pandora_lib_promethion/src/variant/variant.rs

use crate::{
    annotation::Annotations,
    helpers::Hash128,
    positions::{GenomePosition, GetGenomePosition, VcfPosition},
    runners::Run,
    variant::variant_collection::VariantCollection,
};
use anyhow::{anyhow, Context};
use log::warn;
use rayon::prelude::*;
use serde::{Deserialize, Serialize};
use std::{cmp::Ordering, collections::HashSet, fmt, hash::Hash, str::FromStr};

/// Represents a variant in the Variant Call Format (VCF).
#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct VcfVariant {
    /// A 128-bit hash of the variant's key properties for efficient comparison and storage.
    pub hash: Hash128,
    /// The genomic position of the variant.
    pub position: GenomePosition,
    /// The identifier of the variant.
    pub id: String,
    /// The reference allele.
    pub reference: ReferenceAlternative,
    /// The alternative allele.
    pub alternative: ReferenceAlternative,
    /// The quality score of the variant call, if available.
    pub quality: Option<f32>,
    /// The filter status of the variant.
    pub filter: Filter,
    /// Additional information about the variant.
    pub infos: Infos,
    /// Genotype information and other sample-specific data.
    pub formats: Formats,
}

impl PartialEq for VcfVariant {
    /// Compares two VcfVariants for equality.
    ///
    /// Note: This comparison only considers position, reference, and alternative.
    /// It intentionally ignores id, filter, info, format, and quality.
    fn eq(&self, other: &Self) -> bool {
        // Nota bene: id, filter, info, format and quality is intentionally not compared
        self.position == other.position
            && self.reference == other.reference
            && self.alternative == other.alternative
    }
}

impl Eq for VcfVariant {}

impl FromStr for VcfVariant {
    type Err = anyhow::Error;

    /// Parses a VcfVariant from a string representation.
    ///
    /// The input string is expected to be a tab-separated VCF line.
    ///
    /// # Errors
    ///
    /// Returns an error if parsing fails for any field.
    fn from_str(s: &str) -> anyhow::Result<Self> {
        let v: Vec<&str> = s.split('\t').collect();
        let vcf_position: VcfPosition = (
            *v.first().ok_or(anyhow!("Can't get contig from: {s}"))?,
            *v.get(1).ok_or(anyhow!("Can't get position from: {s}"))?,
        )
            .try_into()
            .context(format!("Can't parse position from: {s}"))?;

        let formats = if v.len() >= 10 {
            (
                *v.get(8).ok_or(anyhow!("Can't parse formats from: {s}"))?,
                *v.get(9).ok_or(anyhow!("Can't parse formats from: {s}"))?,
            )
                .try_into()
                .context(format!("Can't parse formats from: {s}"))?
        } else {
            Formats::default()
        };

        let position: GenomePosition = vcf_position.into();
        let reference: ReferenceAlternative = v
            .get(3)
            .ok_or(anyhow!("Can't parse reference from: {s}"))?
            .parse()
            .context(format!("Can't parse reference from: {s}"))?;
        let alternative: ReferenceAlternative = v
            .get(4)
            .ok_or(anyhow!("Can't parse alternative from: {s}"))?
            .parse()
            .context(format!("Can't parse alternative from: {s}"))?;

        // Blake3 128 bytes Hash
        let mut hasher = blake3::Hasher::new();
        hasher.update(&position.contig.to_ne_bytes()); // Convert position to bytes
        hasher.update(&position.position.to_ne_bytes()); // Convert position to bytes
        hasher.update(reference.to_string().as_bytes()); // Reference string as bytes
        hasher.update(alternative.to_string().as_bytes()); // Alternative string as bytes
        let hash = hasher.finalize();
        let hash = Hash128::new(hash.as_bytes()[..16].try_into().unwrap());

        Ok(Self {
            hash,
            position,
            id: v
                .get(2)
                .ok_or(anyhow!("Can't parse id from: {s}"))?
                .to_string(),
            reference,
            alternative,
            quality: v
                .get(5)
                .map(|s| s.parse::<f32>().ok()) // Try to parse as f64; returns Option<f64>
                .unwrap_or(None),
            filter: v
                .get(6)
                .ok_or(anyhow!("Can't parse filter from: {s}"))?
                .parse()
                .context(format!("Can't parse filter from: {s}"))?,
            infos: v
                .get(7)
                .ok_or(anyhow!("Can't parse infos from: {s}"))?
                .parse()
                .context(format!("Can't parse infos from: {s}"))?,
            formats,
        })
    }
}

// #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ADJAGBA_diag
impl VcfVariant {
    /// Converts the VcfVariant into a VCF-formatted row string.
    ///
    /// This method creates a tab-separated string representation of the variant,
    /// suitable for writing to a VCF file.
    pub fn into_vcf_row(&self) -> String {
        let vcf_position: VcfPosition = self.position.clone().into();
        let (contig, position) = vcf_position.into();

        let mut columns = vec![
            contig,
            position,
            self.id.to_string(),
            self.reference.to_string(),
            self.alternative.to_string(),
            self.quality
                .map(|v| v.to_string())
                .unwrap_or(".".to_string()),
            self.filter.to_string(),
            self.infos.to_string(),
        ];

        if !self.formats.0.is_empty() {
            let (format, values) = self.formats.clone().into();
            columns.push(format);
            columns.push(values);
        }

        columns.join("\t")
    }

    /// Returns the hash of the variant.
    pub fn hash(&self) -> Hash128 {
        self.hash
    }

    /// Creates a new VcfVariant with common attributes from DeepVariant and CLAIRS.
    ///
    /// This method generates a new variant with shared properties, resetting some fields
    /// to default or empty values.
    pub fn commun_deepvariant_clairs(&self) -> VcfVariant {
        VcfVariant {
            hash: self.hash,
            position: self.position.clone(),
            id: self.id.clone(),
            reference: self.reference.clone(),
            alternative: self.alternative.clone(),
            quality: self.quality,
            filter: Filter::Other(".".to_string()),
            infos: Infos(vec![Info::Empty]),
            formats: self.formats.commun_deepvariant_clairs(),
        }
    }

    /// Checks if the variant has an SVTYPE info field.
    ///
    /// Returns true if the variant contains structural variation type information.
    pub fn has_svtype(&self) -> bool {
        self.infos.0.iter().any(|i| matches!(i, Info::SVTYPE(_)))
    }

    /// Retrieves the structural variation type of the variant, if present.
    ///
    /// Returns Some(SVType) if the variant has an SVTYPE info field,
    pub fn svtype(&self) -> Option<SVType> {
        self.infos.0.iter().find_map(|e| {
            if let Info::SVTYPE(sv_type) = e {
                Some(sv_type.clone())
            } else {
                None
            }
        })
    }

    /// Determines the alteration category of the variant.
    ///
    /// This method analyzes the reference and alternative alleles to classify
    /// the variant into one of several alteration categories:
    /// - SNV (Single Nucleotide Variant)
    /// - INS (Insertion)
    /// - DEL (Deletion)
    /// - Other (including structural variants and complex alterations)
    ///
    /// The classification is based on the following rules:
    /// 1. If both reference and alternative are single nucleotides, it's an SNV.
    /// 2. If reference is a single nucleotide and alternative is multiple nucleotides, it's an insertion.
    /// 3. If reference is multiple nucleotides and alternative is a single nucleotide, it's a deletion.
    /// 4. For cases where both are multiple nucleotides, the longer one determines if it's an insertion or deletion.
    /// 5. If none of the above apply, it checks for structural variant types.
    /// 6. If no structural variant type is found, it's classified as "Other".
    ///
    /// # Returns
    /// An `AlterationCategory` enum representing the type of alteration.
    pub fn alteration_category(&self) -> AlterationCategory {
        match (&self.reference, &self.alternative) {
            (ReferenceAlternative::Nucleotide(_), ReferenceAlternative::Nucleotide(_)) => {
                AlterationCategory::SNV
            }
            (ReferenceAlternative::Nucleotide(_), ReferenceAlternative::Nucleotides(_)) => {
                AlterationCategory::INS
            }
            (ReferenceAlternative::Nucleotide(_), ReferenceAlternative::Unstructured(_)) => {
                AlterationCategory::Other
            }
            (ReferenceAlternative::Nucleotides(_), ReferenceAlternative::Nucleotide(_)) => {
                AlterationCategory::DEL
            }
            (ReferenceAlternative::Nucleotides(a), ReferenceAlternative::Nucleotides(b))
                if a.len() < b.len() =>
            {
                AlterationCategory::INS
            }
            (ReferenceAlternative::Nucleotides(a), ReferenceAlternative::Nucleotides(b))
                if a.len() > b.len() =>
            {
                AlterationCategory::DEL
            }
            _ => match self.svtype() {
                Some(sv_type) => {
                    if let Ok(bnd_desc) = self.bnd_desc() {
                        if bnd_desc.a_contig != bnd_desc.b_contig {
                            AlterationCategory::TRL
                        } else {
                            AlterationCategory::BND
                        }
                    } else {
                        AlterationCategory::from(sv_type)
                    }
                }
                None => AlterationCategory::Other,
            },
        }
    }

    /// Parses and constructs a BND (breakend) description from the alternative string.
    ///
    /// This function interprets the BND notation in the alternative string and creates
    /// a `BNDDesc` struct containing detailed information about the breakend.
    ///
    /// # Returns
    /// - `Ok(BNDDesc)` if parsing is successful
    /// - `Err` if parsing fails or if the alteration is not a BND
    ///
    /// # Errors
    /// This function will return an error if:
    /// - The alteration category is not BND
    /// - The alternative string cannot be parsed into exactly 3 parts
    /// - The b_position cannot be parsed as a number
    pub fn bnd_desc(&self) -> anyhow::Result<BNDDesc> {
        let alt = self.alternative.to_string();
        if alt.contains('[') || alt.contains(']') {
            let extending_right = alt.contains('[');
            let alt_rep = alt.replace("[", ";").replace("]", ";");
            let alt_is_joined_after = !alt_rep.starts_with(";");
            let parts = alt_rep
                .split(";")
                .filter(|c| !c.is_empty())
                .collect::<Vec<&str>>();

            if alt_is_joined_after {
                // a is ref b is alt
                let a_sens = true;
                let a_contig = self.position.contig();
                let a_position = self.position.position + 1;

                let added_nt = parts[0][1..].to_string();

                let b_sens = alt.contains('[');
                let (contig, pos) = parts[1].split_once(':').unwrap();
                let b_contig = contig.to_string();
                let b_position: u32 = pos.parse()?;

                Ok(BNDDesc {
                    a_contig,
                    a_position,
                    a_sens,
                    b_contig,
                    b_position,
                    b_sens,
                    added_nt,
                })
            } else {
                // a is alt b is ref
                let b_sens = true;
                let b_contig = self.position.contig();
                let b_position = self.position.position + 1;

                let mut added_nt = parts[1].to_string();
                added_nt.pop();

                let a_sens = alt.contains(']');
                let (contig, pos) = parts[0].split_once(':').unwrap();
                let a_contig = contig.to_string();
                let a_position: u32 = pos.parse()?;

                Ok(BNDDesc {
                    a_contig,
                    a_position,
                    a_sens,
                    b_contig,
                    b_position,
                    b_sens,
                    added_nt,
                })
            }

            // let b_sens = alt.contains('[');
            //
            // let a_sens = if b_sens {
            //     !alt.starts_with('[')
            // } else {
            //     !alt.starts_with(']')
            // };
            //
            // let parts: Vec<&str> = alt
            //     .split(&['[', ']', ':'])
            //     .filter(|v| !v.is_empty())
            //     .collect();
            //
            // if parts.len() != 3 {
            //     return Err(anyhow::anyhow!("Failed to parse parts: {parts:?}"));
            // }
            //
            // let (nt, b_contig, b_position) = if a_sens {
            //     (parts[0], parts[1], parts[2])
            // } else {
            //     (parts[2], parts[0], parts[1])
            // };
            //
            // let added_nt = if nt.len() > 1 {
            //     nt[1..].to_string()
            // } else {
            //     nt.to_string()
            // };
            //
            // Ok(BNDDesc {
            //     a_contig: self.position.contig(),
            //     a_position: self.position.position + 1,
            //     a_sens,
            //     b_contig: b_contig.to_string(),
            //     b_position: b_position
            //         .parse()
            //         .map_err(|e| anyhow::anyhow!("Failed to parse: {b_position}\n{e}"))?,
            //     b_sens,
            //     added_nt,
            // })
        } else {
            Err(anyhow::anyhow!("The alteration is not BND: {alt}"))
        }
    }
}

#[derive(Debug, Clone, Serialize, Deserialize, Eq, PartialEq, Hash)]
pub struct BNDDesc {
    pub a_contig: String,
    pub a_position: u32, // 1-based
    pub a_sens: bool,
    pub b_contig: String,
    pub b_position: u32, // 1-based
    pub b_sens: bool,
    pub added_nt: String,
}

#[derive(Debug, Clone, Serialize, Deserialize, Eq, PartialEq, Hash)]
pub enum AlterationCategory {
    SNV,
    DEL,
    INS,
    DUP,
    INV,
    CNV,
    TRL,
    BND,
    Other,
}

impl fmt::Display for AlterationCategory {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        write!(
            f,
            "{}",
            match self {
                AlterationCategory::SNV => "SNV",
                AlterationCategory::DEL => "DEL",
                AlterationCategory::INS => "INS",
                AlterationCategory::DUP => "DUP",
                AlterationCategory::INV => "INV",
                AlterationCategory::CNV => "CNV",
                AlterationCategory::BND | AlterationCategory::TRL => "TRL",
                AlterationCategory::Other => "Other",
            }
        )
    }
}

impl From<SVType> for AlterationCategory {
    fn from(sv_type: SVType) -> Self {
        match sv_type {
            SVType::DEL => AlterationCategory::DEL,
            SVType::INS => AlterationCategory::INS,
            SVType::DUP => AlterationCategory::DUP,
            SVType::INV => AlterationCategory::INV,
            SVType::CNV => AlterationCategory::CNV,
            SVType::BND => AlterationCategory::BND,
        }
    }
}

#[derive(Debug, Clone, Serialize, Deserialize, Eq, PartialEq)]
pub enum SVType {
    DEL,
    INS,
    DUP,
    INV,
    CNV,
    BND,
}

impl FromStr for SVType {
    type Err = anyhow::Error;

    fn from_str(s: &str) -> anyhow::Result<Self> {
        match s {
            "DEL" => Ok(SVType::DEL),
            "INS" => Ok(SVType::INS),
            "DUP" => Ok(SVType::DUP),
            "INV" => Ok(SVType::INV),
            "CNV" => Ok(SVType::CNV),
            "BND" => Ok(SVType::BND),
            _ => Err(anyhow!("Can't parse SVTYPE={s}")),
        }
    }
}

impl fmt::Display for SVType {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        write!(
            f,
            "{}",
            match self {
                SVType::DEL => "DEL",
                SVType::INS => "INS",
                SVType::DUP => "DUP",
                SVType::INV => "INV",
                SVType::CNV => "CNV",
                SVType::BND => "BND",
            }
        )
    }
}

impl VariantId for VcfVariant {
    fn variant_id(&self) -> String {
        format!("{}_{}>{}", self.position, self.reference, self.alternative)
    }
}

impl GetGenomePosition for VcfVariant {
    fn position(&self) -> &GenomePosition {
        &self.position
    }
}

impl PartialOrd for VcfVariant {
    fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
        Some(self.cmp(other))
    }
}

impl Ord for VcfVariant {
    fn cmp(&self, other: &Self) -> Ordering {
        self.position.cmp(&other.position)
    }
}

/// Info
#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Default)]
pub struct Infos(pub Vec<Info>);

impl FromStr for Infos {
    type Err = anyhow::Error;

    fn from_str(s: &str) -> anyhow::Result<Self> {
        Ok(Self(
            s.split(";")
                .map(Info::from_str)
                .collect::<Result<Vec<Info>, _>>()
                .map_err(|e| anyhow::anyhow!("Failed to parse info: {e}"))?,
        ))
    }
}

impl fmt::Display for Infos {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        write!(
            f,
            "{}",
            self.0
                .iter()
                .map(|e| e.to_string())
                .collect::<Vec<String>>()
                .join(";")
        )
    }
}

#[allow(non_camel_case_types)]
#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
pub enum Info {
    Empty,
    H,
    F,
    P,
    FAU(u32),
    FCU(u32),
    FGU(u32),
    FTU(u32),
    RAU(u32),
    RCU(u32),
    RGU(u32),
    RTU(u32),
    SVTYPE(SVType),
    MATEID(String),
    NORMAL_READ_SUPPORT(u32),
    TUMOUR_READ_SUPPORT(u32),
    NORMAL_ALN_SUPPORT(u32),
    TUMOUR_ALN_SUPPORT(u32),
    SVLEN(i32),
    TUMOUR_DP_BEFORE(Vec<u32>),
    TUMOUR_DP_AT(Vec<u32>),
    TUMOUR_DP_AFTER(Vec<u32>),
    NORMAL_DP_BEFORE(Vec<u32>),
    NORMAL_DP_AT(Vec<u32>),
    NORMAL_DP_AFTER(Vec<u32>),
    TUMOUR_AF(Vec<f32>),
    NORMAL_AF(Vec<f32>),
    BP_NOTATION(String),
    SOURCE(String),
    CLUSTERED_READS_TUMOUR(u32),
    CLUSTERED_READS_NORMAL(u32),
    TUMOUR_ALT_HP(Vec<u32>),
    TUMOUR_PS(Vec<String>),
    NORMAL_ALT_HP(Vec<u32>),
    NORMAL_PS(Vec<String>),
    TUMOUR_TOTAL_HP_AT(Vec<u32>),
    NORMAL_TOTAL_HP_AT(Vec<u32>),
    ORIGIN_STARTS_STD_DEV(f32),
    ORIGIN_MAPQ_MEAN(f32),
    ORIGIN_EVENT_SIZE_STD_DEV(f32),
    ORIGIN_EVENT_SIZE_MEDIAN(f32),
    ORIGIN_EVENT_SIZE_MEAN(f32),
    END_STARTS_STD_DEV(f32),
    END_MAPQ_MEAN(f32),
    END_EVENT_SIZE_STD_DEV(f32),
    END_EVENT_SIZE_MEDIAN(f32),
    END_EVENT_SIZE_MEAN(f32),
    CLASS(String),
    END(u32),
    SVINSLEN(u32),
    SVINSSEQ(String),
}

impl FromStr for Info {
    type Err = anyhow::Error;

    fn from_str(s: &str) -> anyhow::Result<Self> {
        if s.contains('=') {
            let (key, value) = s
                .split_once('=')
                .context(format!("Can't split with `=` in string: {s}"))?;

            Ok(match key {
                "FAU" => Info::FAU(parse_value(value, key)?),
                "FCU" => Info::FCU(parse_value(value, key)?),
                "FGU" => Info::FGU(parse_value(value, key)?),
                "FTU" => Info::FTU(parse_value(value, key)?),
                "RAU" => Info::RAU(parse_value(value, key)?),
                "RCU" => Info::RCU(parse_value(value, key)?),
                "RGU" => Info::RGU(parse_value(value, key)?),
                "RTU" => Info::RTU(parse_value(value, key)?),
                "SVLEN" => Info::SVLEN(parse_value(value, key)?),
                "END" => Info::END(parse_value(value, key)?),
                "SVINSLEN" => Info::SVINSLEN(parse_value(value, key)?),
                "SVTYPE" => Info::SVTYPE(value.parse()?),
                "MATEID" => Info::MATEID(value.to_string()),
                "NORMAL_READ_SUPPORT" => Info::NORMAL_READ_SUPPORT(parse_value(value, key)?),
                "TUMOUR_READ_SUPPORT" => Info::TUMOUR_READ_SUPPORT(parse_value(value, key)?),
                "NORMAL_ALN_SUPPORT" => Info::NORMAL_ALN_SUPPORT(parse_value(value, key)?),
                "TUMOUR_ALN_SUPPORT" => Info::TUMOUR_ALN_SUPPORT(parse_value(value, key)?),
                "SVINSSEQ" => Info::SVINSSEQ(value.to_string()),
                "TUMOUR_DP_BEFORE" => Info::TUMOUR_DP_BEFORE(parse_vec_value(value, key)?),
                "TUMOUR_DP_AT" => Info::TUMOUR_DP_AT(parse_vec_value(value, key)?),
                "TUMOUR_DP_AFTER" => Info::TUMOUR_DP_AFTER(parse_vec_value(value, key)?),
                "NORMAL_DP_BEFORE" => Info::NORMAL_DP_BEFORE(parse_vec_value(value, key)?),
                "NORMAL_DP_AT" => Info::NORMAL_DP_AT(parse_vec_value(value, key)?),
                "NORMAL_DP_AFTER" => Info::NORMAL_DP_AFTER(parse_vec_value(value, key)?),
                "TUMOUR_AF" => Info::TUMOUR_AF(parse_vec_value(value, key)?),
                "NORMAL_AF" => Info::NORMAL_AF(parse_vec_value(value, key)?),
                "BP_NOTATION" => Info::BP_NOTATION(value.to_string()),
                "SOURCE" => Info::SOURCE(value.to_string()),
                "CLUSTERED_READS_TUMOUR" => Info::CLUSTERED_READS_TUMOUR(parse_value(value, key)?),
                "CLUSTERED_READS_NORMAL" => Info::CLUSTERED_READS_NORMAL(parse_value(value, key)?),
                "TUMOUR_ALT_HP" => Info::TUMOUR_ALT_HP(parse_vec_value(value, key)?),
                "TUMOUR_PS" => Info::TUMOUR_PS(parse_vec_value(value, key)?),
                "NORMAL_ALT_HP" => Info::NORMAL_ALT_HP(parse_vec_value(value, key)?),
                "NORMAL_PS" => Info::NORMAL_PS(parse_vec_value(value, key)?),
                "TUMOUR_TOTAL_HP_AT" => Info::TUMOUR_TOTAL_HP_AT(parse_vec_value(value, key)?),
                "NORMAL_TOTAL_HP_AT" => Info::NORMAL_TOTAL_HP_AT(parse_vec_value(value, key)?),
                "ORIGIN_STARTS_STD_DEV" => Info::ORIGIN_STARTS_STD_DEV(parse_value(value, key)?),
                "ORIGIN_MAPQ_MEAN" => Info::ORIGIN_MAPQ_MEAN(parse_value(value, key)?),
                "ORIGIN_EVENT_SIZE_STD_DEV" => {
                    Info::ORIGIN_EVENT_SIZE_STD_DEV(parse_value(value, key)?)
                }
                "ORIGIN_EVENT_SIZE_MEDIAN" => {
                    Info::ORIGIN_EVENT_SIZE_MEDIAN(parse_value(value, key)?)
                }
                "ORIGIN_EVENT_SIZE_MEAN" => Info::ORIGIN_EVENT_SIZE_MEAN(parse_value(value, key)?),
                "END_STARTS_STD_DEV" => Info::END_STARTS_STD_DEV(parse_value(value, key)?),
                "END_MAPQ_MEAN" => Info::END_MAPQ_MEAN(parse_value(value, key)?),
                "END_EVENT_SIZE_STD_DEV" => Info::END_EVENT_SIZE_STD_DEV(parse_value(value, key)?),
                "END_EVENT_SIZE_MEDIAN" => Info::END_EVENT_SIZE_MEDIAN(parse_value(value, key)?),
                "END_EVENT_SIZE_MEAN" => Info::END_EVENT_SIZE_MEAN(parse_value(value, key)?),
                "CLASS" => Info::CLASS(value.to_string()),
                _ => Info::Empty,
            })
        } else {
            Ok(match s {
                "H" => Info::H,
                "F" => Info::F,
                "P" => Info::P,
                _ => Info::Empty,
            })
        }
    }
}

impl fmt::Display for Info {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        match self {
            Info::Empty => write!(f, "."),
            Info::H => write!(f, "H"),
            Info::F => write!(f, "F"),
            Info::P => write!(f, "P"),
            Info::FAU(v) => write!(f, "FAU={v}"),
            Info::FCU(v) => write!(f, "FCU={v}"),
            Info::FGU(v) => write!(f, "FGU={v}"),
            Info::FTU(v) => write!(f, "FTU={v}"),
            Info::RAU(v) => write!(f, "RAU={v}"),
            Info::RCU(v) => write!(f, "RCU={v}"),
            Info::RGU(v) => write!(f, "RGU={v}"),
            Info::RTU(v) => write!(f, "RTU={v}"),
            Info::SVTYPE(v) => write!(f, "SVTYPE={v}"),
            Info::SVLEN(v) => write!(f, "SVLEN={v}"),
            Info::END(v) => write!(f, "END={v}"),
            Info::MATEID(v) => write!(f, "MATEID={v}"),
            Info::SVINSLEN(v) => write!(f, "SVINSLEN={v}"),
            Info::SVINSSEQ(v) => write!(f, "SVINSSEQ={v}"),
            Info::NORMAL_READ_SUPPORT(v) => write!(f, "NORMAL_READ_SUPPORT={v}"),
            Info::TUMOUR_READ_SUPPORT(v) => write!(f, "TUMOUR_READ_SUPPORT={v}"),
            Info::NORMAL_ALN_SUPPORT(v) => write!(f, "NORMAL_ALN_SUPPORT={v}"),
            Info::TUMOUR_ALN_SUPPORT(v) => write!(f, "TUMOUR_ALN_SUPPORT={v}"),
            Info::TUMOUR_DP_BEFORE(v) => write!(f, "TUMOUR_DP_BEFORE={}", concat_numbers(v)),
            Info::TUMOUR_DP_AT(v) => write!(f, "TUMOUR_DP_AT={}", concat_numbers(v)),
            Info::TUMOUR_DP_AFTER(v) => write!(f, "TUMOUR_DP_AFTER={}", concat_numbers(v)),
            Info::NORMAL_DP_BEFORE(v) => write!(f, "NORMAL_DP_BEFORE={}", concat_numbers(v)),
            Info::NORMAL_DP_AT(v) => write!(f, "NORMAL_DP_AT={}", concat_numbers(v)),
            Info::NORMAL_DP_AFTER(v) => write!(f, "NORMAL_DP_AFTER={}", concat_numbers(v)),
            Info::TUMOUR_AF(v) => write!(f, "TUMOUR_AF={}", concat_numbers(v)),
            Info::NORMAL_AF(v) => write!(f, "NORMAL_AF={}", concat_numbers(v)),
            Info::BP_NOTATION(v) => write!(f, "BP_NOTATION={v}"),
            Info::SOURCE(v) => write!(f, "SOURCE={v}"),
            Info::CLUSTERED_READS_TUMOUR(v) => write!(f, "CLUSTERED_READS_TUMOUR={v}"),
            Info::CLUSTERED_READS_NORMAL(v) => write!(f, "CLUSTERED_READS_NORMAL={v}"),
            Info::TUMOUR_ALT_HP(v) => write!(f, "TUMOUR_ALT_HP={}", concat_numbers(v)),
            Info::TUMOUR_PS(v) => write!(f, "TUMOUR_PS={}", v.join(",")),
            Info::NORMAL_ALT_HP(v) => write!(f, "NORMAL_ALT_HP={}", concat_numbers(v)),
            Info::NORMAL_PS(v) => write!(f, "NORMAL_PS={}", v.join(",")),
            Info::TUMOUR_TOTAL_HP_AT(v) => write!(f, "TUMOUR_TOTAL_HP_AT={}", concat_numbers(v)),
            Info::NORMAL_TOTAL_HP_AT(v) => write!(f, "NORMAL_TOTAL_HP_AT={}", concat_numbers(v)),
            Info::ORIGIN_STARTS_STD_DEV(v) => write!(f, "ORIGIN_STARTS_STD_DEV={v}"),
            Info::ORIGIN_MAPQ_MEAN(v) => write!(f, "ORIGIN_MAPQ_MEAN={v}"),
            Info::ORIGIN_EVENT_SIZE_STD_DEV(v) => write!(f, "ORIGIN_EVENT_SIZE_STD_DEV={v}"),
            Info::ORIGIN_EVENT_SIZE_MEDIAN(v) => write!(f, "ORIGIN_EVENT_SIZE_MEDIAN={v}"),
            Info::ORIGIN_EVENT_SIZE_MEAN(v) => write!(f, "ORIGIN_EVENT_SIZE_MEAN={v}"),
            Info::END_STARTS_STD_DEV(v) => write!(f, "END_STARTS_STD_DEV={v}"),
            Info::END_MAPQ_MEAN(v) => write!(f, "END_MAPQ_MEAN={v}"),
            Info::END_EVENT_SIZE_STD_DEV(v) => write!(f, "END_EVENT_SIZE_STD_DEV={v}"),
            Info::END_EVENT_SIZE_MEDIAN(v) => write!(f, "END_EVENT_SIZE_MEDIAN={v}"),
            Info::END_EVENT_SIZE_MEAN(v) => write!(f, "END_EVENT_SIZE_MEAN={v}"),
            Info::CLASS(v) => write!(f, "CLASS={v}"),
        }
    }
}

pub fn concat_numbers<T: ToString>(v: &[T]) -> String {
    v.iter()
        .map(|n| n.to_string())
        .collect::<Vec<String>>()
        .join(",")
}

/// Format
#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
pub enum Format {
    // DeepVariant
    GT(String),
    GQ(u32),
    DP(u32),
    AD(Vec<u32>),
    VAF(f32),
    PL(Vec<u32>),

    // Clairs
    // when format begins with N: normal
    // AF(f32),
    // NAF(f32), // DP(u32),
    NDP(u32),
    NAD(Vec<u32>),
    AU(u32),
    CU(u32),
    GU(u32),
    TU(u32),
    NAU(u32),
    NCU(u32),
    NGU(u32),
    NTU(u32),

    // nanomonsv
    TR(u32),
    VR(u32),

    Other((String, String)), // (key, value)
}

#[derive(Debug, Clone, Serialize, Deserialize, PartialEq, Default)]
pub struct Formats(pub Vec<Format>);

impl TryFrom<(&str, &str)> for Formats {
    type Error = anyhow::Error;

    fn try_from((k, v): (&str, &str)) -> anyhow::Result<Self> {
        let keys: Vec<&str> = k.split(':').collect();
        let values: Vec<&str> = v.split(':').collect();

        if keys.len() != values.len() {
            anyhow::bail!("Mismatch between keys and values count for {k} {v}");
        }

        Ok(Self(
            keys.into_iter()
                .zip(values)
                .map(|(key, value)| Format::try_from((key, value)))
                .collect::<Result<Vec<Format>, _>>()
                .map_err(|e| anyhow::anyhow!("Failed to parse format: {e}"))?,
        ))
    }
}

impl From<Formats> for (String, String) {
    fn from(formats: Formats) -> Self {
        let mut keys = Vec::new();
        let mut values = Vec::new();

        for format in formats.0 {
            let (key, value): (String, String) = format.into();
            keys.push(key);
            values.push(value);
        }

        (keys.join(":"), values.join(":"))
    }
}

impl TryFrom<(&str, &str)> for Format {
    type Error = anyhow::Error;

    fn try_from((key, value): (&str, &str)) -> anyhow::Result<Self> {
        let format = match key {
            "GT" => Format::GT(value.to_string()),
            "GQ" => Format::GQ(parse_value(value, key)?),
            "DP" => Format::DP(parse_value(value, key)?),
            "AD" => Format::AD(parse_vec_value(value, key)?),
            "VAF" => Format::VAF(parse_value(value, key)?),
            // "AF" => Format::AF(parse_value(value, key)?),
            // "NAF" => Format::NAF(parse_value(value, key)?),
            "NDP" => Format::NDP(parse_value(value, key)?),
            "NAD" => Format::NAD(parse_vec_value(value, key)?),
            "AU" => Format::AU(parse_value(value, key)?),
            "CU" => Format::CU(parse_value(value, key)?),
            "GU" => Format::GU(parse_value(value, key)?),
            "TU" => Format::TU(parse_value(value, key)?),
            "NAU" => Format::NAU(parse_value(value, key)?),
            "NCU" => Format::NCU(parse_value(value, key)?),
            "NGU" => Format::NGU(parse_value(value, key)?),
            "NTU" => Format::NTU(parse_value(value, key)?),
            "PL" => Format::PL(parse_vec_value(value, key)?),
            "TR" => Format::TR(parse_value(value, key)?),
            "VR" => Format::VR(parse_value(value, key)?),
            _ => Format::Other((key.to_string(), value.to_string())),
        };
        Ok(format)
    }
}

// Helper function to parse a single value (DeepSeek)
fn parse_value<T: std::str::FromStr>(value: &str, key: &str) -> anyhow::Result<T>
where
    T::Err: std::fmt::Debug,
{
    value
        .parse()
        .map_err(|e| anyhow::anyhow!("{:?}", e)) // Convert the error to `anyhow::Error`
        .context(format!("Can't parse {}: {}", key, value)) // Add context
}

// Helper function to parse comma-separated values (DeepSeek)
fn parse_vec_value<T: std::str::FromStr>(value: &str, key: &str) -> anyhow::Result<Vec<T>>
where
    T::Err: std::fmt::Debug,
{
    value
        .split(',')
        .map(|e| {
            e.parse()
                .map_err(|e| anyhow::anyhow!("{:?}", e)) // Convert the error to `anyhow::Error`
                .context(format!("Failed to parse {}: {}", key, e)) // Add context
        })
        .collect()
}

impl From<Format> for (String, String) {
    fn from(format: Format) -> Self {
        let concat = |values: Vec<u32>| -> String {
            values
                .iter()
                .map(|v| v.to_string())
                .collect::<Vec<_>>()
                .join(",")
        };

        match format {
            Format::GT(value) => ("GT".to_string(), value),
            Format::GQ(value) => ("GQ".to_string(), value.to_string()),
            Format::DP(value) => ("DP".to_string(), value.to_string()),
            Format::AD(values) => ("AD".to_string(), concat(values)),
            Format::VAF(value) => ("VAF".to_string(), value.to_string()),
            Format::PL(values) => ("PL".to_string(), concat(values)),
            Format::Other((key, value)) => (key, value),
            // Format::AF(value) => ("AF".to_string(), value.to_string()),
            // Format::NAF(value) => ("NAF".to_string(), value.to_string()),
            Format::NDP(value) => ("NDP".to_string(), value.to_string()),
            Format::NAD(values) => ("NAD".to_string(), concat(values)),
            Format::AU(value) => ("AU".to_string(), value.to_string()),
            Format::CU(value) => ("CU".to_string(), value.to_string()),
            Format::GU(value) => ("GU".to_string(), value.to_string()),
            Format::TU(value) => ("TU".to_string(), value.to_string()),
            Format::NAU(value) => ("NAU".to_string(), value.to_string()),
            Format::NCU(value) => ("NCU".to_string(), value.to_string()),
            Format::NGU(value) => ("NGU".to_string(), value.to_string()),
            Format::NTU(value) => ("NTU".to_string(), value.to_string()),
            Format::TR(value) => ("TR".to_string(), value.to_string()),
            Format::VR(value) => ("VR".to_string(), value.to_string()),
        }
    }
}

impl Formats {
    pub fn commun_deepvariant_clairs(&self) -> Self {
        let filtered_vec: Vec<Format> = self
            .0
            .clone()
            .into_iter()
            .map(|e| {
                if let Format::VAF(_v) = e {
                    e
                    // Format::AF(v)
                } else {
                    e
                }
            })
            .filter(|format| {
                matches!(
                    format,
                    Format::GT(_) | Format::GQ(_) | Format::DP(_) | Format::AD(_) /* | Format::AF(_) */
                )
            })
            .collect();

        Formats(filtered_vec)
    }
}

/// Filter
#[derive(Debug, Clone, Serialize, Deserialize, Eq, PartialEq)]
pub enum Filter {
    PASS,
    Other(String),
}

impl FromStr for Filter {
    type Err = anyhow::Error;

    fn from_str(s: &str) -> anyhow::Result<Self> {
        match s {
            "PASS" => Ok(Filter::PASS),
            _ => Ok(Filter::Other(s.to_string())),
        }
    }
}

impl fmt::Display for Filter {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        match self {
            Filter::PASS => write!(f, "PASS"),
            Filter::Other(ref s) => write!(f, "{}", s),
        }
    }
}

#[derive(Debug, Clone, Serialize, Deserialize, Eq, PartialEq, Hash)]
pub enum ReferenceAlternative {
    Nucleotide(Base),
    Nucleotides(Vec<Base>),
    Unstructured(String),
}

impl FromStr for ReferenceAlternative {
    type Err = anyhow::Error;

    fn from_str(s: &str) -> anyhow::Result<Self> {
        let possible_bases = s.as_bytes().iter();
        let mut res: Vec<Base> = Vec::new();
        for &base in possible_bases {
            match base.try_into() {
                std::result::Result::Ok(b) => res.push(b),
                Err(_) => {
                    return Ok(Self::Unstructured(s.to_string()));
                }
            }
        }

        if res.len() == 1 {
            Ok(Self::Nucleotide(res.pop().unwrap()))
        } else {
            Ok(Self::Nucleotides(res))
        }
    }
}

impl fmt::Display for ReferenceAlternative {
    fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
        let string = match self {
            ReferenceAlternative::Nucleotide(b) => b.to_string(),
            ReferenceAlternative::Nucleotides(bases) => bases
                .iter()
                .fold(String::new(), |acc, e| format!("{}{}", acc, e)),
            ReferenceAlternative::Unstructured(s) => s.to_string(),
        };
        write!(f, "{}", string)
    }
}

#[derive(Debug, Clone, Serialize, Deserialize, Eq, PartialEq, Hash)]
pub enum Base {
    A,
    T,
    C,
    G,
    N,
}

impl TryFrom<u8> for Base {
    type Error = anyhow::Error;
    fn try_from(base: u8) -> anyhow::Result<Self> {
        match base {
            b'A' => Ok(Base::A),
            b'T' => Ok(Base::T),
            b'C' => Ok(Base::C),
            b'G' => Ok(Base::G),
            b'N' => Ok(Base::N),
            _ => Err(anyhow::anyhow!(
                "Unknown base: {}",
                String::from_utf8_lossy(&[base])
            )),
        }
    }
}

impl Base {
    pub fn into_u8(self) -> u8 {
        match self {
            Base::A => b'A',
            Base::T => b'T',
            Base::C => b'C',
            Base::G => b'G',
            Base::N => b'N',
        }
    }
}

impl fmt::Display for Base {
    fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
        // Use `self.number` to refer to each positional data point.
        let str = match self {
            Base::A => "A",
            Base::T => "T",
            Base::C => "C",
            Base::G => "G",
            Base::N => "N",
        };
        write!(f, "{}", str)
    }
}

pub trait Variants {
    fn variants(&self, annotations: &Annotations) -> anyhow::Result<VariantCollection>;
}

pub trait VariantId {
    fn variant_id(&self) -> String;
}

pub trait RunnerVariants: Run + Variants + Send + Sync {}

pub type CallerBox = Box<dyn RunnerVariants + Send + Sync>;

#[macro_export]
macro_rules! init_somatic_callers {
    ($id:expr, $config:expr, $($runner:ty),+ $(,)?) => {
        vec![
            $(
                Box::new(<$runner>::initialize($id, $config.clone())?) as CallerBox
            ),+
        ]
    };
}
#[macro_export]
macro_rules! init_solo_callers {
    ($id:expr, $config:expr, $($runner:ty, $arg:expr),+ $(,)?) => {
        vec![
            $(
                Box::new(<$runner>::initialize($id, $arg, $config.clone())?) as CallerBox
            ),+
        ]
    };
}

pub fn run_variants(iterable: &mut [CallerBox]) -> anyhow::Result<()> {
    iterable
        .iter_mut()
        .try_for_each(|runner| runner.run())
        .map_err(|e| anyhow::anyhow!("Error while calling run_variants.\n{e}"))
}

pub fn load_variants(
    iterable: &mut [CallerBox],
    annotations: &Annotations,
) -> anyhow::Result<Vec<VariantCollection>> {
    iterable
        .par_iter()
        .map(|runner| {
            let r = runner.variants(annotations);
            if let Err(ref e) = r {
                warn!("{e}");
            };
            r
        })
        .filter(|r| r.is_ok())
        .collect::<anyhow::Result<Vec<_>>>()
        .map_err(|e| anyhow::anyhow!("Failed to load variants.\n{e}"))
}

pub fn parallel_intersection<T: Hash + Eq + Clone + Send + Sync>(
    vec1: &[T],
    vec2: &[T],
) -> (Vec<T>, Vec<T>, Vec<T>) {
    let set1: HashSet<_> = vec1.par_iter().cloned().collect();
    let set2: HashSet<_> = vec2.par_iter().cloned().collect();

    let common: Vec<T> = set1
        .par_iter()
        .filter(|item| set2.contains(item))
        .cloned()
        .collect();

    let only_in_first: Vec<T> = set1
        .par_iter()
        .filter(|item| !set2.contains(item))
        .cloned()
        .collect();

    let only_in_second: Vec<T> = set2
        .par_iter()
        .filter(|item| !set1.contains(item))
        .cloned()
        .collect();

    (common, only_in_first, only_in_second)
}