Package org.snpeff.fileIterator
Class VcfHapMapFileIterator
- java.lang.Object
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- org.snpeff.fileIterator.FileIterator<M>
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- org.snpeff.fileIterator.MarkerFileIterator<VcfEntry>
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- org.snpeff.fileIterator.VcfHapMapFileIterator
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public class VcfHapMapFileIterator extends MarkerFileIterator<VcfEntry>
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
Fields Modifier and Type Field Description protected Genome
genome
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Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, ignoreChromosomeErrors, inOffset
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Constructor Summary
Constructors Constructor Description VcfHapMapFileIterator(java.lang.String hapMapFileName, java.lang.String fatsaFileName, Genome genome)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected VcfEntry
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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Field Detail
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genome
protected Genome genome
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Constructor Detail
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VcfHapMapFileIterator
public VcfHapMapFileIterator(java.lang.String hapMapFileName, java.lang.String fatsaFileName, Genome genome)
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Method Detail
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readNext
protected VcfEntry readNext()
Description copied from class:FileIterator
Read next element- Specified by:
readNext
in classFileIterator<VcfEntry>
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