AlignedReadStoreElement

| Class AlignedReadStoreElement Represents an alignment between read and contig. AlignedReadStoreElement<> AlignedReadStoreElement<TPos[, TGapAnchor[, TSpec]]> Parameters
TPos | Type to store gap-space positions.
TGapAnchor | Type of a read gap anchor. Types: GapAnchor
TSpec | The specialization type. Default: void
Remarks Value type of the alignedReadStore string. Typedefs
TGapAnchors | Type of the gaps member.
TPos | Type of the beginPos and endPos members.
TSpec | The specialization type.
Data Members
beginPos | Begin position of the alignment in gap-space.
contigId | Refers to the contig in the contigStore the read is aligned with.
endPos | End position of the alignment in gap-space.
gaps | String of read gap anchors. Can be used to create a Spec.AnchorGaps alignment row.
id | The alignment id refers to associated alignment information in alignQualityStore or alignedReadTagStore.
INVALID_ID | Constant to represent an invalid id.
pairMatchId | Two read alignments having the same pairMatchId form a valid pair match. If INVALID_ID the read is either not paired or could not be aligned as part of a pair match.
readId | Refers to the aligned read in the readStore.
Member Functions
AlignedReadStoreElement | Constructor
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