Configuration file

We are using toml file as configuration file. Please refer to its documentation.

To overwrite arguments from command line, just specify the values directly in the configuration file. For example:

devpars = {width = 1000, height = 1000, res = 100}
passed = true

To specify multiple plots, we do:

passed = true

[[instance]]
formula = 'DEPTHs{0} ~ CHROM'
title = 'Depth distribution on each chromosome'
ggs = 'theme_minimal()'
devpars = {width = 1000, height = 1000, res = 100}

[[instance]]
formula = 'AAF ~ CHROM'
title = 'Allele frequency distribution on each chromosome'
ggs = 'theme_bw()'
devpars = {width = 2000, height = 2000, res = 300}

When you have a configuration file provided, --title and --formula are optional.

The instances specified by --title and --formula will be used together with the ones provided in the configuration file.