genomicframe-core 0.2.0

//! Genomic interval operations
//!
//! Core data structures and operations for working with genomic intervals.
//! Used across all formats for region-based queries, overlap detection, and filtering.
//!
//! # Design Philosophy
//!
//! - **0-based coordinates**: All intervals use 0-based, half-open [start, end) coordinates
//!   - This matches BED, BAM, and internal representations
//!   - VCF uses 1-based coordinates but is converted during parsing
//! - **Efficient operations**: Overlap and containment checks are O(1)
//! - **Immutable by default**: Intervals are cheap to clone (just 3 fields)
//! - **Cross-format compatibility**: Can convert from any genomic record type
//!
//! # Examples
//!
//! ```
//! use genomicframe_core::interval::GenomicInterval;
//!
//! // Create intervals
//! let interval1 = GenomicInterval::new("chr1", 1000, 2000);
//! let interval2 = GenomicInterval::new("chr1", 1500, 2500);
//!
//! // Check overlap
//! assert!(interval1.overlaps(&interval2));
//!
//! // Compute overlap length
//! assert_eq!(interval1.overlap_length(&interval2), 500);
//!
//! // Get intersection
//! let intersection = interval1.intersect(&interval2).unwrap();
//! assert_eq!(intersection.start, 1500);
//! assert_eq!(intersection.end, 2000);
//! ```

use crate::error::{Error, Result};
use std::cmp::{max, min};
use std::fmt;

// Conversions from format-specific records
pub mod conversions;

// Annotation infrastructure
pub mod annotation;

/// A genomic interval representing a region on a chromosome
///
/// Uses 0-based, half-open [start, end) coordinates:
/// - `start` is inclusive (0-based)
/// - `end` is exclusive (0-based)
///
/// This matches BED format and is the standard for genomic intervals.
#[derive(Debug, Clone, PartialEq, Eq, Hash)]
pub struct GenomicInterval {
    /// Chromosome/contig name (e.g., "chr1", "chrX", "1")
    pub chrom: String,

    /// Start position (0-based, inclusive)
    pub start: u64,

    /// End position (0-based, exclusive)
    pub end: u64,
}

impl GenomicInterval {
    /// Create a new genomic interval
    ///
    /// # Arguments
    /// * `chrom` - Chromosome name
    /// * `start` - Start position (0-based, inclusive)
    /// * `end` - End position (0-based, exclusive)
    ///
    /// # Panics
    /// Panics if `start > end`
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let interval = GenomicInterval::new("chr1", 1000, 2000);
    /// assert_eq!(interval.len(), 1000);
    /// ```
    pub fn new<S: Into<String>>(chrom: S, start: u64, end: u64) -> Self {
        let interval = Self {
            chrom: chrom.into(),
            start,
            end,
        };
        assert!(
            start <= end,
            "Invalid interval: start ({}) > end ({})",
            start,
            end
        );
        interval
    }

    /// Try to create a new genomic interval, returning an error if invalid
    ///
    /// This is the fallible version of `new()`.
    pub fn try_new<S: Into<String>>(chrom: S, start: u64, end: u64) -> Result<Self> {
        if start > end {
            return Err(Error::InvalidInput(format!(
                "Invalid interval: start ({}) > end ({})",
                start, end
            )));
        }
        Ok(Self {
            chrom: chrom.into(),
            start,
            end,
        })
    }

    /// Create a point interval (length 1) at the given position
    ///
    /// Useful for representing SNPs or single positions.
    pub fn point<S: Into<String>>(chrom: S, pos: u64) -> Self {
        Self {
            chrom: chrom.into(),
            start: pos,
            end: pos + 1,
        }
    }

    /// Get the length of this interval
    ///
    /// Returns `end - start`.
    #[inline]
    pub fn len(&self) -> u64 {
        self.end - self.start
    }

    /// Check if this is an empty interval (start == end)
    #[inline]
    pub fn is_empty(&self) -> bool {
        self.start == self.end
    }

    /// Check if this interval is a point (length 1)
    #[inline]
    pub fn is_point(&self) -> bool {
        self.len() == 1
    }

    /// Check if two intervals overlap (share at least one base)
    ///
    /// Returns `false` if intervals are on different chromosomes.
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let a = GenomicInterval::new("chr1", 100, 200);
    /// let b = GenomicInterval::new("chr1", 150, 250);
    /// assert!(a.overlaps(&b));
    ///
    /// let c = GenomicInterval::new("chr1", 200, 300);
    /// assert!(!a.overlaps(&c)); // Adjacent but not overlapping
    /// ```
    #[inline]
    pub fn overlaps(&self, other: &GenomicInterval) -> bool {
        self.chrom == other.chrom && self.start < other.end && other.start < self.end
    }

    /// Check if this interval completely contains another interval
    ///
    /// Returns `false` if intervals are on different chromosomes.
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let a = GenomicInterval::new("chr1", 100, 300);
    /// let b = GenomicInterval::new("chr1", 150, 200);
    /// assert!(a.contains(&b));
    /// assert!(!b.contains(&a));
    /// ```
    #[inline]
    pub fn contains(&self, other: &GenomicInterval) -> bool {
        self.chrom == other.chrom && self.start <= other.start && other.end <= self.end
    }

    /// Check if this interval contains a specific position
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let interval = GenomicInterval::new("chr1", 100, 200);
    /// assert!(interval.contains_pos("chr1", 150));
    /// assert!(!interval.contains_pos("chr1", 200)); // end is exclusive
    /// ```
    #[inline]
    pub fn contains_pos(&self, chrom: &str, pos: u64) -> bool {
        self.chrom == chrom && self.start <= pos && pos < self.end
    }

    /// Compute the length of overlap between two intervals
    ///
    /// Returns 0 if intervals don't overlap or are on different chromosomes.
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let a = GenomicInterval::new("chr1", 100, 200);
    /// let b = GenomicInterval::new("chr1", 150, 250);
    /// assert_eq!(a.overlap_length(&b), 50);
    /// ```
    pub fn overlap_length(&self, other: &GenomicInterval) -> u64 {
        if !self.overlaps(other) {
            0
        } else {
            min(self.end, other.end) - max(self.start, other.start)
        }
    }

    /// Compute the intersection of two intervals
    ///
    /// Returns `None` if intervals don't overlap or are on different chromosomes.
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let a = GenomicInterval::new("chr1", 100, 200);
    /// let b = GenomicInterval::new("chr1", 150, 250);
    /// let intersection = a.intersect(&b).unwrap();
    /// assert_eq!(intersection.start, 150);
    /// assert_eq!(intersection.end, 200);
    /// ```
    pub fn intersect(&self, other: &GenomicInterval) -> Option<GenomicInterval> {
        if !self.overlaps(other) {
            None
        } else {
            Some(GenomicInterval {
                chrom: self.chrom.clone(),
                start: max(self.start, other.start),
                end: min(self.end, other.end),
            })
        }
    }

    /// Compute the union (span) of two intervals
    ///
    /// Returns the smallest interval that contains both intervals.
    /// Returns `None` if intervals are on different chromosomes.
    ///
    /// Note: This may include regions not covered by either original interval.
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let a = GenomicInterval::new("chr1", 100, 200);
    /// let b = GenomicInterval::new("chr1", 300, 400);
    /// let union = a.union(&b).unwrap();
    /// assert_eq!(union.start, 100);
    /// assert_eq!(union.end, 400);
    /// assert_eq!(union.len(), 300); // Includes gap!
    /// ```
    pub fn union(&self, other: &GenomicInterval) -> Option<GenomicInterval> {
        if self.chrom != other.chrom {
            None
        } else {
            Some(GenomicInterval {
                chrom: self.chrom.clone(),
                start: min(self.start, other.start),
                end: max(self.end, other.end),
            })
        }
    }

    /// Compute the distance between two intervals
    ///
    /// Returns:
    /// - `Some(0)` if intervals overlap
    /// - `Some(n)` where n > 0 is the gap size between intervals
    /// - `None` if intervals are on different chromosomes
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let a = GenomicInterval::new("chr1", 100, 200);
    /// let b = GenomicInterval::new("chr1", 250, 300);
    /// assert_eq!(a.distance(&b), Some(50)); // 250 - 200 = 50
    ///
    /// let c = GenomicInterval::new("chr1", 150, 250);
    /// assert_eq!(a.distance(&c), Some(0)); // Overlapping
    /// ```
    pub fn distance(&self, other: &GenomicInterval) -> Option<u64> {
        if self.chrom != other.chrom {
            None
        } else if self.overlaps(other) {
            Some(0)
        } else if self.end <= other.start {
            Some(other.start - self.end)
        } else {
            Some(self.start - other.end)
        }
    }

    /// Expand this interval by a fixed amount on both sides
    ///
    /// Start is reduced by `amount`, end is increased by `amount`.
    /// Start is clamped to 0 (won't go negative).
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let interval = GenomicInterval::new("chr1", 100, 200);
    /// let expanded = interval.expand(50);
    /// assert_eq!(expanded.start, 50);
    /// assert_eq!(expanded.end, 250);
    /// ```
    pub fn expand(&self, amount: u64) -> GenomicInterval {
        GenomicInterval {
            chrom: self.chrom.clone(),
            start: self.start.saturating_sub(amount),
            end: self.end + amount,
        }
    }

    /// Shrink this interval by a fixed amount on both sides
    ///
    /// Returns `None` if shrinking would make the interval invalid.
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let interval = GenomicInterval::new("chr1", 100, 200);
    /// let shrunk = interval.shrink(25).unwrap();
    /// assert_eq!(shrunk.start, 125);
    /// assert_eq!(shrunk.end, 175);
    /// ```
    pub fn shrink(&self, amount: u64) -> Option<GenomicInterval> {
        let new_start = self.start + amount;
        let new_end = self.end.saturating_sub(amount);

        if new_start <= new_end {
            Some(GenomicInterval {
                chrom: self.chrom.clone(),
                start: new_start,
                end: new_end,
            })
        } else {
            None
        }
    }

    /// Convert to BED format string (0-based, tab-separated)
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let interval = GenomicInterval::new("chr1", 100, 200);
    /// assert_eq!(interval.to_bed_string(), "chr1\t100\t200");
    /// ```
    pub fn to_bed_string(&self) -> String {
        format!("{}\t{}\t{}", self.chrom, self.start, self.end)
    }

    /// Parse from BED format string (0-based, tab-separated)
    ///
    /// # Example
    /// ```
    /// use genomicframe_core::interval::GenomicInterval;
    ///
    /// let interval = GenomicInterval::from_bed_string("chr1\t100\t200").unwrap();
    /// assert_eq!(interval.chrom, "chr1");
    /// assert_eq!(interval.start, 100);
    /// assert_eq!(interval.end, 200);
    /// ```
    pub fn from_bed_string(s: &str) -> Result<Self> {
        let parts: Vec<&str> = s.split('\t').collect();
        if parts.len() < 3 {
            return Err(Error::Parse(format!(
                "Invalid BED string: expected at least 3 fields, got {}",
                parts.len()
            )));
        }

        let chrom = parts[0].to_string();
        let start = parts[1].parse::<u64>().map_err(|_| {
            Error::Parse(format!("Invalid start position: {}", parts[1]))
        })?;
        let end = parts[2].parse::<u64>().map_err(|_| {
            Error::Parse(format!("Invalid end position: {}", parts[2]))
        })?;

        Self::try_new(chrom, start, end)
    }
}

impl fmt::Display for GenomicInterval {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        write!(f, "{}:{}-{}", self.chrom, self.start, self.end)
    }
}

/// Helper for sorting intervals
impl PartialOrd for GenomicInterval {
    fn partial_cmp(&self, other: &Self) -> Option<std::cmp::Ordering> {
        Some(self.cmp(other))
    }
}

impl Ord for GenomicInterval {
    fn cmp(&self, other: &Self) -> std::cmp::Ordering {
        // Sort by chromosome, then start, then end
        (&self.chrom, self.start, self.end).cmp(&(&other.chrom, other.start, other.end))
    }
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_new() {
        let interval = GenomicInterval::new("chr1", 100, 200);
        assert_eq!(interval.chrom, "chr1");
        assert_eq!(interval.start, 100);
        assert_eq!(interval.end, 200);
        assert_eq!(interval.len(), 100);
    }

    #[test]
    #[should_panic]
    fn test_invalid_interval() {
        GenomicInterval::new("chr1", 200, 100); // start > end
    }

    #[test]
    fn test_try_new() {
        assert!(GenomicInterval::try_new("chr1", 200, 100).is_err());
        assert!(GenomicInterval::try_new("chr1", 100, 200).is_ok());
    }

    #[test]
    fn test_point() {
        let interval = GenomicInterval::point("chr1", 100);
        assert_eq!(interval.start, 100);
        assert_eq!(interval.end, 101);
        assert!(interval.is_point());
    }

    #[test]
    fn test_overlaps() {
        let a = GenomicInterval::new("chr1", 100, 200);
        let b = GenomicInterval::new("chr1", 150, 250);
        let c = GenomicInterval::new("chr1", 200, 300);
        let d = GenomicInterval::new("chr2", 100, 200);

        assert!(a.overlaps(&b));
        assert!(!a.overlaps(&c)); // Adjacent
        assert!(!a.overlaps(&d)); // Different chromosome
    }

    #[test]
    fn test_contains() {
        let a = GenomicInterval::new("chr1", 100, 300);
        let b = GenomicInterval::new("chr1", 150, 200);

        assert!(a.contains(&b));
        assert!(!b.contains(&a));
    }

    #[test]
    fn test_contains_pos() {
        let interval = GenomicInterval::new("chr1", 100, 200);
        assert!(interval.contains_pos("chr1", 100));
        assert!(interval.contains_pos("chr1", 150));
        assert!(!interval.contains_pos("chr1", 200)); // end is exclusive
        assert!(!interval.contains_pos("chr2", 150));
    }

    #[test]
    fn test_overlap_length() {
        let a = GenomicInterval::new("chr1", 100, 200);
        let b = GenomicInterval::new("chr1", 150, 250);
        let c = GenomicInterval::new("chr1", 200, 300);

        assert_eq!(a.overlap_length(&b), 50);
        assert_eq!(a.overlap_length(&c), 0);
    }

    #[test]
    fn test_intersect() {
        let a = GenomicInterval::new("chr1", 100, 200);
        let b = GenomicInterval::new("chr1", 150, 250);

        let intersection = a.intersect(&b).unwrap();
        assert_eq!(intersection.start, 150);
        assert_eq!(intersection.end, 200);

        let c = GenomicInterval::new("chr1", 200, 300);
        assert!(a.intersect(&c).is_none());
    }

    #[test]
    fn test_union() {
        let a = GenomicInterval::new("chr1", 100, 200);
        let b = GenomicInterval::new("chr1", 300, 400);

        let union = a.union(&b).unwrap();
        assert_eq!(union.start, 100);
        assert_eq!(union.end, 400);

        let c = GenomicInterval::new("chr2", 100, 200);
        assert!(a.union(&c).is_none());
    }

    #[test]
    fn test_distance() {
        let a = GenomicInterval::new("chr1", 100, 200);
        let b = GenomicInterval::new("chr1", 250, 300);
        let c = GenomicInterval::new("chr1", 150, 250);

        assert_eq!(a.distance(&b), Some(50));
        assert_eq!(a.distance(&c), Some(0)); // Overlapping
    }

    #[test]
    fn test_expand() {
        let interval = GenomicInterval::new("chr1", 100, 200);
        let expanded = interval.expand(50);
        assert_eq!(expanded.start, 50);
        assert_eq!(expanded.end, 250);

        // Test saturation at 0
        let small = GenomicInterval::new("chr1", 10, 20);
        let expanded = small.expand(50);
        assert_eq!(expanded.start, 0);
    }

    #[test]
    fn test_shrink() {
        let interval = GenomicInterval::new("chr1", 100, 200);
        let shrunk = interval.shrink(25).unwrap();
        assert_eq!(shrunk.start, 125);
        assert_eq!(shrunk.end, 175);

        // Shrink too much
        assert!(interval.shrink(100).is_none());
    }

    #[test]
    fn test_bed_string() {
        let interval = GenomicInterval::new("chr1", 100, 200);
        assert_eq!(interval.to_bed_string(), "chr1\t100\t200");

        let parsed = GenomicInterval::from_bed_string("chr1\t100\t200").unwrap();
        assert_eq!(parsed, interval);
    }

    #[test]
    fn test_display() {
        let interval = GenomicInterval::new("chr1", 100, 200);
        assert_eq!(format!("{}", interval), "chr1:100-200");
    }

    #[test]
    fn test_sorting() {
        let mut intervals = vec![
            GenomicInterval::new("chr2", 100, 200),
            GenomicInterval::new("chr1", 300, 400),
            GenomicInterval::new("chr1", 100, 200),
        ];

        intervals.sort();

        assert_eq!(intervals[0].chrom, "chr1");
        assert_eq!(intervals[0].start, 100);
        assert_eq!(intervals[1].chrom, "chr1");
        assert_eq!(intervals[1].start, 300);
        assert_eq!(intervals[2].chrom, "chr2");
    }
}