Package org.snpeff.fileIterator
Class VariantFileIterator
- java.lang.Object
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- org.snpeff.fileIterator.FileIterator<M>
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- org.snpeff.fileIterator.MarkerFileIterator<Variant>
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- org.snpeff.fileIterator.VariantFileIterator
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- Direct Known Subclasses:
BedFileIterator
,BigBedFileIterator
,VariantTxtFileIterator
public abstract class VariantFileIterator extends MarkerFileIterator<Variant>
Opens a sequence change file and iterates over all sequence changes- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, inOffset
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Constructor Summary
Constructors Constructor Description VariantFileIterator(java.lang.String fileName)
VariantFileIterator(java.lang.String fileName, Genome genome)
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Method Summary
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Methods inherited from class org.snpeff.fileIterator.MarkerFileIterator
getChromosome, getGenome, init, isIgnoreChromosomeErrors, loadMarkers, parsePosition, sanityCheckChromo, setCreateChromos, setIgnoreChromosomeErrors, setInOffset
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Methods inherited from class org.snpeff.fileIterator.FileIterator
close, countNewLineChars, getFilePointer, getLine, getLineNum, guessNewLineChars, hasNext, hasSeek, isDebug, iterator, load, next, readLine, readNext, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString
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Constructor Detail
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VariantFileIterator
public VariantFileIterator(java.lang.String fileName, Genome genome)
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VariantFileIterator
public VariantFileIterator(java.lang.String fileName)
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