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use anyhow::Result;
use clap::Parser;
mod select;
mod split;
mod stats;
mod concat;
use select::*;
use split::*;
use stats::*;
use concat::*;
#[derive(Parser, Debug)]
#[command(
author = "size_t",
version = "version 0.1",
about = "vcfkit: a simple program for vcf/bcf file manipulation",
long_about = "vcfkit: a simple program for vcf/bcf file manipulation\nrepo: https::github.com/sharkLoc/vcfkit.git\nemail: dwood8146@gmail.com"
)]
struct Args {
#[clap(subcommand)]
command: Subcli,
}
#[derive(Parser, Debug)]
#[allow(non_camel_case_types)]
enum Subcli {
/// concatenate VCF/BCF files from the same set of samples
concat {
/// input VCF/BCF file list, containing the path to the files, one per line and no blank line.
#[arg(short= 'l', long = "list")]
list: String,
/// if specified, output bgzip compressed file.
#[arg(short = 'z', long = "gzip")]
gzip: bool,
/// output vcf file name, or write to stdout.
out: Option<String>,
},
/// convert BCF file to VCF file formats
convert {
/// input bcf file, or read from stdin.
bcf: Option<String>,
/// if specified, output bgzip compressed file.
#[arg(short = 'z', long = "gzip")]
gzip: bool,
/// output vcf file name, or write to stdout.
#[arg(short = 'o', long = "out")]
out : String
},
/// select SNP/INDEL variants from a VCF file
select {
/// input vcf[.gz] file, or read from stdin.
vcf: Option<String>,
/// select variant type: SNP/INDEL
#[arg(short = 'k', long = "keep", default_value_t = String::from("SNP") )]
keep: String,
/// if specified, output bgzip compressed file.
#[arg(short = 'z', long = "gzip")]
gzip: bool,
/// output vcf file name, or write to stdout.
out: Option<String>,
},
/// split vcf file by chromosome name
split {
/// input vcf[.gz] file, or read from stdin.
vcf: Option<String>,
/// split vcf file output dir.
#[arg(short = 'o', long = "out")]
outdir: String,
},
///statistics including alleles frequence, missing rate, etc.
stats {
/// input vcf[.gz] file, or read from stdin.
vcf: Option<String>,
},
}
fn main() -> Result<(), anyhow::Error> {
let arg = Args::parse();
match arg.command {
Subcli::select {
vcf,
keep,
gzip,
out,
} => match vcf {
Some(v) => {
if let Some(o) = out {
let _x = select_sites(&Some(&v), &keep, gzip, &Some(&o))?;
} else {
let _x = select_sites(&Some(&v), &keep, gzip, &None)?;
}
}
None => {
if let Some(o) = out {
let _x = select_sites(&None, &keep, gzip, &Some(&o))?;
} else {
let _x = select_sites(&None, &keep, gzip, &None)?;
}
}
}
Subcli::split {
vcf,
outdir,
} => match vcf {
Some(v) => { let _x = split_by_chr(&Some(&v), &outdir)?; }
None => { let _x = split_by_chr(&None, &outdir)?; }
}
Subcli::concat {
list,
gzip,
out
} => match out {
Some(x) => { let _x = concat_vcfs(&list, gzip, &Some(&x))?;}
None => { let _x = concat_vcfs(&list, gzip, &None)?; }
}
Subcli::convert {
bcf,
gzip,
out
} => match bcf {
Some(v) => { let _x = bcf2vcf(&Some(&v), gzip, &out)?; }
None => { let _x = bcf2vcf(&None, gzip, &out)?; }
}
Subcli::stats {vcf} => match vcf {
Some(v) => { let _x = calc_sites(&Some(&v));}
None => { let _x = calc_sites(&None);}
}
}
Ok(())
}