Package org.snpeff.fileIterator
Class BedFileIterator
java.lang.Object
org.snpeff.fileIterator.FileIterator<M>
org.snpeff.fileIterator.MarkerFileIterator<Variant>
org.snpeff.fileIterator.VariantFileIterator
org.snpeff.fileIterator.BedFileIterator
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
Fields inherited from class org.snpeff.fileIterator.MarkerFileIterator
createChromos, genome, ignoreChromosomeErrors, inOffset
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Constructor Summary
ConstructorsConstructorDescriptionBedFileIterator
(String fileName) BedFileIterator
(String fileName, 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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Constructor Details
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BedFileIterator
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BedFileIterator
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Method Details
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load
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readNext
Description copied from class:FileIterator
Read next element- Specified by:
readNext
in classFileIterator<Variant>
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