Package org.snpeff.fileIterator
Class Gff3FileIterator
Opens a sequence change file and iterates over all intervals in GFF3 format.
- Author:
- pcingola
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Field Summary
Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, inOffset
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Constructor Summary
ConstructorsConstructorDescriptionGff3FileIterator
(String fileName) Gff3FileIterator
(String fileName, Genome genome) Gff3FileIterator
(String fileName, Genome genome, int inOffset) -
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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Constructor Details
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Gff3FileIterator
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Gff3FileIterator
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Gff3FileIterator
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Method Details
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readNext
Description copied from class:FileIterator
Read next element- Specified by:
readNext
in classFileIterator<GffMarker>
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