Class
AlignedReadStoreElementRepresents an alignment of a read to a contig.
Represents an alignment of a read to a contig.
Defined in | <seqan/store.h> |
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Signature |
template <typename TPos, typename TGapAnchors[, typename TSpec]>
struct AlignedReadStoreElement;
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Template Parameters
TPos |
The position type to use. |
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TGapAnchors |
Type of a read GapAnchor. |
TSpec |
The specializing type. Default: void. |
Member Function Overview
Member Typedef Overview
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typedef (..) TAlignedReadStoreElement::TGapAnchors;
Type of the gaps member. -
typedef (..) TAlignedReadStoreElement::TId;
Type of all store ids. -
typedef (..) TAlignedReadStoreElement::TPos;
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typedef (..) TAlignedReadStoreElement::TSpec;
The specializing type.
Member Variable Overview
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TPos AlignedReadStoreElement::beginPos
Begin position in gap-space. -
TId AlignedReadStoreElement::contigId
Refers to the contig in the contigStore that the read is aligned with. -
TPos AlignedReadStoreElement::endPos
End position in gap-space. -
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.
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
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The alignment id refers to associated alignment information in alignQualityStore or alignedReadTagStore. |
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readId
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Refers to the aligned read in the readStore. |
contigID
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Refers to the contig in the contigStore the read is aligned to. |
beginPos
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Begin position of the alignment in gap-space. |
endPos
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End position of the alignment in gap-space. |
gaps
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A String of GapAnchor objects. |
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;
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.