BcftoolsStatsFile R6 Class

Contains methods for reading and displaying contents of the bcftools_stats.txt file (QUAL section) output from running bcftools stats.

Super class

dracarys::File -> BcftoolsStatsFile

Methods

Public methods

• BcftoolsStatsFile$read()

• BcftoolsStatsFile$write()

• BcftoolsStatsFile$clone()

Inherited methods

• dracarys::File$bname()
• dracarys::File$initialize()
• dracarys::File$print()
• dracarys::File$type()

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Method read()

Reads the QUAL section from the bcftools_stats.txt file.

Usage

BcftoolsStatsFile$read()

Returns

A tibble.

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Method write()

Writes a tidy version of the bcftools_stats.txt (only QUAL section) file output from TSO.

Usage

BcftoolsStatsFile$write(
  d,
  out_dir = NULL,
  prefix,
  out_format = "tsv",
  drid = NULL
)

Arguments

d

Parsed object from self$read().

out_dir

Output directory.

prefix

Prefix of output file(s).

out_format

Format of output file(s).

drid

dracarys ID to use for the dataset (e.g. wfrid.123, prid.456).

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Method clone()

The objects of this class are cloneable with this method.

Usage

BcftoolsStatsFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{
x <- "/path/to/bcftools_stats.txt"
d <- BcftoolsStatsFile$new(x)
d_parsed <- d$read()
d$write(d_parsed, out_dir = tempdir(), prefix = "sample123", out_format = "tsv")
} # }