Class AlignedReadStoreElement
Represents an alignment of a read to a contig.

Defined in <seqan/store.h>
Signature template <typename TPos, typename TGapAnchors[, typename TSpec]> struct AlignedReadStoreElement;

Template Parameters

TPos The position type to use.
TGapAnchors Type of a read GapAnchor.
TSpec The specializing type. Default: void.

Member Function Overview

Member Typedef Overview

Member Variable Overview

Detailed Description

Value type of the alignedReadStore. In contrast to all other FragmentStore stores, the id of an aligned read is explicitely stored as a member to allow for reordering the alignedReadStore and still recover the id.

Member Functions Detail

AlignedReadStoreElement::AlignedReadStoreElement(); AlignedReadStoreElement::AlignedReadStoreElement(id, readId, contigId, beginPos, endPos[, gaps]);

Constructor.

Parameters

id The alignment id refers to associated alignment information in alignQualityStore or alignedReadTagStore.
readId Refers to the aligned read in the readStore.
contigID Refers to the contig in the contigStore the read is aligned to.
beginPos Begin position of the alignment in gap-space.
endPos End position of the alignment in gap-space.
gaps A String of GapAnchor objects.

The default constructors sets all ids to AlignedReadStoreElement::INVALID_ID and beginPos and endPos to 0.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

Member Typedef Detail

typedef (..) TAlignedReadStoreElement::TGapAnchors;

Type of the gaps member.

typedef (..) TAlignedReadStoreElement::TId;

Type of all store ids.

TId is the result of Id≶AlignedReadStoreElement&lgt;> >::Type, see Id.

typedef (..) TAlignedReadStoreElement::TPos;

Type of the beginPos and endPos.

typedef (..) TAlignedReadStoreElement::TSpec;

The specializing type.

Member Variables Detail

TPos AlignedReadStoreElement::beginPos

Begin position in gap-space.

If beginPos < endPos then the read is aligned to the reverse strand where beginPos and endPos are the corresponding positions on the forward strand.

TId AlignedReadStoreElement::contigId

Refers to the contig in the contigStore that the read is aligned with.

TPos AlignedReadStoreElement::endPos

End position in gap-space.

If beginPos < endPos then the read is aligned to the reverse strand where beginPos and endPos are the corresponding positions on the forward strand.

TGaps AlignedReadStoreElement::gaps

String of read GapAnchor objects. Can be used to create a AnchorGaps alignment row.

TId AlignedReadStoreElement::id

The alignment id refers to associated alignment information in alignQualityStore or alignedReadTagStore.

TId AlignedReadStoreElement::INVALID_ID

Constant expression that is the value of an invalid id.

TId AlignedReadStoreElement::pairMatchId

Two read alignments having the same pairMatchId form a valid pair match. If it equals INVALID_ID then the read is either not paired or could not be aligned as part of a pair.

TId AlignedReadStoreElement::readId

Refers to the aligned read in readStore.