name: d4-stat - Run statistics on D4 file
author: Hao Hou <haohou302@gmail.com>
args:
- stat:
short: s
long: stat
value_name: stat_type
help: "The type of statistics we want to perform, by default average. You can specify statistic methods: mean, median, hist, percentile=X%, sum, count (If this is not specified d4utils will use mean by default)"
- region:
short: r
long: region
value_name: bed_file_path
help: A bed file that describes the region on which we want to run the stat
- threads:
short: t
long: threads
value_name: num_of_threads
help: Number of threads
- max-bin:
long: max-bin
value_name: maximum bin
help: "Set the upper bound of max bin (default: 1000)"
- input:
required: true
value_name: input_d4_file
- first:
short: f
long: first
help: "Show first data track from the given file"
- no-index:
long: no-index
help: "Do not use index even it's present"
- filter:
short: F
long: filter
value_name: 'TRACK-PATTERN'
help: "A regex that matches all the track labels to be printed"
- header:
short: H
long: header
help: "Print the column header"