Decode compact BamScale sequence output

Decodes seq values returned by bam_read(..., seqqual_mode = "compact") back to ordinary character strings.

Usage

decode_compact_seq(seq, qwidth)

Arguments

seq

A list (or list-column) of raw vectors produced by compact BamScale sequence extraction.

qwidth

Integer vector of read widths. This is required because compact sequence bytes use BAM's 4-bit packed encoding (two bases per byte).

Value

A character vector containing decoded sequence strings.

See also

decode_compact_qual(), decode_seqqual_compact(), bam_read()

Examples

decode_compact_seq(
  seq = list(as.raw(c(0x12, 0x48))),
  qwidth = 4L
)
#> [1] "ACGT"