Package org.snpeff.fileIterator
Class VcfHapMapFileIterator
Opens a Hapmap phased file and iterates over all entries, returning VcfEntries for each line
Note: Each HapMap file has one chromosome. The reference sequence for the chromosome is read from a fasta file
- Author:
- pcingola
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Field Summary
FieldsFields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, ignoreChromosomeErrors, inOffset -
Constructor Summary
ConstructorsConstructorDescriptionVcfHapMapFileIterator(String hapMapFileName, String fatsaFileName, Genome genome) -
Method Summary
Methods inherited from class org.snpeff.fileIterator.MarkerFileIterator
getChromosome, getGenome, init, isIgnoreChromosomeErrors, loadMarkers, parsePosition, sanityCheckChromo, setCreateChromos, setIgnoreChromosomeErrors, setInOffsetMethods 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, toStringMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitMethods inherited from interface java.lang.Iterable
forEach, spliteratorMethods inherited from interface java.util.Iterator
forEachRemaining
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Field Details
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genome
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Constructor Details
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VcfHapMapFileIterator
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Method Details
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readNext
Description copied from class:FileIteratorRead next element- Specified by:
readNextin classFileIterator<VcfEntry>
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