pandora_lib_variants/src/config.rs

use std::path::PathBuf;

use serde::{Serialize, Deserialize};
use anyhow::Result;

#[derive(Serialize, Deserialize, Clone, Debug)]
pub struct Config {
    pub db: String,
    pub reference_fa: String,
    pub longreads_results_dir: String,
    pub panel_results_dir: String,
    pub dict_file: String,
    pub gff_path: String,
    pub min_loh_diff: f32,
    pub deepvariant_loh_pval: f64,
    pub min_mrd_depth: u32,
    pub min_diversity: f64,
    pub vep_chunk_size: usize,
    pub max_gnomad_af: f64,
}

impl ::std::default::Default for Config {
    fn default() -> Self {
        Self {
            db: "/data/db_results.sqlite".to_string(),
            reference_fa: "/data/ref/hs1/chm13v2.0.fa".to_string(),
            longreads_results_dir: "/data/longreads_basic_pipe".to_string(),
            panel_results_dir: "/data/oncoT".to_string(),
            dict_file: "/data/ref/hs1/chm13v2.0.dict".to_string(),
            gff_path: "/data/ref/hs1/features_not_in_vep.gff.gz".to_string(),
            min_loh_diff: 0.25,
            deepvariant_loh_pval: 0.001,
            min_mrd_depth: 6,
            min_diversity: 1.6,
            vep_chunk_size: 1_000,
            max_gnomad_af: 0.01,
        }
    }
}

impl Config {
    pub fn get() -> Result<Self> {
        Ok(confy::load("pandora_lib_variants", None)?)
    }
    pub fn path() -> Result<PathBuf> {
        Ok(confy::get_configuration_file_path("pandora_lib_variants", None)?)
    } 
}