// Copyright (C) 2022  Osma S. Rautila

//

// This program is free software: you can redistribute it and/or modify

// it under the terms of the GNU General Public License as published by

// the Free Software Foundation, either version 3 of the License, or

// (at your option) any later version.

//

// This program is distributed in the hope that it will be useful,

// but WITHOUT ANY WARRANTY; without even the implied warranty of

// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

// GNU General Public License for more details.

//

// You should have received a copy of the GNU General Public License

// along with this program.  If not, see <http://www.gnu.org/licenses/>.

//

//

//

// #![doc(

//     html_logo_url = "https://raw.githubusercontent.com/rust-bio/rust-bio/master/img/bioferris.svg",

//     html_favicon_url = "https://raw.githubusercontent.com/rust-bio/rust-bio/master/img/bioferris.svg"

// )]

//! HATK - Haplotype analysis toolkit

//!

//! This library and program provides a multitude of tools designed for the analysis of phased and

//! imputed genomes.

//! All provided tools are tested via continuous integration.

//!

//! For navigating the documentation of the available modules, see [the `Modules` section below](#modules).

//! If you want to contribute to `hatk`, see [the `Contribute` section in the repo]()

//!

//! HATK toolkit commands

//!

//! * Check for haplotype

//! * Find the longest common haplotype at a locus

//! * Contrahomozygosity

//! * Random sampled contrahomozygosity

//! * Decay of shared ancestral haplotype

//! * Recursive decay of shared ancestral haplotypes

//! * Most recent common ancestor estimation using the Gamma method

//! * Pairwise Identity-By-Descent at a specific locus

//! * Sample homozygosity

//! * Utils to check VCF coverage and sample names

//!

//! # Getting started

//!

//! Users who already know `HATK` might want to jump right into the [modules docs](https://docs.rs/bio/#modules)

//!

//! ## Installing HATK

//!

//! Rust and its package manager cargo can be installed following the instruction for [rustup](https://rustup.rs/).

//!

//! After installing cargo, run the following command

//!

//! ```bash

//! cargo install hatk

//! ```

//!

//! ## Running HATK

//!

//! To print the available commands use (more about the commands in the subcommnds section):

//! ```bash

//! hatk --help

//! ```

//! To run for example the longest common haplotype at a specific locus tool use:

//! ```bash

//! hatk common-haplotype $file --coords $coords > ${outdir}/longest_haplotype.tsv

//! ```

//!

//! For a full analysis of a given locus using only the longest shared haplotypes run the following:

//! ```bash

//!hatk common-haplotype $file --coords $coords --only-longest > ${outdir}/longest_haplotype.tsv

//!

//!hatk decay $file --coords $coords --only-longest > ${outdir}/decay.csv

//!

//!hatk multi-decay $file --coords $coords --only-longest -o "${outdir}/decay_graph"

//!

//!hatk mrca $file --coords $coords --only-longest > ${outdir}/age.txt

//!

//!hatk ibs $file --coords $coords --only-longest -o "${outdir}/ibs.png"

//!

//!hatk rand-homozygosity $file -t 8 --iters 300 > ${outdir}/rand_homozygosity.csv

//!

//!hatk sample-homozygosity \

//!  $file --coords $coords -t 8 --iters 100 > ${outdir}/sampled-homozygosity.csv

//!

//!hatk homozygosity $file -t 8 > ${outdir}/homozygosity.csv

//!

//!hatk check-for-haplotype $file --coords $coords --haplotype ${outdir}/longest_haplotype.tsv

//!

//!

//!```

//!

pub mod libs;

pub use libs::{args, io, read_vcf, structs, utils, core};

#[cfg(feature = "clap")]

pub use libs::clap;

pub mod graphs;

pub mod subcommands;