Class
AlignedReadStoreElement
Represents an alignment between read and contig.
Include Headers
seqan/store.h
Parameters
Type to store (gap-space) positions. | |
Type of a read gap anchor. Types: GapAnchor | |
The specialization type. Default: |
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
Type of the gaps member. | |
Type of all stored ids. | |
Type of the beginPos and endPos members. | |
The specialization type. |
Data Members
Begin position of the alignment in gap-space. | |
Refers to the contig in the contigStore the read is aligned with. | |
End 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. | |
String of read gap anchors. Can be used to create a AnchorGaps alignment row. | |
The alignment id refers to associated alignment information in alignQualityStore or alignedReadTagStore. | |
Constant to represent an invalid id. | |
Two 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. | |
Refers to the aligned read in the readStore. |
Member Functions
Constructor |
Functions
Get the "clear" range of a read alignment. |
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