Package org.snpsift.annotate
Class MarkerFile
java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpsift.annotate.MarkerFile
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<org.snpeff.interval.Interval>
,org.snpeff.serializer.TxtSerializable
public class MarkerFile
extends org.snpeff.interval.Marker
Represents a marker in a file (located at 'fileIdx' bytes since the beginning of the file)
- Author:
- pcingola
- See Also:
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Field Summary
FieldsFields inherited from class org.snpeff.interval.Marker
type
Fields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
ConstructorsConstructorDescriptionMarkerFile
(org.snpeff.interval.Marker parent, int start, int end, long fileIdx) -
Method Summary
Methods inherited from class org.snpeff.interval.Marker
adjust, apply, applyDel, applyDup, applyIns, applyMixed, clone, cloneShallow, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, isShowWarningIfParentDoesNotInclude, minus, query, query, readTxt, serializeParse, serializeSave, shouldApply, union, variantEffect, variantEffectNonRef
Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, hashCode, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, setStrandMinus, shiftCoordinates, size, toStr, toStringAsciiArt, toStrPos
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Field Details
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fileIdx
protected long fileIdx
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Constructor Details
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MarkerFile
public MarkerFile(org.snpeff.interval.Marker parent, int start, int end, long fileIdx)
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Method Details
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getFileIdx
public long getFileIdx() -
toString
- Overrides:
toString
in classorg.snpeff.interval.Marker
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