Alignments Object

Alignments file parsing and manipulation.

Super class

nemo::Tool -> Alignments

Methods

Public methods

• Alignments$new()

• Alignments$parse_markdup()

Inherited methods

• nemo::Tool$filter_files()
• nemo::Tool$get_globs()
• nemo::Tool$get_metadata()
• nemo::Tool$get_tbls()
• nemo::Tool$list_files()
• nemo::Tool$print()
• nemo::Tool$run()
• nemo::Tool$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 is ignored.

files_tbl

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

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Method parse_markdup()

Read md.metrics file.

Usage

Alignments$parse_markdup(x)

Arguments

x

(character(1))
Path to file.

Examples

cls <- Alignments; tool <- "alignments"
indir <- system.file("extdata/oa", tool, package = "tidywigits")
odir <- tempdir()
id <- paste0(tool, "_run1")
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = id)
(lf <- list.files(odir, pattern = paste0(tool, "_.*parquet"), full.names = FALSE))
#> [1] "sample1_2_alignments_dupfreq.parquet"
#> [2] "sample1_alignments_dupfreq.parquet"  
#> [3] "sample1_alignments_markdup.parquet"