Class
ConsensusAlignmentOptionsConfiguration for consensusAlignment
Configuration for consensusAlignment
Defined in | <seqan/consensus.h> |
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Signature |
struct ConsensusAlignmentOptions;
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Member Variable Overview
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unsigned ConsensusAlignmentOptions::contigID
The id of the contig to compute the consensus for, defaults to INVALID. -
unsigned ConsensusAlignmentOptions::INVALID
Static member variable with a marker for invalid contig ids. -
unsigned ConsensusAlignmentOptions::posDelta
Positions are considered with an environment of posDelta (default is 30). -
bool ConsensusAlignmentOptions::runRealignment
Perform a realignment using standard parameters, depending on the sequence length (default is true). -
bool ConsensusAlignmentOptions::useContigID
Whether or not to use the value of contigID (default is true). -
bool ConsensusAlignmentOptions::usePositions
Whether or not to use positions of the in the alignedReadStore (default is true).
Member Variables Detail
unsigned ConsensusAlignmentOptions::contigID
The id of the contig to compute the consensus for, defaults to INVALID.
Set to INVALID for all.
unsigned ConsensusAlignmentOptions::INVALID
Static member variable with a marker for invalid contig ids.
unsigned ConsensusAlignmentOptions::posDelta
Positions are considered with an environment of posDelta (default is 30).
When positions are not used then this value is ignored.
See consensusAlignment for more details.
bool ConsensusAlignmentOptions::runRealignment
Perform a realignment using standard parameters, depending on the sequence length (default is true).
Defaults to true.
bool ConsensusAlignmentOptions::useContigID
Whether or not to use the value of contigID (default is true).
When this variable is set to false then the value of contigID is ignored and treated as if it was INVALID.
bool ConsensusAlignmentOptions::usePositions
Whether or not to use positions of the in the alignedReadStore (default is true).
When set to false, then the alignedReadStore will be cleared and filled with new entries, one for each read.