BclconvertReports375 R6 Class

Reads and writes tidy versions of files within the Reports directory output from BCLConvert v4.2.7. See the DRAGEN v4.2 documentation at https://support-docs.illumina.com/SW/dragen_v42/Content/SW/DRAGEN/OutputFiles.htm.

Public fields

path

Path to the Reports directory.

contents

Tibble with file path, basename, and size.

Methods

Public methods

• BclconvertReports375$new()

• BclconvertReports375$print()

• BclconvertReports375$read_adaptermetrics()

• BclconvertReports375$read_demultiplexstats()

• BclconvertReports375$read_indexhoppingcounts()

• BclconvertReports375$read_topunknownbarcodes()

• BclconvertReports375$read_fastqlist()

• BclconvertReports375$read()

• BclconvertReports375$write()

• BclconvertReports375$clone()

---

Method new()

Create a new BclconvertReports375 object.

Usage

BclconvertReports375$new(path = NULL)

Arguments

path

Path to the Reports directory.

---

Method print()

Print details about the BclconvertReports375 directory.

Usage

BclconvertReports375$print(...)

Arguments

...

(ignored).

---

Method read_adaptermetrics()

Read Adapter_Metrics.csv file.

Usage

BclconvertReports375$read_adaptermetrics(x)

Arguments

x

(character(1))
Path to Adapter_Metrics.csv file.

---

Method read_demultiplexstats()

Read Demultiplex_Stats.csv file.

Usage

BclconvertReports375$read_demultiplexstats(x)

Arguments

x

(character(1))
Path to Demultiplex_Stats.csv file.

---

Method read_indexhoppingcounts()

Read Index_Hopping_Counts.csv file.

Usage

BclconvertReports375$read_indexhoppingcounts(x)

Arguments

x

(character(1))
Path to Index_Hopping_Counts.csv file.

---

Method read_topunknownbarcodes()

Read Top_Unknown_Barcodes.csv file.

Usage

BclconvertReports375$read_topunknownbarcodes(x)

Arguments

x

(character(1))
Path to Top_Unknown_Barcodes.csv file.

---

Method read_fastqlist()

Read fastq_list.csv file.

• rgid: read group.

• rgsm: sample ID.

• rglb: library.

• lane: flow cell lane.

• readnum: read number (1 or 2).

• filepath: path to the FASTQ file.

Usage

BclconvertReports375$read_fastqlist(x)

Arguments

x

(character(1))
Path to fastq_list.csv file.

---

Method read()

Reads contents of Reports directory output by BCLConvert.

Usage

BclconvertReports375$read()

Returns

A list of tibbles.

---

Method write()

Writes tidied contents of Reports directory output by BCLConvert.

Usage

BclconvertReports375$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

BclconvertReports375$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{
p1 <- "nogit/bcl_convert/WGS_TsqNano/Reports"
b <- here::here(p1) |>
  BclconvertReports375$new()
b$path
b$contents
d <- b$read()
b$write(d, out_dir = tempdir(), prefix = "sampleA", out_format = "tsv")
} # }