Package org.snpeff.fileIterator
Class RegulationBedFileIterator
java.lang.Object
org.snpeff.fileIterator.FileIterator<Regulation>
org.snpeff.fileIterator.MarkerFileIterator<Regulation>
org.snpeff.fileIterator.RegulationFileIterator
org.snpeff.fileIterator.RegulationBedFileIterator
- All Implemented Interfaces:
Iterable<Regulation>
,Iterator<Regulation>
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
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Field Summary
FieldsFields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, inOffset
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Constructor Summary
ConstructorsConstructorDescriptionRegulationBedFileIterator
(String fileName, String name, String cellType) RegulationBedFileIterator
(String fileName, Genome genome, String name, String cellType) -
Method Summary
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
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Field Details
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BED_OFFSET
public static final int BED_OFFSET- See Also:
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Constructor Details
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RegulationBedFileIterator
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RegulationBedFileIterator
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Method Details
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readNext
Description copied from class:FileIterator
Read next element- Specified by:
readNext
in classFileIterator<Regulation>
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