generate_cost_matrix: Generate a simple cost matrix
Description
Generate a cost matrix for use with the search method.
Usage
generate_cost_matrix(charset, ambiguity_base = NULL, match = 0L, mismatch = 1L)
Value
A square cost matrix with row- and column-names given by charset, plus the optional ambiguity_base. Gap costs are no longer included here; pass gap_cost and gap_open_cost to distance/search functions.
Arguments
charset
A string of all allowed characters in both query and target sequences (e.g. "ACGT").
ambiguity_base
A single character (e.g. "N") that will match any character in charset at the cost of match. Defaults to NULL.