Package org.snpeff.fileIterator
Class BigBedFileIterator
- 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.BigBedFileIterator
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public class BigBedFileIterator extends VariantFileIterator
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
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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 BigBedFileIterator(java.lang.String fileName)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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, hasNext, hasSeek, isDebug, iterator, load, next, readLine, ready, remove, seek, setAutoClose, setDebug, setVerbose, toString
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Method Detail
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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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