VariantFileIterator (SnpEff 5.1 API)

java.lang.Object

org.snpeff.fileIterator.FileIterator<M>

org.snpeff.fileIterator.MarkerFileIterator<Variant>

org.snpeff.fileIterator.VariantFileIterator

All Implemented Interfaces:: Iterable<Variant>, Iterator<Variant>

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

Field Summary

Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, inOffset

Fields inherited from class org.snpeff.fileIterator.FileIterator
autoClose, countNewLineChars, debug, fileName, fileSize, line, lineNum, next, nextLine, reader, verbose
Constructor Summary

Constructors

Constructor

Description

VariantFileIterator(String fileName)

VariantFileIterator(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, hasNext, hasSeek, isDebug, iterator, load, next, readLine, readNext, 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

Constructor Details
- VariantFileIterator
  
  public VariantFileIterator(String fileName, Genome genome)
- VariantFileIterator
  
  public VariantFileIterator(String fileName)