Function
bandedChainAlignment
Calculates a banded alignment around a chain of seeds.
bandedChainAlignment(seedChain, k, alignment, scoreMatrix);
Parameters
seedChain
A chain of seeds.
k
Half of the width of the band.
alignment
The alignment where the result is stored.
Types: Align
scoreMatrix
The score matrix.
Types: Simple Score
Remarks: Depending on the score matrix the Needleman-Wunsch or the Gotoh algorithm is used.
Return Values
The score of the alignment.
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