BclconvertReports R6 Class

Reads and writes tidy versions of files within the Reports directory output from BCLConvert.

Public fields

path

Path to the Reports directory.

contents

Tibble with file path, basename, and size.

Methods

Public methods

• BclconvertReports$new()

• BclconvertReports$print()

• BclconvertReports$read()

• BclconvertReports$write()

• BclconvertReports$clone()

---

Method new()

Create a new BclconvertReports object.

Usage

BclconvertReports$new(path = NULL)

Arguments

path

Path to the Reports directory.

---

Method print()

Print details about the BclconvertReports directory.

Usage

BclconvertReports$print(...)

Arguments

...

(ignored).

---

Method read()

Reads contents of Reports directory output by BCLConvert.

Usage

BclconvertReports$read()

Returns

A list of tibbles.

---

Method write()

Writes tidied contents of Reports directory output by BCLConvert.

Usage

BclconvertReports$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).

---

Method clone()

The objects of this class are cloneable with this method.

Usage

BclconvertReports$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) {
b <- BclconvertReports$new(here::here("nogit/bcl_convert/WGS_TsqNano/Reports"))
b$path
b$contents
d <- b$read()
b$write(d, out_dir = tempdir(), prefix = "sampleA", out_format = "tsv")
}