Class
AlignedReadStoreElement
Represents an alignment between read and contig.
AlignedReadStoreElement<>
AlignedReadStoreElement<TPos[, TGapAnchor[, TSpec]]>
Include Headers
seqan/store.h
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. In contrast to all other FragmentStore stores, the id of an aligned read is explicitly stored as a member to allow for random reordering of the alignedReadStore, e.g. sorting by genomic position via sortAlignedReads.
Typedefs
TGapAnchorsType of the gaps member.
TIdType of all stored ids.
TPosType of the beginPos and endPos members.
TSpecThe specialization type.
Data Members
beginPosBegin position of the alignment in gap-space.
contigIdRefers to the contig in the contigStore the read is aligned with.
endPosEnd position of the alignment in gap-space. If endPos < beginPos, the read is aligned to the reverse strand, where beginPos and endPos are the corresponding positions on the forward strand.
gapsString of read gap anchors. Can be used to create a AnchorGaps alignment row.
idThe alignment id refers to associated alignment information in alignQualityStore or alignedReadTagStore.
INVALID_IDConstant to represent an invalid id.
pairMatchIdTwo read alignments having the same pairMatchId form a valid pair match. If it equals INVALID_ID, the read is either not paired or could not be aligned as part of a pair match.
readIdRefers to the aligned read in the readStore.
Member Functions
AlignedReadStoreElementConstructor
Functions
getClrRangeGet the "clear" range of a read alignment.
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