Package org.snpeff.fileIterator
Class BedFileIterator
- 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.BedFileIterator
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public class BedFileIterator extends VariantFileIterator
Opens a sequence change file and iterates over all intervals in BED format. Reference: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The first three required BED fields are: 1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671). 2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0. 3. chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99. There are 9 additional optional BED fields, but we only use one: 4. name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode. 5. score - A score used for that interval- Author:
- pcingola
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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 BedFileIterator(java.lang.String fileName)
BedFileIterator(java.lang.String fileName, Genome genome)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static Markers
load(java.lang.String bedFileName, boolean verbose)
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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Constructor Detail
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BedFileIterator
public BedFileIterator(java.lang.String fileName)
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BedFileIterator
public BedFileIterator(java.lang.String fileName, Genome genome)
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Method Detail
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load
public static Markers load(java.lang.String bedFileName, boolean verbose)
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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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