pad_bed: Pad a BED file

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Pad a BED file

Description

This function takes a BED file and pad each regions in both directions

Usage

pad_bed(
  bin_bedtools = build_default_tool_binary_list()$bin_bedtools,
  bed = "",
  pad = 10,
  output_name = "Padded",
  output_dir = ".",
  genome = "",
  verbose = FALSE,
  batch_config = build_default_preprocess_config(),
  threads = 3,
  ram = 1,
  coord_sort = TRUE,
  mode = "local",
  executor_id = make_unique_id("padBED"),
  task_name = "padBED",
  time = "48:0:0",
  update_time = 60,
  wait = FALSE,
  hold = NULL
)

Arguments

bin_bedtools	Path to bedtools executable. Default path tools/bedtools2/bin/bedtools.
bed	Path to the input file with the sequence.
pad	Pad distance. Default 10
output_name	Output file name.
output_dir	Path to output directory
genome	Path to genome fa.fai file
verbose	OPTIONAL Enables progress messages. Default False.#
threads	Number of threads . Default 4
ram	RAM memory. Default 4
mode	REQUIRED Where to parallelize. Default local. Options "local","batch"
executor_id	Task EXECUTOR ID. Default "mardupsGATK"
task_name	Task name. Default "mardupsGATK"
time	OPTIONAL If batch mode. Max run time per job. Default "48:0:0"
update_time	OPTIONAL If batch mode. Job update time in seconds. Default 60.
wait	OPTIONAL If batch mode wait for batch to finish. Default FALSE
hold	OPTIONAL Hold job until job is finished. Job ID.

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.