pandora_lib_promethion/src/positions.rs

use std::{
    cmp::{max, Ordering},
    fmt::Display,
    ops::Range,
    str::FromStr,
};

use anyhow::Context;
use bitcode::{Decode, Encode};
use rayon::prelude::*;
use serde::{Deserialize, Serialize};

/// Represents a position in the genome using 0-based coordinates.
///
/// This struct encapsulates a genomic position, consisting of a contig (chromosome)
/// identifier and a position within that contig.
///
/// # Fields
/// * `contig` - An 8-bit unsigned integer representing the contig/chromosome
/// * `position` - A 32-bit unsigned integer representing the 0-based position within the contig
///
/// # Derives
/// This struct derives the following traits:
/// * `Debug` for easier debugging and logging
/// * `PartialEq` and `Eq` for equality comparisons
/// * `Clone` for creating deep copies
/// * `Serialize` and `Deserialize` for serialization (e.g., to JSON or other formats)
/// * `Hash` for use in hash-based collections
/// * `Default` for creating a default instance
///
/// # Note
/// The position is 0-based, meaning the first position in a contig is represented as 0.
///
/// # Usage
/// This struct is typically used to precisely locate genomic features or variants
/// within a reference genome.
///
/// # Example
/// ```
/// let position = GenomePosition {
///     contig: 1,  // Representing chromosome 1
///     position: 1000,  // 1001st base pair in the chromosome (remember it's 0-based)
/// };
/// ```
#[derive(Debug, PartialEq, Eq, Clone, Serialize, Deserialize, Hash, Default, Encode, Decode)]
pub struct GenomePosition {
    pub contig: u8,
    pub position: u32,
}

impl GenomePosition {
    /// Returns the contig (chromosome) identifier as a human-readable string.
    ///
    /// This method converts the internal numeric representation of the contig
    /// to a string format commonly used in genomics, such as "chr1", "chrX", etc...
    ///
    /// # Returns
    /// A `String` representing the contig identifier.
    ///
    /// # Examples
    ///
    /// ```
    /// let pos = GenomePosition { contig: 1, position: 1000 };
    /// assert_eq!(pos.contig(), "chr1");
    ///
    /// let pos_x = GenomePosition { contig: 23, position: 500 };
    /// assert_eq!(pos_x.contig(), "chrX");
    /// ```
    ///
    /// # Note
    /// This method uses the `num_to_contig` function to perform the conversion.
    /// Special cases like X, Y chromosomes and mitochondrial DNA are handled appropriately.
    pub fn contig(&self) -> String {
        num_to_contig(self.contig)
    }
}

/// Implements the `Display` trait for `GenomePosition`.
///
/// This implementation allows a `GenomePosition` to be formatted as a string
/// in the form "contig:position", where contig is the string representation
/// of the chromosome (e.g., "chr1", "chrX") and position is the 0-based position.
///
/// # Example
/// ```
/// let pos = GenomePosition { contig: 1, position: 1000 };
/// assert_eq!(format!("{}", pos), "chr1:1000");
/// ```
impl Display for GenomePosition {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
        write!(f, "{}:{}", self.contig(), self.position)
    }
}

/// Implements the `FromStr` trait for `GenomePosition`.
///
/// This allows creating a `GenomePosition` from a string in the format "contig:position".
///
/// # Errors
/// Returns an `anyhow::Error` if:
/// - The input string doesn't contain a ':' character
/// - The contig part can't be converted to a numeric representation
/// - The position part can't be parsed as a `u32`
///
/// # Example
/// ```
/// use std::str::FromStr;
/// let pos = GenomePosition::from_str("chr1:1000").unwrap();
/// assert_eq!(pos.contig, 1);
/// assert_eq!(pos.position, 1000);
/// ```
impl FromStr for GenomePosition {
    type Err = anyhow::Error;

    fn from_str(s: &str) -> anyhow::Result<Self> {
        let (c, p) = s
            .split_once(":")
            .ok_or(anyhow::anyhow!("Can't split {s}"))?;
        Ok(Self {
            contig: contig_to_num(c),
            position: p.parse()?,
        })
    }
}

/// Implements `TryFrom<(&str, &str)>` for `GenomePosition`.
///
/// This allows creating a `GenomePosition` from a tuple of two string slices,
/// where the first represents the contig and the second represents the position.
///
/// # Errors
/// Returns an `anyhow::Error` if:
/// - The contig part can't be converted to a numeric representation
/// - The position part can't be parsed as a `u32`
///
/// # Example
/// ```
/// use std::convert::TryFrom;
/// let pos = GenomePosition::try_from(("chr1", "1000")).unwrap();
/// assert_eq!(pos.contig, 1);
/// assert_eq!(pos.position, 1000);
/// ```
impl TryFrom<(&str, &str)> for GenomePosition {
    type Error = anyhow::Error;

    fn try_from((c, p): (&str, &str)) -> anyhow::Result<Self> {
        Ok(GenomePosition {
            contig: contig_to_num(c),
            position: p.parse().context(format!("Can't parse {p} into u32."))?,
        })
    }
}

/// Implements conversion from `VcfPosition` to `GenomePosition`.
///
/// This conversion adjusts for the difference between 1-based VCF coordinates
/// and 0-based genomic coordinates. It also handles the special case of
/// position 0 in VCF, which represents a variant inside telomeres.
///
/// # Note
/// This implementation assumes that `VcfPosition` uses 1-based coordinates.
///
/// # Example
/// ```
/// let vcf_pos = VcfPosition { contig: 1, position: 1001 };
/// let genome_pos: GenomePosition = vcf_pos.into();
/// assert_eq!(genome_pos.contig, 1);
/// assert_eq!(genome_pos.position, 1000);
/// ```
impl From<VcfPosition> for GenomePosition {
    fn from(value: VcfPosition) -> Self {
        let position = if value.position == 0 {
            // position 0 is a variant inside telomeres
            0
        } else {
            value.position - 1
        };
        Self {
            contig: value.contig,
            position,
        }
    }
}

/// Implements conversion from `GenomePosition` to `(String, String)`.
///
/// This conversion creates a tuple where the first element is the string
/// representation of the contig (e.g., "chr1", "chrX") and the second
/// element is the string representation of the position.
///
/// # Example
/// ```
/// let pos = GenomePosition { contig: 1, position: 1000 };
/// let (contig, position): (String, String) = pos.into();
/// assert_eq!(contig, "chr1");
/// assert_eq!(position, "1000");
/// ```
impl From<GenomePosition> for (String, String) {
    fn from(val: GenomePosition) -> Self {
        (num_to_contig(val.contig), val.position.to_string())
    }
}

/// Implements `PartialOrd` for `GenomePosition`.
///
/// This implementation allows `GenomePosition` instances to be compared
/// and ordered based first on their contig, then on their position.
impl PartialOrd for GenomePosition {
    fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
        Some(self.cmp(other))
    }
}

/// Implements `Ord` for `GenomePosition`.
///
/// This implementation defines a total ordering for `GenomePosition` instances.
/// Positions are first compared by their contig, and if the contigs are equal,
/// then by their position.
///
/// # Example
/// ```
/// let pos1 = GenomePosition { contig: 1, position: 1000 };
/// let pos2 = GenomePosition { contig: 1, position: 2000 };
/// let pos3 = GenomePosition { contig: 2, position: 500 };
/// assert!(pos1 < pos2);
/// assert!(pos2 < pos3);
/// ```
impl Ord for GenomePosition {
    fn cmp(&self, other: &Self) -> Ordering {
        match self.contig.cmp(&other.contig) {
            Ordering::Equal => self.position.cmp(&other.position),
            other => other,
        }
    }
}

/// Converts a contig (chromosome) identifier string to its numeric representation.
///
/// # Arguments
/// * `contig` - A string slice representing the contig identifier (e.g., "chr1", "chrX")
///
/// # Returns
/// A `u8` representing the numeric value of the contig:
/// * 1-22 for autosomes
/// * 23 for X chromosome
/// * 24 for Y chromosome
/// * 25 for mitochondrial DNA
/// * `u8::MAX` (255) for any unrecognized input
///
/// # Examples
/// ```
/// assert_eq!(contig_to_num("chr1"), 1);
/// assert_eq!(contig_to_num("chrX"), 23);
/// assert_eq!(contig_to_num("chrM"), 25);
/// assert_eq!(contig_to_num("chr_unknown"), u8::MAX);
/// ```
///
/// # Note
/// This function assumes the input string starts with "chr" for standard chromosomes.
/// The "chr" prefix is trimmed before parsing numeric values.
pub fn contig_to_num(contig: &str) -> u8 {
    match contig {
        "chrX" => 23,
        "chrY" => 24,
        "chrM" => 25,
        c => c.trim_start_matches("chr").parse().unwrap_or(u8::MAX),
    }
}

/// Converts a numeric contig (chromosome) representation to its string identifier.
///
/// # Arguments
/// * `num` - A `u8` representing the numeric value of the contig
///
/// # Returns
/// A `String` representing the contig identifier:
/// * "chr1" to "chr22" for autosomes
/// * "chrX" for 23
/// * "chrY" for 24
/// * "chrM" for 25
/// * "chr{num}" for any other input
///
/// # Examples
/// ```
/// assert_eq!(num_to_contig(1), "chr1");
/// assert_eq!(num_to_contig(23), "chrX");
/// assert_eq!(num_to_contig(25), "chrM");
/// ```
///
/// # Note
/// This function always prepends "chr" to the output string.
pub fn num_to_contig(num: u8) -> String {
    match num {
        23 => "chrX".to_string(),
        24 => "chrY".to_string(),
        25 => "chrM".to_string(),
        c => format!("chr{c}"),
    }
}

/// Represents a position in a VCF (Variant Call Format) file using 1-based coordinates.
///
/// This struct encapsulates a genomic position as represented in VCF files, consisting of a contig (chromosome)
/// identifier and a position within that contig.
///
/// # Fields
/// * `contig` - An 8-bit unsigned integer representing the contig/chromosome
/// * `position` - A 32-bit unsigned integer representing the 1-based position within the contig
///
/// # Derives
/// This struct derives the following traits:
/// * `Debug` for easier debugging and logging
/// * `PartialEq` and `Eq` for equality comparisons
/// * `Clone` for creating deep copies
/// * `Serialize` and `Deserialize` for serialization (e.g., to JSON or other formats)
///
/// # Note
/// The position is 1-based, as per VCF file format specifications.
#[derive(Debug, PartialEq, Eq, Clone, Serialize, Deserialize)]
pub struct VcfPosition {
    pub contig: u8,
    pub position: u32,
}

/// Implements `TryFrom<(&str, &str)>` for `VcfPosition`.
///
/// This allows creating a `VcfPosition` from a tuple of two string slices,
/// where the first represents the contig and the second represents the position.
///
/// # Errors
/// Returns an `anyhow::Error` if:
/// - The contig part can't be converted to a numeric representation
/// - The position part can't be parsed as a `u32`
///
/// # Example
/// ```
/// use std::convert::TryFrom;
/// let pos = VcfPosition::try_from(("chr1", "1000")).unwrap();
/// assert_eq!(pos.contig, 1);
/// assert_eq!(pos.position, 1000);
/// ```
impl TryFrom<(&str, &str)> for VcfPosition {
    type Error = anyhow::Error;

    fn try_from((c, p): (&str, &str)) -> anyhow::Result<Self> {
        Ok(VcfPosition {
            contig: contig_to_num(c),
            position: p.parse().context(format!("Can't parse {p} into u32."))?,
        })
    }
}

/// Implements conversion from `GenomePosition` to `VcfPosition`.
///
/// This conversion adjusts for the difference between 0-based genomic coordinates
/// and 1-based VCF coordinates.
///
/// # Example
/// ```
/// let genome_pos = GenomePosition { contig: 1, position: 999 };
/// let vcf_pos: VcfPosition = genome_pos.into();
/// assert_eq!(vcf_pos.contig, 1);
/// assert_eq!(vcf_pos.position, 1000);
/// ```
impl From<GenomePosition> for VcfPosition {
    fn from(value: GenomePosition) -> Self {
        Self {
            contig: value.contig,
            position: value.position + 1,
        }
    }
}

/// Implements conversion from `VcfPosition` to `(String, String)`.
///
/// This conversion creates a tuple where the first element is the string
/// representation of the contig (e.g., "chr1", "chrX") and the second
/// element is the string representation of the position.
///
/// # Example
/// ```
/// let pos = VcfPosition { contig: 1, position: 1000 };
/// let (contig, position): (String, String) = pos.into();
/// assert_eq!(contig, "chr1");
/// assert_eq!(position, "1000");
/// ```
impl From<VcfPosition> for (String, String) {
    fn from(val: VcfPosition) -> Self {
        (num_to_contig(val.contig), val.position.to_string())
    }
}

/// Represents a range in the genome using 0-based, half-open coordinates [start, end).
///
/// This struct encapsulates a genomic range, consisting of a contig (chromosome)
/// identifier and a range of positions within that contig.
///
/// # Fields
/// * `contig` - An 8-bit unsigned integer representing the contig/chromosome
/// * `range` - A `Range<u32>` representing the start (inclusive) and end (exclusive) positions
///
/// # Derives
/// This struct derives the following traits:
/// * `Debug` for easier debugging and logging
/// * `PartialEq` and `Eq` for equality comparisons
/// * `Clone` for creating deep copies
/// * `Serialize` and `Deserialize` for serialization (e.g., to JSON or other formats)
///
/// # Note
/// The range is 0-based and half-open, meaning the start position is included but the end position is not.
/// This is consistent with many programming languages and bioinformatics tools.
#[derive(Debug, PartialEq, Eq, Clone, Serialize, Deserialize)]
pub struct GenomeRange {
    pub contig: u8,
    pub range: Range<u32>,
}

/// Implements `TryFrom<(&str, &str, &str)>` for `GenomeRange`.
///
/// This allows creating a `GenomeRange` from a tuple of three string slices,
/// where the first represents the contig, the second the start position,
/// and the third the end position.
///
/// # Errors
/// Returns an `anyhow::Error` if:
/// - The contig part can't be converted to a numeric representation
/// - Either the start or end position can't be parsed as a `u32`
///
/// # Example
/// ```
/// use std::convert::TryFrom;
/// let range = GenomeRange::try_from(("chr1", "1000", "2000")).unwrap();
/// assert_eq!(range.contig, 1);
/// assert_eq!(range.range.start, 1000);
/// assert_eq!(range.range.end, 2000);
/// ```
impl TryFrom<(&str, &str, &str)> for GenomeRange {
    type Error = anyhow::Error;

    fn try_from((c, s, e): (&str, &str, &str)) -> anyhow::Result<Self> {
        Ok(Self {
            contig: contig_to_num(c),
            range: Range {
                start: s.parse().context(format!("Can't parse {s} into u32."))?,
                end: e.parse().context(format!("Can't parse {e} into u32."))?,
            },
        })
    }
}

impl GenomeRange {
    pub fn new(contig: &str, start: u32, end: u32) -> Self {
        Self {
            contig: contig_to_num(contig),
            range: start..end,
        }
    }
    /// Creates a `GenomeRange` from 1-based inclusive start and end positions.
    ///
    /// This method is useful when working with data sources that use 1-based coordinates
    /// and inclusive ranges. It converts the input to the 0-based, half-open format used by `GenomeRange`.
    ///
    /// # Arguments
    /// * `contig` - A string slice representing the contig/chromosome
    /// * `start` - A string slice representing the 1-based inclusive start position
    /// * `end` - A string slice representing the 1-based inclusive end position
    ///
    /// # Returns
    /// A `Result` containing the `GenomeRange` if successful, or an `anyhow::Error` if parsing fails.
    ///
    /// # Errors
    /// Returns an `anyhow::Error` if:
    /// - The contig can't be converted to a numeric representation
    /// - Either the start or end position can't be parsed as a `u32`
    ///
    /// # Example
    /// ```
    /// let range = GenomeRange::from_1_inclusive("chr1", "1000", "2000").unwrap();
    /// assert_eq!(range.contig, 1);
    /// assert_eq!(range.range.start, 999);  // Converted to 0-based
    /// assert_eq!(range.range.end, 2000);   // End is exclusive in 0-based
    /// ```
    pub fn from_1_inclusive_str(contig: &str, start: &str, end: &str) -> anyhow::Result<Self> {
        Ok(Self {
            contig: contig_to_num(contig),
            range: Range {
                start: start
                    .parse::<u32>()
                    .context(format!("Can't parse {start} into u32."))?
                    .saturating_sub(1),
                end: end
                    .parse()
                    .context(format!("Can't parse {end} into u32."))?,
            },
        })
    }

    pub fn from_1_inclusive(contig: &str, start: u32, end: u32) -> Self {
        Self {
            contig: contig_to_num(contig),
            range: Range {
                start: start.saturating_sub(1),
                end,
            },
        }
    }

    pub fn length(&self) -> u32 {
        self.range.end - self.range.start
    }
}

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

impl GetGenomeRange for GenomeRange {
    fn range(&self) -> &GenomeRange {
        self
    }
}

pub fn merge_overlapping_genome_ranges(ranges: &[GenomeRange]) -> Vec<GenomeRange> {
    if ranges.is_empty() {
        return vec![];
    }

    // ranges.par_sort_by_key(|r| (r.contig, r.range.start));

    let chunk_size = (ranges.len() / rayon::current_num_threads()).max(1);

    ranges
        .par_chunks(chunk_size)
        .map(|chunk| {
            let mut merged = Vec::new();
            let mut current = chunk[0].clone();

            for range in chunk.iter().skip(1) {
                if current.contig == range.contig && current.range.end >= range.range.start {
                    current.range.end = max(current.range.end, range.range.end);
                } else {
                    merged.push(current);
                    current = range.clone();
                }
            }
            merged.push(current);
            merged
        })
        .reduce(Vec::new, |mut acc, mut chunk| {
            if let (Some(last), Some(first)) = (acc.last_mut(), chunk.first()) {
                if last.contig == first.contig && last.range.end >= first.range.start {
                    last.range.end = max(last.range.end, first.range.end);
                    chunk.remove(0);
                }
            }
            acc.extend(chunk);
            acc
        })
}

/// Finds overlaps between a list of genome positions and a list of genome ranges in parallel.
///
/// This function uses Rayon for parallel processing, dividing the positions into chunks
/// and processing them concurrently.
///
/// # Arguments
/// * `positions` - A slice of references to `GenomePosition`s
/// * `ranges` - A slice of references to `GenomeRange`s
///
/// # Returns
/// A `Vec<usize>` containing the indices of positions that overlap with any range.
///
/// # Performance
/// This function is optimized for scenarios where both `positions` and `ranges` are sorted
/// by contig and position/range start. It uses this ordering to avoid unnecessary comparisons.
///
/// # Example
/// ```
/// let positions = vec![
///     &GenomePosition { contig: 1, position: 100 },
///     &GenomePosition { contig: 1, position: 200 },
///     &GenomePosition { contig: 2, position: 150 },
/// ];
/// let ranges = vec![
///     &GenomeRange { contig: 1, range: 50..150 },
///     &GenomeRange { contig: 2, range: 100..200 },
/// ];
/// let overlaps = overlaps_par(&positions, &ranges);
/// assert_eq!(overlaps, vec!);
/// ```
pub fn overlaps_par(positions: &[&GenomePosition], ranges: &[&GenomeRange]) -> Vec<usize> {
    let chunk_size = (positions.len() / rayon::current_num_threads()).max(1);

    positions
        .par_chunks(chunk_size)
        .enumerate()
        .flat_map(|(chunk_idx, chunk)| {
            let mut result = Vec::new();
            let mut range_idx = ranges.partition_point(|r| r.contig < chunk[0].contig);

            for (pos_idx, pos) in chunk.iter().enumerate() {
                while range_idx < ranges.len() && ranges[range_idx].contig < pos.contig {
                    range_idx += 1;
                }

                if range_idx < ranges.len() && ranges[range_idx].contig == pos.contig {
                    while range_idx < ranges.len()
                        && ranges[range_idx].contig == pos.contig
                        && ranges[range_idx].range.end <= pos.position
                    {
                        range_idx += 1;
                    }

                    if range_idx < ranges.len()
                        && ranges[range_idx].contig == pos.contig
                        && ranges[range_idx].range.contains(&pos.position)
                    {
                        result.push(chunk_idx * chunk_size + pos_idx);
                    }
                }
            }
            result
        })
        .collect()
}
//
// pub fn range_intersection_par(a: &[GenomeRange], b: &[GenomeRange]) -> Vec<GenomeRange> {
//     // Group ranges by contig for both inputs
//     let mut a_map = std::collections::HashMap::new();
//     for range in a {
//         a_map.entry(&range.contig).or_insert(Vec::new()).push(range);
//     }
//
//     let mut b_map = std::collections::HashMap::new();
//     for range in b {
//         b_map.entry(&range.contig).or_insert(Vec::new()).push(range);
//     }
//
//     // Process common contigs in parallel
//     a_map
//         .into_par_iter()
//         .filter_map(|(contig, mut a_ranges)| {
//             // Sort ranges by start position (end is only used for tie-breaking)
//             a_ranges.sort_by_key(|r| (r.range.start, r.range.end));
//
//             // Get corresponding ranges from b
//             let mut b_ranges = match b_map.get(contig) {
//                 Some(ranges) => ranges.clone(),
//                 None => return None,
//             };
//             b_ranges.sort_by_key(|r| (r.range.start, r.range.end));
//
//             let mut intersections = Vec::new();
//             let mut i = 0;
//             let mut j = 0;
//
//             // Two-pointer intersection algorithm for 0-based, end-exclusive ranges
//             while i < a_ranges.len() && j < b_ranges.len() {
//                 let a_range = &a_ranges[i];
//                 let b_range = &b_ranges[j];
//
//                 // Check if ranges are completely non-overlapping
//                 if a_range.range.end <= b_range.range.start {
//                     // |a_range| ends before |b_range| starts
//                     i += 1;
//                 } else if b_range.range.end <= a_range.range.start {
//                     // |b_range| ends before |a_range| starts
//                     j += 1;
//                 } else {
//                     // Calculate intersection of overlapping ranges
//                     let start = a_range.range.start.max(b_range.range.start);
//                     let end = a_range.range.end.min(b_range.range.end);
//
//                     // Only create a range if start < end (non-zero length)
//                     if start < end {
//                         intersections.push(GenomeRange {
//                             contig: *contig,
//                             range: start..end,
//                         });
//                     }
//
//                     // Move the pointer with the earlier end coordinate
//                     if a_range.range.end < b_range.range.end {
//                         i += 1;
//                     } else {
//                         j += 1;
//                     }
//                 }
//             }
//
//             Some(intersections)
//         })
//         .flatten()
//         .collect()
// }

/// Returns every region that **overlaps** between two sorted
/// slices of genome ranges, distributing the work across
/// threads with **Rayon**.
///
/// Both inputs **must**
/// - be sorted by `(contig, start)`
/// - contain non-overlapping, half-open ranges (`start < end`)
/// - use the same coordinate system.
///
/// # Parameters
/// * `a` – Slice of references to `GenomeRange`.
/// * `b` – Slice of references to `GenomeRange`.
///
/// # Returns
/// A `Vec<GenomeRange>` containing one entry for each pairwise
/// intersection.  
/// The output is *not* guaranteed to be sorted.
///
/// # Complexity
/// `O(|a| + |b|)` total work; memory ≤ the number of produced
/// intersections.  Work is split per contig and executed in
/// parallel.
///
/// # Panics
/// Never panics if the pre-conditions above are met.
///
/// # Example
/// ```
/// # use pandora_lib_promethion::{GenomeRange, range_intersection_par};
/// let a_range = GenomeRange { contig: 1, range: 100..200 };
/// let b_range = GenomeRange { contig: 1, range: 150..250 };
///
/// let out = range_intersection_par(&[&a_range], &[&b_range]);
/// assert_eq!(out, vec![GenomeRange { contig: 1, range: 150..200 }]);
/// ```
pub fn range_intersection_par(a: &[&GenomeRange], b: &[&GenomeRange]) -> Vec<GenomeRange> {
    let (a_contigs, b_contigs) = rayon::join(
        || extract_contig_indices(a),
        || extract_contig_indices(b),
    );

    a_contigs.into_par_iter()
        .filter_map(|(contig, a_start, a_end)| {
            let (b_start, b_end) = find_contig_indices(&b_contigs, contig)?;

            let a_ranges = &a[a_start..a_end];
            let b_ranges = &b[b_start..b_end];
            
            let mut intersections = Vec::new();
            let (mut i, mut j) = (0, 0);

            while i < a_ranges.len() && j < b_ranges.len() {
                let a_range = &a_ranges[i].range;
                let b_range = &b_ranges[j].range;

                match (a_range.end <= b_range.start, b_range.end <= a_range.start) {
                    (true, _) => i += 1,
                    (_, true) => j += 1,
                    _ => {
                        let start = a_range.start.max(b_range.start);
                        let end = a_range.end.min(b_range.end);
                        if start < end {
                            intersections.push(GenomeRange {
                                contig,
                                range: start..end,
                            });
                        }

                        if a_range.end < b_range.end {
                            i += 1;
                        } else {
                            j += 1;
                        }
                    }
                }
            }

            Some(intersections)
        })
        .flatten()
        .collect()
}

// Helper to create (contig, start index, end index) tuples
pub fn extract_contig_indices(ranges: &[&GenomeRange]) -> Vec<(u8, usize, usize)> {
    let mut indices = Vec::new();
    let mut current_contig = None;
    let mut start_idx = 0;

    for (i, range) in ranges.iter().enumerate() {
        if current_contig != Some(range.contig) {
            if let Some(contig) = current_contig {
                indices.push((contig, start_idx, i));
            }
            current_contig = Some(range.contig);
            start_idx = i;
        }
    }

    if let Some(contig) = current_contig {
        indices.push((contig, start_idx, ranges.len()));
    }

    indices
}

// Binary search to find contig indices in precomputed list
pub fn find_contig_indices(contigs: &[(u8, usize, usize)], target: u8) -> Option<(usize, usize)> {
    contigs.binary_search_by(|(c, _, _)| c.cmp(&target))
        .ok()
        .map(|idx| (contigs[idx].1, contigs[idx].2))
}

/// A parallel version of the overlap finding function that works with any types
/// implementing `GetGenomePosition` and `GetGenomeRange` traits.
///
/// This function first converts the input slices to vectors of `GenomePosition` and `GenomeRange`,
/// then calls `overlaps_par`.
///
/// # Arguments
/// * `a` - A slice of items implementing `GetGenomePosition`
/// * `b` - A slice of items implementing `GetGenomeRange`
///
/// # Returns
/// A `Vec<usize>` containing the indices of positions that overlap with any range.
///
/// # Example
/// ```
/// struct MyPosition(GenomePosition);
/// impl GetGenomePosition for MyPosition {
///     fn position(&self) -> &GenomePosition { &self.0 }
/// }
///
/// struct MyRange(GenomeRange);
/// impl GetGenomeRange for MyRange {
///     fn range(&self) -> &GenomeRange { &self.0 }
/// }
///
/// let positions = vec![
///     MyPosition(GenomePosition { contig: 1, position: 100 }),
///     MyPosition(GenomePosition { contig: 1, position: 200 }),
/// ];
/// let ranges = vec![
///     MyRange(GenomeRange { contig: 1, range: 50..150 }),
/// ];
/// let overlaps = par_overlaps(&positions, &ranges);
/// assert_eq!(overlaps, vec!);
/// ```
pub fn par_overlaps(a: &[impl GetGenomePosition], b: &[impl GetGenomeRange]) -> Vec<usize> {
    let a: Vec<_> = a.iter().map(|e| e.position()).collect();
    let b: Vec<_> = b.iter().map(|e| e.range()).collect();
    overlaps_par(&a, &b)
}

/// A trait for types that can provide a reference to a `GenomePosition`.
///
/// Implement this trait for types that contain or can compute a `GenomePosition`.
pub trait GetGenomePosition {
    // Returns a reference to the `GenomePosition` for this item.
    fn position(&self) -> &GenomePosition;
}

/// A trait for types that can provide a reference to a `GenomeRange`.
///
/// Implement this trait for types that contain or can compute a `GenomeRange`.
pub trait GetGenomeRange {
    /// Returns a reference to the `GenomeRange` for this item.
    fn range(&self) -> &GenomeRange;
}

pub fn sort_ranges(ranges: &mut [GenomeRange]) {
    ranges.par_sort_by_key(|r| (r.contig, r.range.start, r.range.end));
}