org.snpeff.fileIterator.RegulationBedFileIterator

All Implemented Interfaces:: Iterable<Regulation>, Iterator<Regulation>

public class RegulationBedFileIterator extends RegulationFileIterator

Opens a GFF3 file and create regulatory elements. Example of regulatory GFF file: ftp://ftp.ensembl.org/pub/release-63/regulation/homo_sapiens/AnnotatedFeatures.gff.gz References (GFF3) : http://www.sequenceontology.org/gff3.shtml

Author:: pcingola

Field Summary

Fields

Modifier and Type

Field

Description

static final int

BED_OFFSET

Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, inOffset

Fields inherited from class org.snpeff.fileIterator.FileIterator
autoClose, countNewLineChars, debug, fileName, fileSize, line, lineNum, next, nextLine, reader, verbose
Constructor Summary

Constructors

Constructor

Description

RegulationBedFileIterator(String fileName, String name, String cellType)

RegulationBedFileIterator(String fileName, Genome genome, String name, String cellType)
Method Summary

Modifier and Type

Method

Description

protected Regulation

readNext()

Read next element

Methods inherited from class org.snpeff.fileIterator.MarkerFileIterator
getChromosome, getGenome, init, isIgnoreChromosomeErrors, loadMarkers, parsePosition, sanityCheckChromo, setCreateChromos, setIgnoreChromosomeErrors, setInOffset

Methods inherited from class org.snpeff.fileIterator.FileIterator
close, countNewLineChars, getFilePointer, getLine, getLineNum, guessNewLineChars, hasNext, hasSeek, isDebug, iterator, load, next, readLine, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from interface java.util.Iterator
forEachRemaining

Field Details
- BED_OFFSET
  
  public static final int BED_OFFSET
  See Also:
  
  Constant Field Values
Constructor Details
- RegulationBedFileIterator
  
  public RegulationBedFileIterator(String fileName, Genome genome, String name, String cellType)
- RegulationBedFileIterator
  
  public RegulationBedFileIterator(String fileName, String name, String cellType)
Method Details
- readNext
  
  protected Regulation readNext()
  
  Description copied from class: FileIterator
  
  Read next element
  
  Specified by:
  
  readNext in class FileIterator<Regulation>

Class RegulationBedFileIterator

Field Summary

Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator

Fields inherited from class org.snpeff.fileIterator.FileIterator

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.fileIterator.MarkerFileIterator

Methods inherited from class org.snpeff.fileIterator.FileIterator

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Methods inherited from interface java.util.Iterator

Field Details

BED_OFFSET

Constructor Details

RegulationBedFileIterator

RegulationBedFileIterator

Method Details

readNext