Package org.snpeff.fileIterator
Class VariantTxtFileIterator
java.lang.Object
org.snpeff.fileIterator.FileIterator<M>
org.snpeff.fileIterator.MarkerFileIterator<Variant>
org.snpeff.fileIterator.VariantFileIterator
org.snpeff.fileIterator.VariantTxtFileIterator
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
Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, inOffset
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Constructor Summary
ConstructorsConstructorDescriptionVariantTxtFileIterator
(String fileName) VariantTxtFileIterator
(String fileName, Genome genome) -
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, hasSeek, isDebug, iterator, load, 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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VariantTxtFileIterator
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VariantTxtFileIterator
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Method Details
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hasNext
public boolean hasNext() -
next
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readNext
Description copied from class:FileIterator
Read next element- Specified by:
readNext
in classFileIterator<Variant>
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