Package ngs
Interface Pileup
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- All Superinterfaces:
PileupEvent
,PileupEventIterator
- All Known Subinterfaces:
PileupIterator
public interface Pileup extends PileupEventIterator
Represents a slice through a stack of Alignments at a given position on the Reference
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Field Summary
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Fields inherited from interface ngs.PileupEvent
alignment_minus_strand, alignment_start, alignment_stop, deletion, insertion, insertion_before_deletion, insertion_before_match, insertion_before_mismatch, intron_minus, intron_plus, intron_unknown, match, mismatch, normal_indel, read_gap, read_overlap, replacement
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description int
getPileupDepth()
getPileupDepthchar
getReferenceBase()
long
getReferencePosition()
getReferencePositionjava.lang.String
getReferenceSpec()
getReferenceSpec-
Methods inherited from interface ngs.PileupEvent
getAlignmentBase, getAlignmentId, getAlignmentPosition, getAlignmentQuality, getEventIndelType, getEventRepeatCount, getEventType, getFirstAlignmentPosition, getInsertionBases, getInsertionQualities, getLastAlignmentPosition, getMappingQuality
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Methods inherited from interface ngs.PileupEventIterator
nextPileupEvent, resetPileupEvent
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Method Detail
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getReferenceSpec
java.lang.String getReferenceSpec() throws ErrorMsg
getReferenceSpec- Returns:
- name of the Reference
- Throws:
ErrorMsg
- upon an error accessing data
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getReferencePosition
long getReferencePosition() throws ErrorMsg
getReferencePosition- Returns:
- current position on the Reference
- Throws:
ErrorMsg
- upon an error accessing data
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getReferenceBase
char getReferenceBase() throws ErrorMsg
- Returns:
- base at current Reference position
- Throws:
ErrorMsg
- upon an error accessing data
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