Package ngs
Interface Pileup
- All Superinterfaces:
PileupEvent,PileupEventIterator
- All Known Subinterfaces:
PileupIterator
Represents a slice through a stack of Alignments at a given position on the Reference
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Field Summary
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 -
Method Summary
Modifier and TypeMethodDescriptionintgetPileupDepthcharlonggetReferencePositiongetReferenceSpecMethods inherited from interface ngs.PileupEvent
getAlignmentBase, getAlignmentId, getAlignmentPosition, getAlignmentQuality, getEventIndelType, getEventRepeatCount, getEventType, getFirstAlignmentPosition, getInsertionBases, getInsertionQualities, getLastAlignmentPosition, getMappingQualityMethods inherited from interface ngs.PileupEventIterator
nextPileupEvent, resetPileupEvent
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Method Details
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getReferenceSpec
getReferenceSpec- Returns:
- name of the Reference
- Throws:
ErrorMsg- upon an error accessing data
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getReferencePosition
getReferencePosition- Returns:
- current position on the Reference
- Throws:
ErrorMsg- upon an error accessing data
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getReferenceBase
- Returns:
- base at current Reference position
- Throws:
ErrorMsg- upon an error accessing data
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getPileupDepth
getPileupDepth- Returns:
- the coverage depth at the current reference position
- Throws:
ErrorMsg- upon an error accessing data
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