Package ngs
Interface PileupEvent
- All Known Subinterfaces:
Pileup
,PileupEventIterator
,PileupIterator
public interface PileupEvent
Represents a single cell of a sparse 2D matrix with Reference coordinates on one axis
and stacked Alignments on the other axis
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
EventTypestatic final int
static final int
EventIndelTypestatic final int
static final int
static final int
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Method Summary
Modifier and TypeMethodDescriptionchar
getAlignmentBasegetAlignmentIdlong
getAlignmentPositionchar
getAlignmentQualityint
getEventIndelTypeint
getEventRepeatCountint
getEventTypelong
getFirstAlignmentPositiongetInsertionBasesgetInsertionQualitieslong
getLastAlignmentPositionint
getMappingQuality
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Field Details
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match
static final int matchEventType- See Also:
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mismatch
static final int mismatch- See Also:
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deletion
static final int deletion- See Also:
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insertion
static final int insertion- See Also:
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insertion_before_match
static final int insertion_before_match- See Also:
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insertion_before_mismatch
static final int insertion_before_mismatch- See Also:
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insertion_before_deletion
static final int insertion_before_deletion- See Also:
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replacement
static final int replacement- See Also:
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alignment_start
static final int alignment_start- See Also:
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alignment_stop
static final int alignment_stop- See Also:
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alignment_minus_strand
static final int alignment_minus_strand- See Also:
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normal_indel
static final int normal_indelEventIndelType- See Also:
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intron_plus
static final int intron_plus- See Also:
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intron_minus
static final int intron_minus- See Also:
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intron_unknown
static final int intron_unknown- See Also:
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read_overlap
static final int read_overlap- See Also:
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read_gap
static final int read_gap- See Also:
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Method Details
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getMappingQuality
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getAlignmentId
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getAlignmentPosition
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getFirstAlignmentPosition
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getLastAlignmentPosition
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getEventType
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getAlignmentBase
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getAlignmentQuality
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getInsertionBases
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getInsertionQualities
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getEventRepeatCount
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getEventIndelType
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