umcg.genetica.io.bed

Class BedFile

java.lang.Object

umcg.genetica.io.bed.BedFile

All Implemented Interfaces:

Iterable<BedEntry>

public class BedFile
extends Object
implements Iterable<BedEntry>

Author:

Patrick Deelen

Constructor Summary

Constructors

Constructor and Description
BedFile(File bedFile)
BedFile(File bedFile, boolean omitChr, boolean makeOneBased)
BedFile(String bedFilePath)
BedFile(String bedFilePath, boolean omitChr, boolean makeOneBased)

Method Summary

Modifier and Type	Method and Description
PerChrIntervalTree<BedEntry>	createIntervalTree()
Map<String,String>	getTrackInfo()
Iterator<BedEntry>	iterator()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

BedFile

public BedFile(String bedFilePath)
        throws FileNotFoundException,
               IOException

Throws:

FileNotFoundException

IOException

BedFile

public BedFile(String bedFilePath,
               boolean omitChr,
               boolean makeOneBased)
        throws FileNotFoundException,
               IOException

Throws:

FileNotFoundException

IOException

BedFile

public BedFile(File bedFile)
        throws FileNotFoundException,
               IOException

Throws:

FileNotFoundException

IOException

BedFile

public BedFile(File bedFile,
               boolean omitChr,
               boolean makeOneBased)
        throws FileNotFoundException,
               IOException

Throws:

FileNotFoundException

IOException

Method Detail

iterator

public Iterator<BedEntry> iterator()

Specified by:

iterator in interface Iterable<BedEntry>

createIntervalTree

public PerChrIntervalTree<BedEntry> createIntervalTree()
                                                throws Exception

Throws:

Exception

getTrackInfo

public Map<String,String> getTrackInfo()