange(java.lang.String chr, int pos)` Returns the next range that has its beginning closest to the given position.
	`boolean`	`overlaps(java.lang.String chr, int from, int to)` Return true if the given region overlaps any range in this Regions
	`boolean`	`overlaps(IRegion r)` Return true if the given region overlaps any range in this Regions
	`boolean`	`overlaps(Regions other)` Returns true if at least one region in r overlaps at least one region in this Regions object
	`boolean`	`overlaps(java.lang.Iterable<IRegion> other)` Returns true if at least one region in r overlaps at least one region in this Regions object
	`Regions`	`plus(Regions other)`
	`groovy.lang.IntRange`	`previousRange(java.lang.String chr, int pos)` Returns the prior range that has its end closest to the given position.
	`Regions`	`reduce(groovy.lang.Closure reducer)` Simplify all overlapping regions down to a single region, with an optional closure as a callback to combine the attributes of combined regions
	`java.util.List<gngs.Region>`	`regionsEndingAt(java.lang.String chr, int pos)` Return a list of ranges that end exactly at the specified position.
	`java.util.List<gngs.Region>`	`regionsStartingAt(java.lang.String chr, int pos)`
	`void`	`remove(java.lang.String chr, groovy.lang.Range r)`
	`void`	`save(java.lang.String fileName)`
	`void`	`save(java.util.Map options, java.lang.String fileName)` Save the regions in BED format.
	`void`	`save(java.util.Map options, java.io.Writer w)` Save the regions in BED format.
	`long`	`size()`
	`java.util.List<groovy.lang.IntRange>`	`startingAt(java.lang.String chr, int pos)`
	`Regions`	`subtract(Regions other)`
	`java.util.List<gngs.Region>`	`subtractFrom(gngs.Region region)`
	`java.util.List<groovy.lang.IntRange>`	`subtractFrom(java.lang.String chr, int start, int end)` Remove all of the regions belonging to this Regions object from the interval specified, and return the list of Ranges that results.
	`Regions`	`thin(int desiredRanges, int minRangesPerChromosme)` Select the given number of ranges from these, approximately evenly spaced
	`java.util.List<java.lang.Integer>`	`thinnedIndices(int desiredRanges, int minRangesPerChromosme)` The same as thin(int,int) but returns the indices of the regions to keep.
	`java.lang.String`	`toHTML()`
	`java.util.List<java.util.Map<java.lang.String, java.lang.Object>>`	`toListMap()` A convenience method to return the contained regions as a list of Map objects.
	`java.lang.String`	`toString()`
	`Regions`	`uniquify()` Return a new Regions that contains the same regions as this one, but ensuring each identical region is only present once.
	`Regions`	`widen(int bp)` Return a new Regions object that has `bp` bases added to the beginning and end of each interval.
	`java.util.List<gngs.Region>`	`window(gngs.Region r, int n)` Return a window of n regions upstream and downstream of the given region

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
  - java.util.Map<java.lang.String, java.util.List<groovy.lang.IntRange>> allRanges
    
    A list of ranges in the order they were loaded
  - java.util.Map<java.lang.String, RangeIndex> index
    
    Index for looking up overlaps
- Constructor Detail
  - Regions(java.util.Map attributes)
    
    Create new empty set of regions
  - Regions(java.util.Map attributes, java.lang.String chr, java.lang.Iterable<groovy.lang.Range> ranges)
    
    Create a Regions from a list of Ranges
  - Regions(java.util.Map attributes, java.lang.Iterable<IRegion> regions)
    
    Create a Regions from a list of regions
- Method Detail
  - @groovy.transform.CompileStatic Regions addRegion(java.lang.String chr, int start, int end, java.lang.Object extra)
    
    Add the specified range to this Regions file.
    NOTE: the 'end' is treated as exclusive of the range covered. This is consistent with BED file notation, but different to Groovy ranges. Since most methods in this class use Groovy ranges, you will generally get a Range object out that has end one less than the end you put in with add. Thus if you are iterating through one BED file and adding the ranges to another with this method, you must add one to the end position that you pass to this method!
    Will trigger the flag to indicate this BED is loaded in memory.
  - @groovy.transform.CompileStatic Regions addRegion(gngs.Region r)
    
    Adds the region to this Regions object in such a way that the same Region object is returned in iteration, preserving any expando properties set on the region. @return
    Parameters:
    r
  - groovy.lang.IntRange backward(java.lang.String chr, int pos, int count)
    
    Returns the region that is count regions backwards from the given position
  - @groovy.transform.CompileStatic java.util.List<Regions> balancedSplit()
    
    Divide these regions into two regions objects with approximately the same total bp in each half @return
  - java.util.List<java.util.Map> bkr()
  - @groovy.transform.CompileStatic boolean contains(java.lang.String chr, int position)
    
    Return true iff the given chromosome and position fall into a range covered by this BED file
  - Regions coverage()
    
    Return a new regions object that has each distinct region of this object with a "coverage" value assigned. @return
  - @groovy.transform.CompileStatic int distanceTo(java.lang.String chr, int pos)
    
    Returns:
    the distance to the nearest region in this Regions object, or -1 if there is no region in the same contig, if a region onverlaps, returns 0
  - @groovy.transform.CompileStatic int distanceTo(gngs.Region r)
    
    Returns:
    the distance to the nearest region in this Regions object, or -1 if there is no region in the same contig, if a region onverlaps, returns 0
  - @groovy.transform.CompileStatic void eachOverlap(java.lang.String chr, int pos, groovy.lang.Closure c)
    
    Call closure c for each range that overlaps the given position
  - @groovy.transform.CompileStatic void eachRange(groovy.lang.Closure c)
  - void eachRange(java.util.Map options, groovy.lang.Closure c)
  - java.util.List<groovy.lang.Range> endingAt(java.lang.String chr, int pos)
    
    Return a list of ranges that end exactly at the specified position.
    NOTE: the position is considered inclusive to the range. This is different to BED file notation. @return
    Parameters:
    chr
    pos
  - @groovy.transform.CompileStatic Regions enhance()
  - groovy.lang.IntRange forward(java.lang.String chr, int pos, int count)
    
    Returns the region that is count regions forward of the given position
  - @groovy.transform.CompileStatic java.lang.Object getAt(java.lang.Object obj)
  - @groovy.transform.CompileStatic java.lang.Object getAtIndex(java.lang.Object obj)
  - @groovy.transform.CompileStatic Regions getContigRegions(java.lang.String chr)
  - java.util.List<java.lang.Object> getExtrasAtPosition(java.lang.String chr, int position)
  - int getNumberOfRanges()
  - @groovy.transform.CompileStatic java.util.List<gngs.Region> getOverlapRegions(IRegion r)
    
    Returns the overlaps with with the given region as region objects.
    Note: all the internal ranges must be stored as full Region objects, or this operation will throw an exception.
  - @groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> getOverlaps(IRegion r)
    
    Find the ranges that have at least 1bp overlap with the given region
    Note that this method returns a list of groovy.lang.IntRange objects. Where these belong to Region objects they will be instances of GRange objects with the Region set as the gngs.Region#extra field.
    If you want to get the gngs.Region objects back directly, use gngs.Region#getOverlapRegions().
    See Also:
    gngs.Region#getOverlapRegions()
    Parameters:
    the - region to locate overlaps for0
  - @groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> getOverlaps(java.lang.String chr, int start, int end)
    
    Return a list of ranges that overlap the specified range. Note: both ends of the range are *inclusive*. The Range objects returned all belong to the reference sequence chr. Note, if the internal ranges are GRanges objects (as they will be often) then you can get full Region objects out from the 'extra' property:
```
 List overlaps = regions.getOverlaps('chrX',10000,20000)*.extra
```
    Parameters:
    start - first position to look for overlaps
    end - last position to look for overlaps (inclusive)
    Returns:
    List of ranges overlapping the specified start -> end range
  - @groovy.transform.CompileStatic gngs.Region getSpan(java.lang.String contig)
    
    Returns the total span from the beginning of the first region to the end of the last region on the given contig (chromosome). @return
  - @groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> intersect(IRegion region)
  - @groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> intersect(java.lang.String chr, int start, int end)
  - @groovy.transform.CompileStatic Regions intersect(BED other)
  - @groovy.transform.CompileStatic Regions intersect(Regions other)
  - @groovy.transform.CompileStatic Regions intersectImpl(Regions other)
    
    Returns a set of regions representing each region in this Regions intersected with the Regions in the other regions.
    Note: nothing is done to deal specially with overlapping ranges. Thus if there are overlapping ranges in this Regions then you will find overlapping ranges in the results wherever those overlaps intersect with the other Regions. The same applies with respect to the other Regions. For a "flat" intersection of the two Regions, you should use reduce() to flatten the source and target first before calling this method.
  - @groovy.transform.CompileStatic Regions intersectRegion(gngs.Region other)
  - @groovy.transform.CompileStatic Regions intersectRegions(Regions other)
  - boolean isEmpty()
  - @java.lang.Override @groovy.transform.CompileStatic java.util.Iterator<gngs.Region> iterator()
  - groovy.lang.IntRange nearest(java.lang.String chr, int pos)
    
    Returns the range that is "closest" to the given position. 1. if no range overlaps, the closer of a) the end of the nearest prior range vs b) the start of the nearest following range is returned. 2. if one or more ranges overlap, returns the overlapping range with the start or end closest to the specified position @return
    Parameters:
    chr
    pos
  - @groovy.transform.CompileStatic groovy.lang.IntRange nextRange(java.lang.String chr, int pos)
    
    Returns the next range that has its beginning closest to the given position.
  - @groovy.transform.CompileStatic boolean overlaps(java.lang.String chr, int from, int to)
    
    Return true if the given region overlaps any range in this Regions
    Parameters:
    r - Region to test for overlaps
    Returns:
    true iff the region overlaps at least one region in this Regions
  - @groovy.transform.CompileStatic boolean overlaps(IRegion r)
    
    Return true if the given region overlaps any range in this Regions
    Parameters:
    r - Region to test for overlaps
    Returns:
    true iff the region overlaps at least one region in this Regions
  - @groovy.transform.CompileStatic boolean overlaps(Regions other)
    
    Returns true if at least one region in r overlaps at least one region in this Regions object @return
    Parameters:
    r
  - @groovy.transform.CompileStatic boolean overlaps(java.lang.Iterable<IRegion> other)
    
    Returns true if at least one region in r overlaps at least one region in this Regions object @return
    Parameters:
    r
  - @groovy.transform.CompileStatic Regions plus(Regions other)
  - groovy.lang.IntRange previousRange(java.lang.String chr, int pos)
    
    Returns the prior range that has its end closest to the given position.
  - @groovy.transform.CompileStatic Regions reduce(groovy.lang.Closure reducer)
    
    Simplify all overlapping regions down to a single region, with an optional closure as a callback to combine the attributes of combined regions
    The closure is passed two IntRange / GRange objects to combine. The callback shoud return the new gngs.GRange#extra object to assign to the result region.
    Returns:
    a new Regions that consists of all the overlapping regions of this Regions merged together.
  - java.util.List<gngs.Region> regionsEndingAt(java.lang.String chr, int pos)
    
    Return a list of ranges that end exactly at the specified position. @return
    Parameters:
    chr
    pos
  - @groovy.transform.CompileStatic java.util.List<gngs.Region> regionsStartingAt(java.lang.String chr, int pos)
  - @groovy.transform.CompileStatic void remove(java.lang.String chr, groovy.lang.Range r)
  - void save(java.lang.String fileName)
  - @groovy.transform.CompileStatic void save(java.util.Map options, java.lang.String fileName)
    
    Save the regions in BED format. If an 'extra' option is provided, this is called as a closure to return an id field to use for each region.
    Parameters:
    options
    fileName
  - void save(java.util.Map options, java.io.Writer w)
    
    Save the regions in BED format. If an 'extra' option is provided, this is called as a closure to return an id field to use for each region.
    Parameters:
    options - extra: closure returning data to write into 4th column, sorted: true to sort lexically, Comparator to sort custom (see {@link NumericRegionComparator)
    fileName
  - @groovy.transform.CompileStatic long size()
  - @groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> startingAt(java.lang.String chr, int pos)
  - @groovy.transform.CompileStatic Regions subtract(Regions other)
  - @groovy.transform.CompileStatic java.util.List<gngs.Region> subtractFrom(gngs.Region region)
  - @groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> subtractFrom(java.lang.String chr, int start, int end)
    
    Remove all of the regions belonging to this Regions object from the interval specified, and return the list of Ranges that results.
    Note: the end attribute is considered exclusive of the range to be subtracted from. @return
    Parameters:
    chr - chromsome of range
    start - start of interval to subtract from (inclusive)
    end - end of interval to subtract from (exclusive)
  - @groovy.transform.CompileStatic Regions thin(int desiredRanges, int minRangesPerChromosme)
    
    Select the given number of ranges from these, approximately evenly spaced @return
    Parameters:
    desiredRanges - target number of ranges to preserve
    minRanges - the minimum number of ranges to preserve on each chromosome
  - @groovy.transform.CompileStatic java.util.List<java.lang.Integer> thinnedIndices(int desiredRanges, int minRangesPerChromosme)
    
    The same as thin(int,int) but returns the indices of the regions to keep.
  - java.lang.String toHTML()
  - @groovy.transform.CompileStatic java.util.List<java.util.Map<java.lang.String, java.lang.Object>> toListMap()
    
    A convenience method to return the contained regions as a list of Map objects.
    This is primarily aimed at interactive use in shell or notebook environments, it is not performant or memory efficient.
  - java.lang.String toString()
  - Regions uniquify()
    
    Return a new Regions that contains the same regions as this one, but ensuring each identical region is only present once. @return
  - @groovy.transform.CompileStatic Regions widen(int bp)
    
    Return a new Regions object that has bp bases added to the beginning and end of each interval. If this causes overlaps then these are left in the resulting Objects.
    Parameters:
    bp
    Returns:
    a new Regions with bp wider intervals
  - java.util.List<gngs.Region> window(gngs.Region r, int n)
    
    Return a window of n regions upstream and downstream of the given region

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation

[Groovy] Class Regions

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Property Detail

java.util.Map<java.lang.String, java.util.List<groovy.lang.IntRange>> allRanges

java.util.Map<java.lang.String, RangeIndex> index

Constructor Detail

Regions(java.util.Map attributes)

Regions(java.util.Map attributes, java.lang.String chr, java.lang.Iterable<groovy.lang.Range> ranges)

Regions(java.util.Map attributes, java.lang.Iterable<IRegion> regions)

Method Detail

@groovy.transform.CompileStatic Regions addRegion(java.lang.String chr, int start, int end, java.lang.Object extra)

@groovy.transform.CompileStatic Regions addRegion(gngs.Region r)

groovy.lang.IntRange backward(java.lang.String chr, int pos, int count)

@groovy.transform.CompileStatic java.util.List<Regions> balancedSplit()

java.util.List<java.util.Map> bkr()

@groovy.transform.CompileStatic boolean contains(java.lang.String chr, int position)

Regions coverage()

@groovy.transform.CompileStatic int distanceTo(java.lang.String chr, int pos)

@groovy.transform.CompileStatic int distanceTo(gngs.Region r)

@groovy.transform.CompileStatic void eachOverlap(java.lang.String chr, int pos, groovy.lang.Closure c)

@groovy.transform.CompileStatic void eachRange(groovy.lang.Closure c)

void eachRange(java.util.Map options, groovy.lang.Closure c)

java.util.List<groovy.lang.Range> endingAt(java.lang.String chr, int pos)

@groovy.transform.CompileStatic Regions enhance()

groovy.lang.IntRange forward(java.lang.String chr, int pos, int count)

@groovy.transform.CompileStatic java.lang.Object getAt(java.lang.Object obj)

@groovy.transform.CompileStatic java.lang.Object getAtIndex(java.lang.Object obj)

@groovy.transform.CompileStatic Regions getContigRegions(java.lang.String chr)

java.util.List<java.lang.Object> getExtrasAtPosition(java.lang.String chr, int position)

int getNumberOfRanges()

@groovy.transform.CompileStatic java.util.List<gngs.Region> getOverlapRegions(IRegion r)

@groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> getOverlaps(IRegion r)

@groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> getOverlaps(java.lang.String chr, int start, int end)

@groovy.transform.CompileStatic gngs.Region getSpan(java.lang.String contig)

@groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> intersect(IRegion region)

@groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> intersect(java.lang.String chr, int start, int end)

@groovy.transform.CompileStatic Regions intersect(BED other)

@groovy.transform.CompileStatic Regions intersect(Regions other)

@groovy.transform.CompileStatic Regions intersectImpl(Regions other)

@groovy.transform.CompileStatic Regions intersectRegion(gngs.Region other)

@groovy.transform.CompileStatic Regions intersectRegions(Regions other)

boolean isEmpty()

@java.lang.Override @groovy.transform.CompileStatic java.util.Iterator<gngs.Region> iterator()

groovy.lang.IntRange nearest(java.lang.String chr, int pos)

@groovy.transform.CompileStatic groovy.lang.IntRange nextRange(java.lang.String chr, int pos)

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

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

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

@groovy.transform.CompileStatic boolean overlaps(java.lang.Iterable<IRegion> other)

@groovy.transform.CompileStatic Regions plus(Regions other)

groovy.lang.IntRange previousRange(java.lang.String chr, int pos)

@groovy.transform.CompileStatic Regions reduce(groovy.lang.Closure reducer)

java.util.List<gngs.Region> regionsEndingAt(java.lang.String chr, int pos)

@groovy.transform.CompileStatic java.util.List<gngs.Region> regionsStartingAt(java.lang.String chr, int pos)

@groovy.transform.CompileStatic void remove(java.lang.String chr, groovy.lang.Range r)

void save(java.lang.String fileName)

@groovy.transform.CompileStatic void save(java.util.Map options, java.lang.String fileName)

void save(java.util.Map options, java.io.Writer w)

@groovy.transform.CompileStatic long size()

@groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> startingAt(java.lang.String chr, int pos)

@groovy.transform.CompileStatic Regions subtract(Regions other)

@groovy.transform.CompileStatic java.util.List<gngs.Region> subtractFrom(gngs.Region region)

@groovy.transform.CompileStatic java.util.List<groovy.lang.IntRange> subtractFrom(java.lang.String chr, int start, int end)

@groovy.transform.CompileStatic Regions thin(int desiredRanges, int minRangesPerChromosme)

@groovy.transform.CompileStatic java.util.List<java.lang.Integer> thinnedIndices(int desiredRanges, int minRangesPerChromosme)

java.lang.String toHTML()

@groovy.transform.CompileStatic java.util.List<java.util.Map<java.lang.String, java.lang.Object>> toListMap()

java.lang.String toString()

Regions uniquify()

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

java.util.List<gngs.Region> window(gngs.Region r, int n)