Alignments Object

Alignments file parsing and manipulation.

Super class

tidywigits::Tool -> Alignments

Methods

Public methods

• Alignments$new()

• Alignments$parse_dupfreq()

• Alignments$tidy_dupfreq()

• Alignments$parse_markdup()

• Alignments$tidy_markdup()

• Alignments$clone()

Inherited methods

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

---

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 list_files_dir.

---

Method parse_dupfreq()

Read duplicate_freq.tsv file.

Usage

Alignments$parse_dupfreq(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_dupfreq()

Tidy duplicate_freq.tsv file.

Usage

Alignments$tidy_dupfreq(x)

Arguments

x

(character(1))
Path to file.

---

Method parse_markdup()

Read md.metrics file.

Usage

Alignments$parse_markdup(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_markdup()

Tidy md.metrics file.

Usage

Alignments$tidy_markdup(x)

Arguments

x

(character(1))
Path to file.

---

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

if (FALSE) { # \dontrun{
path <- here::here(
  "nogit/oa_v2"
)
a <- Alignments$new(path)
a$nemofy(
    odir = "nogit/test_data",
    format = "parquet",
    id = "run1",
    include = NULL,
    exclude = NULL
)
} # }