BED

gngs.BED

```
class BED
extends Regions
```
Support for parsing, filtering, and manipuulating BED files.
This class provides and implementation for Regions that is backed by a file in BED format.
Some methods hit the file directly, while others rely on reading it into memory. In cases where the data set will not fit into memory, you should check how the method is going to operate and choose accordingly.
Note that the constructor does not load the contents of the BED file. To actually load the BED file you need to call load().
The fourth column of the BED file is referred to as the extra attribute. This is not loaded by default. You can request that it be loaded by adding the option withExtra to either the constructor or the load() method.
Authors:
simon.sadedin@mcri.edu.au

Nested Class Summary

Nested classes
Modifiers	Name	Description
`class`	`BED.1`

Properties Summary

Properties
Type	Name and description
`java.io.File`	`bedFile` File from which bed is read
`java.io.InputStream`	`bedFileStream` The stream from which bed line will be read
`int`	`chrColumn` Columns for reading the position data - these can be overridden to allow loading of any "bed-like" file
`java.util.List<java.lang.String>`	`columnNames`
`int`	`endColumn`
`boolean`	`isLoaded` Some functions require loading of the BED file into memory.
`boolean`	`readColumnNames`
`int`	`startColumn`
`boolean`	`withExtra` Use 'extra' field to allow additional data to be attached to ranges in the bed file
`boolean`	`withProperties` If true, column names will be set as properties on the regions

Constructor Summary

Constructors
Constructor and description
`BED (java.util.Map attributes)` Empty bed file
`BED (java.util.Map attributes, java.lang.String fileName)`
`BED (java.util.Map attributes, java.io.File file, groovy.lang.Closure c)`
`BED (java.util.Map attributes, java.io.InputStream inStream, groovy.lang.Closure c)`
`BED (java.util.Map attributes, java.lang.Iterable<gngs.Region> regions)` Create a BED from a list of regions

Methods Summary

Methods
Type Params	Return Type	Name and description
	`BED`	`add(java.lang.String chr, int start, int end, java.lang.Object extra)` Add the specified range to this BED file.
	`static BED`	`eachInputRange(groovy.lang.Closure c)`
	`void`	`eachLoadedRange(groovy.lang.Closure c)`
	`void`	`eachLoadedRange(java.util.Map options, groovy.lang.Closure c)`
	`void`	`eachOverlap(java.lang.String chr, int pos, groovy.lang.Closure c)` Call closure c for each range that overlaps the given position
	`void`	`eachPosition(groovy.lang.Closure c)` Iterate each position in a BED file and call the given closure with it
	`static void`	`eachPosition(java.lang.String fileName, groovy.lang.Closure c)` Iterate every single base in the regions of the specified bed file
	`void`	`eachRange(java.util.Map options, groovy.lang.Closure c)` Iterate over each line in the BED file and invoke the specified closure with bed file information for the line.
	`boolean`	`isCase(IRegion region)`
	`BED`	`load(java.util.Map options)` Load the data for this BED file into memory.
	`static BED`	`parse()`
	`static BED`	`parse(java.lang.String fileName)`
	`java.lang.String`	`toString()`

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class Regions`	addRegion, addRegion, backward, balancedSplit, bkr, contains, coverage, distanceTo, distanceTo, eachOverlap, eachRange, eachRange, endingAt, enhance, forward, getAt, getAtIndex, getContigRegions, getExtrasAtPosition, getNumberOfRanges, getOverlapRegions, getOverlaps, getOverlaps, getSpan, intersect, intersect, intersect, intersect, intersectImpl, intersectRegion, intersectRegions, isEmpty, iterator, nearest, nextRange, overlaps, overlaps, overlaps, overlaps, plus, previousRange, reduce, regionsEndingAt, regionsStartingAt, remove, save, save, save, size, startingAt, subtract, subtractFrom, subtractFrom, thin, thinnedIndices, toHTML, toListMap, toString, uniquify, widen, window

- Property Detail
  - java.io.File bedFile
    
    File from which bed is read
  - java.io.InputStream bedFileStream
    
    The stream from which bed line will be read
  - int chrColumn
    
    Columns for reading the position data - these can be overridden to allow loading of any "bed-like" file
  - java.util.List<java.lang.String> columnNames
  - int endColumn
  - boolean isLoaded
    
    Some functions require loading of the BED file into memory. Others can use it optionally. So keep a flag to know if the BED was loaded, and if it was, use memory for all operations to be faster.
  - boolean readColumnNames
  - int startColumn
  - boolean withExtra
    
    Use 'extra' field to allow additional data to be attached to ranges in the bed file
  - boolean withProperties
    
    If true, column names will be set as properties on the regions
- Constructor Detail
  - BED(java.util.Map attributes)
    
    Empty bed file
  - BED(java.util.Map attributes, java.lang.String fileName)
  - BED(java.util.Map attributes, java.io.File file, groovy.lang.Closure c)
  - BED(java.util.Map attributes, java.io.InputStream inStream, groovy.lang.Closure c)
  - BED(java.util.Map attributes, java.lang.Iterable<gngs.Region> regions)
    
    Create a BED from a list of regions
- Method Detail
  - @groovy.transform.CompileStatic BED add(java.lang.String chr, int start, int end, java.lang.Object extra)
    
    Add the specified range to this BED 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.
  - static BED eachInputRange(groovy.lang.Closure c)
  - void eachLoadedRange(groovy.lang.Closure c)
  - void eachLoadedRange(java.util.Map options, groovy.lang.Closure c)
  - @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 eachPosition(groovy.lang.Closure c)
    
    Iterate each position in a BED file and call the given closure with it
    NOTE: this only works on an actual BED file, not in-memory BED file. @TODO: merge overlapping regions
  - static void eachPosition(java.lang.String fileName, groovy.lang.Closure c)
    
    Iterate every single base in the regions of the specified bed file
    Parameters:
    fileName
  - @groovy.transform.CompileStatic void eachRange(java.util.Map options, groovy.lang.Closure c)
    
    Iterate over each line in the BED file and invoke the specified closure with bed file information for the line.
    Options can be provided as a Map argument, including:
  - unique (whether identical ranges should be included multiple times or only once)
  - boolean isCase(IRegion region)
  - @groovy.transform.CompileStatic BED load(java.util.Map options)
    
    Load the data for this BED file into memory.
    If withExtra is false, only the range data will be loaded. This is very compact and fast. Otherwise, the optional 4th column will be loaded as well and stored in memory too, as the 'extra' attribute on the GRange objects.
    Note: this method returns the same BED object as a result to enable chaining
  - static BED parse()
  - static BED parse(java.lang.String fileName)
  - java.lang.String toString()

Summary:
Nested
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation

[Groovy] Class BED

Nested Class Summary

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Property Detail

java.io.File bedFile

java.io.InputStream bedFileStream

int chrColumn

java.util.List<java.lang.String> columnNames

int endColumn

boolean isLoaded

boolean readColumnNames

int startColumn

boolean withExtra

boolean withProperties

Constructor Detail

BED(java.util.Map attributes)

BED(java.util.Map attributes, java.lang.String fileName)

BED(java.util.Map attributes, java.io.File file, groovy.lang.Closure c)

BED(java.util.Map attributes, java.io.InputStream inStream, groovy.lang.Closure c)

BED(java.util.Map attributes, java.lang.Iterable<gngs.Region> regions)

Method Detail

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

static BED eachInputRange(groovy.lang.Closure c)

void eachLoadedRange(groovy.lang.Closure c)

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

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

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

static void eachPosition(java.lang.String fileName, groovy.lang.Closure c)

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

boolean isCase(IRegion region)

@groovy.transform.CompileStatic BED load(java.util.Map options)

static BED parse()

static BED parse(java.lang.String fileName)

java.lang.String toString()