Class ConsensusAlignmentOptions
Configuration for consensusAlignment

Defined in <seqan/consensus.h>
Signature struct ConsensusAlignmentOptions;

Member Variable Overview

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.