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
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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, 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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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:FileIterator
Read next element- Specified by:
readNext
in classFileIterator<VcfEntry>
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