Package org.snpeff.fileIterator
Class BigBedFileIterator
java.lang.Object
org.snpeff.fileIterator.FileIterator<M>
org.snpeff.fileIterator.MarkerFileIterator<Variant>
org.snpeff.fileIterator.VariantFileIterator
org.snpeff.fileIterator.BigBedFileIterator
FileIterator for BigBed features
WARNING: Removed in 2022-01 due to dependency on IGV's code (which depends on Log4j, which has a major security issue)
Note: I use Broad's IGV code to do all the work, this is just a wrapper
- Author:
- pablocingolani
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Field Summary
Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, inOffset
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Constructor Summary
Constructors -
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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BigBedFileIterator
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Method Details
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readNext
Description copied from class:FileIterator
Read next element- Specified by:
readNext
in classFileIterator<Variant>
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