DragenMap Object

Parses and tidies DRAGEN mapping/alignment outputs: mapping metrics, run-time metrics, and the fragment-length histogram.

Super classes

nemo::Tool -> tidydragen::DragenTool -> DragenMap

Public fields

flat_tidy_names

(logical(1))
TRUE: fan-out sub-tables are named <tool>_<tidy_name> (parser token dropped). Needed for the umimain/umihist and gcmain/gcbias splits.

Methods

Public methods

• DragenMap$new()

• DragenMap$tidy_metrics()

• DragenMap$tidy_umimain()

• DragenMap$tidy_gcmain()

• DragenMap$tidy_time()

• DragenMap$parse_fraglenhist()

Inherited methods

• nemo::Tool$filter_files()
• nemo::Tool$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 DragenMap object.

Usage

DragenMap$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 tidy_metrics()

Tidy mapping_metrics.csv. Both id columns retained (drop_constant = character()).

Usage

DragenMap$tidy_metrics(x)

Arguments

x

(character(1) or tibble())
Path to file or parsed tibble.

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Method tidy_umimain()

Tidy umi_metrics.csv into umimain (summary, wide) and umihist (the {a|b|c} histograms, long).

Usage

DragenMap$tidy_umimain(x)

Arguments

x

(character(1) or tibble())
Path to file or parsed tibble.

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Method tidy_gcmain()

Tidy gc_metrics.csv into gcmain (GC METRICS SUMMARY, wide) and gcbias (per-GC-window GC BIAS DETAILS, long — GC 0-100).

Usage

DragenMap$tidy_gcmain(x)

Arguments

x

(character(1) or tibble())
Path to file or parsed tibble.

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Method tidy_time()

Tidy time_metrics.csv, using seconds (not HH:MM:SS) as the metric value and surfacing total_runtime first.

Usage

DragenMap$tidy_time(x)

Arguments

x

(character(1) or tibble())
Path to file or parsed tibble.

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Method parse_fraglenhist()

Parse fragment_length_hist.csv into a long tibble.

Usage

DragenMap$parse_fraglenhist(x)

Arguments

x

(character(1))
Path to file.

Examples

cls <- DragenMap; tool <- "dragenmap"
indir <- system.file("extdata", tool, package = "tidydragen")
odir <- tempdir()
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = "run1")
(lf <- list.files(odir, pattern = "dragenmap_.*parquet", full.names = FALSE))
#> [1] "sampleA_dragenmap_fraglenhist.parquet"
#> [2] "sampleA_dragenmap_gcbias.parquet"     
#> [3] "sampleA_dragenmap_gcmain.parquet"     
#> [4] "sampleA_dragenmap_metrics.parquet"    
#> [5] "sampleA_dragenmap_time.parquet"       
#> [6] "sampleA_dragenmap_trimmer.parquet"    
#> [7] "sampleA_dragenmap_umihist.parquet"    
#> [8] "sampleA_dragenmap_umimain.parquet"