Decode compact seq and qual columns in BamScale output — decode_seqqual_compact • BamScale

Convenience wrapper for converting a compact bam_read() result back to ordinary sequence and quality strings.

Usage

decode_seqqual_compact(
  x,
  seq_col = "seq",
  qual_col = "qual",
  qwidth_col = "qwidth"
)

Arguments

x: A data.frame, S4Vectors::DataFrame, or list-like object containing compact BamScale seq and/or qual columns.
seq_col: Name of the compact sequence column.
qual_col: Name of the compact quality column.
qwidth_col: Name of the read-width column used to decode compact sequence bytes.

Value

x with compact seq and/or qual columns replaced by decoded character vectors. The input class is preserved.

See also

decode_compact_seq(), decode_compact_qual(), bam_read()

Examples

x <- data.frame(qwidth = 4L)
x$seq <- I(list(as.raw(c(0x12, 0x48))))
x$qual <- I(list(as.raw(c(0L, 1L, 2L, 3L))))
decode_seqqual_compact(x)
#>   qwidth  seq qual
#> 1      4 ACGT !"#$