generate_cost_matrix {seqtrie}

Generate a simple cost matrix

Description

Generate a cost matrix for use with the search method

Usage

generate_cost_matrix(
  charset,
  match = 0L,
  mismatch = 1L,
  gap = NULL,
  gap_open = NULL
)

Arguments

charset

A string representing all possible characters in both query and target sequences (e.g. "ACGT")

match

The cost of a match

mismatch

The cost of a mismatch

gap

The cost of a gap or NULL if this parameter will be set later.

gap_open

The cost of a gap opening or NULL. If this parameter is set, gap must also be set.

Value

A cost matrix

Examples

generate_cost_matrix("ACGT", match = 0, mismatch = 1)