Format matches in SAM-compatible text direction

Rsassy normally follows the upstream sassy TSV convention: reverse-strand match_region values are reverse-complemented and CIGAR strings are oriented in the input pattern direction. sassy_as_sam() converts reverse-strand rows to the text direction used by SAM and by upstream sassy --sam output.

Usage

sassy_as_sam(x, alphabet = "dna")

Arguments

x

A sassy_matches data frame.

alphabet

Alphabet profile used for the search. One of "dna" or "iupac" when x includes match_region.

Value

A copy of x with reverse-strand cigar values reversed and, when present, reverse-strand match_region values reverse-complemented back to text direction.

Examples

sassy_as_sam(
  sassy_search(list("ACGA"), list("TTTCGTTT"), 0, alphabet = "dna", match_region = TRUE),
  alphabet = "dna"
)
#> <sassy_matches> 1 match
#> pattern_idx text_idx text_start text_end pattern_start pattern_end cost strand cigar match_region
#>           0        0          2        6             0           4    0      -    4=         TCGT