fn() reAlign
Perform realignment using the Anson-Myers realignment.

Defined in <seqan/consensus.h>
Signature void reAlign(fragStore, consensusScore, contigID, [realignmentMethod,] bandwidth, includeReference);


fragStore The FragmentStore with the alignment to realign.
consensusScore The Score to use for scoring alignments.
contigID The integer id of the contig to realign.
bandwidth The integer bandwidth to use for realignment.
includeReference A bool flag that indicates whether to include the reference as a pseudo-read.

Detailed Description


Do not use this function but use the new function reAlignment instead.

If includeReference then the reference of the given contig will be used as a pseudo-read. In this case, the reference will be replaced by the consensus. When included as a pseudo-read, the alignment of the consensus relative to the original refernence can be used to call variants.