Alignments Object

Alignments file parsing and manipulation.

Super class

nemo::Tool -> Alignments

Methods

Public methods

• Alignments$new()

• Alignments$parse_dupfreq()

• Alignments$tidy_dupfreq()

• Alignments$parse_markdup()

• Alignments$tidy_markdup()

• Alignments$clone()

Inherited methods

• nemo::Tool$.eval_func()
• nemo::Tool$.parse_file()
• nemo::Tool$.parse_file_nohead()
• nemo::Tool$.tidy_file()
• nemo::Tool$filter_files()
• nemo::Tool$list_files()
• nemo::Tool$nemofy()
• nemo::Tool$print()
• nemo::Tool$tidy()
• nemo::Tool$write()

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Method new()

Create a new Alignments object.

Usage

Alignments$new(path = NULL, files_tbl = NULL)

Arguments

path

(character(1))
Output directory of tool. If files_tbl is supplied, this basically gets ignored.

files_tbl

(tibble(n))
Tibble of files from nemo::list_files_dir().

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Method parse_dupfreq()

Read duplicate_freq.tsv file.

Usage

Alignments$parse_dupfreq(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_dupfreq()

Tidy duplicate_freq.tsv file.

Usage

Alignments$tidy_dupfreq(x)

Arguments

x

(character(1))
Path to file.

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Method parse_markdup()

Read md.metrics file.

Usage

Alignments$parse_markdup(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_markdup()

Tidy md.metrics file.

Usage

Alignments$tidy_markdup(x)

Arguments

x

(character(1))
Path to file.

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Method clone()

The objects of this class are cloneable with this method.

Usage

Alignments$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

cls <- Alignments
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "alignments_run1"
obj <- cls$new(indir)
obj$nemofy(odir = odir, format = "parquet", id = id)
#> NULL
(lf <- list.files(odir, pattern = "alignments.*parquet", full.names = FALSE))
#> character(0)