Package org.snpeff.fileIterator
Class VariantTxtFileIterator
- 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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- org.snpeff.fileIterator.VariantTxtFileIterator
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public class VariantTxtFileIterator extends VariantFileIterator
Opens a sequence change file and iterates over all sequence changes TXT Format: Tab-separated format, containing five columns that correspond to: chr \t position \t refSeq \t newSeq \t strand \t quality \t coverage \t id \n Fields strand, quality, coverage and id are optional E.g. 5 140532 T C + 31 12 1017956 T A + 2 946507 G C + 21 16 Very_important_Snp 14 19584687 C T - 19 66520 G A + 27 8 150029 A T + 31- 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 VariantTxtFileIterator(java.lang.String fileName)
VariantTxtFileIterator(java.lang.String fileName, Genome genome)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
hasNext()
Variant
next()
protected Variant
readNext()
Read next element-
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, hasSeek, isDebug, iterator, load, readLine, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString
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Constructor Detail
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VariantTxtFileIterator
public VariantTxtFileIterator(java.lang.String fileName)
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VariantTxtFileIterator
public VariantTxtFileIterator(java.lang.String fileName, Genome genome)
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Method Detail
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hasNext
public boolean hasNext()
- Specified by:
hasNext
in interfacejava.util.Iterator<Variant>
- Overrides:
hasNext
in classFileIterator<Variant>
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next
public Variant next()
- Specified by:
next
in interfacejava.util.Iterator<Variant>
- Overrides:
next
in classFileIterator<Variant>
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readNext
protected Variant readNext()
Description copied from class:FileIterator
Read next element- Specified by:
readNext
in classFileIterator<Variant>
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