Perform Smith-Waterman alignment of a read against a reference sequence

Usage

align(
  read,
  reference,
  gap_open = 3L,
  gap_extension = 1L,
  start_idx = 0L,
  end_idx = 0L,
  match_score = 2L,
  mismatch_penalty = 2L
)

read: A character string of the read.
reference: A character string of the reference.
gap_open: Penalty for opening a gap. Default is 3.
gap_extension: Penalty for extending a gap. Default is 1.
start_idx: Index to start the alignment search. Default is 0.
end_idx: Index to end the alignment search. The default value 0 means using the entire reference length.
match_score: An integer for scoring matches, ranging from 0 to 255. Default is 2.
mismatch_penalty: An integer for mismatch penalties, ranging from 0 to 255. Default is 2.

A list of class ssw containing the ssw aligner object and the alignment results.

if (FALSE) { # is_installed_ssw_py()
a <- align("ACGT", "TTTTACGTCCCCC")
a
a$alignment$optimal_score
a$alignment$sub_optimal_score
}