twitcher 0.6.9

use std::{error::Error, fmt::Display, time::Duration};

use anyhow::bail;
use generic_a_star::AStarResult;

use itertools::Itertools as _;
use lib_tsalign::{
    a_star_aligner::{
        alignment_result::{AlignmentResult, AlignmentStatistics, alignment::Alignment},
        template_switch_distance::{AlignmentType, EqualCostRange},
    },
    costs::U64Cost,
};
use serde::{Deserialize, Serialize};

use crate::common::{
    aligner::fpa::FpaAlignmentStatistics,
    alignment::consumed_reference,
    coords::{GenomePosition, GenomeRegion},
};

/// The result of an alignment. This is the output of the whole `aligner` module.
pub type TwitcherAlignmentResult = Result<TwitcherAlignmentWithStatistics, AlignmentFailure>;

/// The result of a call to the aligner which completed successfully.
#[derive(Debug, Clone, Deserialize, Serialize)]
pub struct TwitcherAlignmentWithStatistics {
    pub alignment: AlignmentWithCost,
    pub stats: TwitcherAlignmentStatistics,
}

#[derive(Debug, Clone, Deserialize, Serialize)]
/// Statistics that are returned by the aligner
pub enum TwitcherAlignmentStatistics {
    FPAStats(Box<FpaAlignmentStatistics>),
    TSAlign(Box<AlignmentStatistics<U64Cost>>),
}

#[derive(Debug, Clone, Deserialize, Serialize)]
pub struct AlignmentWithCost {
    pub alignment: Alignment<AlignmentType>,
    pub cost: U64Cost,
}

impl AlignmentWithCost {
    pub const fn new(alignment: Alignment<AlignmentType>, cost: U64Cost) -> Self {
        Self { alignment, cost }
    }
    pub fn has_ts(&self) -> bool {
        self.alignment
            .iter_compact()
            .any(|(_, ty)| matches!(ty, AlignmentType::TemplateSwitchEntrance { .. }))
    }
}

/// The two ways an aligner can fail: expectedly or unexpectedly.
#[derive(Debug, Clone, Deserialize, Serialize)]
pub enum AlignmentFailure {
    SoftFailure { reason: SoftFailureReason },
    Error { error: String },
}

#[derive(Debug, Clone, Deserialize, Serialize)]
pub enum SoftFailureReason {
    OutOfMemory,
    Timeout(Duration),
    Other(String),
}

impl TwitcherAlignmentWithStatistics {
    pub const fn new(
        alignment: Alignment<AlignmentType>,
        cost: U64Cost,
        stats: TwitcherAlignmentStatistics,
    ) -> Self {
        Self {
            alignment: AlignmentWithCost { alignment, cost },
            stats,
        }
    }

    pub fn has_ts(&self) -> bool {
        self.alignment.has_ts()
    }
}

impl TwitcherAlignmentStatistics {
    pub fn reference_offset(&self) -> usize {
        match self {
            Self::FPAStats(fpa_alignment_statistics) => {
                fpa_alignment_statistics.ranges.reference_offset()
            }
            Self::TSAlign(alignment_statistics) => alignment_statistics.reference_offset,
        }
    }

    pub fn query_offset(&self) -> usize {
        match self {
            Self::FPAStats(fpa_alignment_statistics) => {
                fpa_alignment_statistics.ranges.query_offset()
            }
            Self::TSAlign(alignment_statistics) => alignment_statistics.query_offset,
        }
    }
}

impl AlignmentFailure {
    pub const fn oom() -> Self {
        Self::SoftFailure {
            reason: SoftFailureReason::OutOfMemory,
        }
    }

    pub const fn timeout(duration: Duration) -> Self {
        Self::SoftFailure {
            reason: SoftFailureReason::Timeout(duration),
        }
    }

    pub fn soft_fail<S: ToString>(error: &S) -> Self {
        Self::SoftFailure {
            reason: SoftFailureReason::Other(error.to_string()),
        }
    }

    pub fn error<S: ToString + ?Sized>(error: &S) -> Self {
        Self::Error {
            error: error.to_string(),
        }
    }
}

pub fn from_tsalign(
    tsalign_result: AlignmentResult<AlignmentType, U64Cost>,
) -> TwitcherAlignmentResult {
    let (alignment_cigar, mut statistics) = match tsalign_result {
        AlignmentResult::WithTarget {
            alignment,
            statistics,
        } => (Some(alignment), statistics),
        AlignmentResult::WithoutTarget { statistics } => (None, statistics),
    };

    // Remove the sequences from the statistics, since we handle sequences throughout twitcher as shared references (Arc<[u8]>) elsewhere.
    statistics.sequences.reference = String::new();
    statistics.sequences.reference_rc = String::new();
    statistics.sequences.query = String::new();
    statistics.sequences.query_rc = String::new();

    if let Some(alignment_cigar) = alignment_cigar {
        let cost = statistics.result.cost();
        Ok(TwitcherAlignmentWithStatistics::new(
            alignment_cigar,
            cost,
            statistics.into(),
        ))
    } else {
        let reason = match statistics.result {
            AStarResult::FoundTarget { .. } => {
                anyhow::anyhow!("There should be an alignment available, but it is not reported")
            }
            AStarResult::ExceededCostLimit { cost_limit } => {
                anyhow::anyhow!("Exceeded cost limit. Lower bound for the cost: {cost_limit}")
            }
            AStarResult::ExceededMemoryLimit { .. } => {
                return Err(AlignmentFailure::oom());
            }
            AStarResult::NoTarget => {
                anyhow::anyhow!("There was no target (implementation error?)")
            }
        };
        Err(AlignmentFailure::soft_fail(&reason))
    }
}

impl From<FpaAlignmentStatistics> for TwitcherAlignmentStatistics {
    fn from(value: FpaAlignmentStatistics) -> Self {
        Self::FPAStats(value.into())
    }
}

impl From<AlignmentStatistics<U64Cost>> for TwitcherAlignmentStatistics {
    fn from(value: AlignmentStatistics<U64Cost>) -> Self {
        Self::TSAlign(value.into())
    }
}

impl From<anyhow::Error> for AlignmentFailure {
    fn from(value: anyhow::Error) -> Self {
        Self::Error {
            error: value.to_string(),
        }
    }
}

impl From<std::io::Error> for AlignmentFailure {
    fn from(value: std::io::Error) -> Self {
        Self::Error {
            error: value.to_string(),
        }
    }
}

impl Display for AlignmentFailure {
    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
        match self {
            Self::SoftFailure {
                reason: SoftFailureReason::OutOfMemory,
            } => write!(f, "Expected failure: Out of memory."),
            Self::SoftFailure {
                reason: SoftFailureReason::Timeout(dur),
            } => write!(f, "Expected failure: Timeout ({dur:?})."),
            Self::SoftFailure {
                reason: SoftFailureReason::Other(e),
            } => write!(f, "Expected failure: {e}."),
            Self::Error { error } => write!(f, "Unexpected failure: {error}"),
        }
    }
}

impl Error for AlignmentFailure {}

#[derive(Debug)]
pub struct TSData {
    pub inner_len: usize,
    pub jump_1_2: isize,
    pub er: Option<EqualCostRange>,
    pub inner_aln: Alignment<AlignmentType>,
    pub apg: isize,
    pub pos_1: GenomePosition,
    pub pos_4: GenomePosition,
}

impl TSData {
    pub fn compute(
        region: &GenomeRegion,
        result: &TwitcherAlignmentWithStatistics,
    ) -> anyhow::Result<Vec<Self>> {
        let alignment = &result.alignment.alignment;

        let mut pos = region.start().clone() + result.stats.reference_offset();

        let mut results = Vec::new();
        let mut curr_data = None;
        let mut curr_ts_descendant = None;
        for (n, ty) in alignment.iter_compact() {
            pos += consumed_reference(n, ty, curr_ts_descendant)?;
            match ty {
                AlignmentType::TemplateSwitchEntrance {
                    first_offset,
                    equal_cost_range,
                    descendant,
                    ..
                } => {
                    curr_data = Some(Self {
                        inner_len: 0, // will change
                        jump_1_2: *first_offset,
                        er: (equal_cost_range.is_valid()).then_some(*equal_cost_range),
                        inner_aln: Alignment::new(), // will change
                        apg: 0,                      // will change
                        pos_1: pos.clone(),
                        pos_4: pos.clone(), // Will change
                    });
                    curr_ts_descendant = Some(*descendant);
                }
                AlignmentType::TemplateSwitchExit {
                    anti_descendant_gap,
                } => {
                    let Some(mut current) = curr_data.take() else {
                        bail!("Invalid alignment");
                    };
                    current.apg = *anti_descendant_gap;
                    current.pos_4 = pos.clone();
                    results.push(current);
                    curr_ts_descendant = None;
                }
                AlignmentType::SecondaryInsertion
                | AlignmentType::SecondarySubstitution
                | AlignmentType::SecondaryMatch => {
                    let Some(current) = &mut curr_data else {
                        bail!("Invalid alignment");
                    };
                    current.inner_len += n;
                    current.inner_aln.push_n(n, *ty);
                }
                AlignmentType::SecondaryDeletion => {
                    let Some(current) = &mut curr_data else {
                        bail!("Invalid alignment");
                    };
                    current.inner_aln.push_n(n, *ty);
                }
                _ => {}
            }
        }
        Ok(results)
    }

    pub fn to_field<S: ToString>(data: &[Self], sep: &str, f: impl Fn(&Self) -> S) -> String {
        data.iter().map(|d| f(d).to_string()).join(sep)
    }

    pub fn to_field_fallible<S: ToString>(
        data: &[Self],
        sep: &str,
        f: impl Fn(&Self) -> anyhow::Result<S>,
    ) -> anyhow::Result<String> {
        itertools::process_results(data.iter().map(f), |iter| {
            iter.map(|s| s.to_string()).join(sep)
        })
    }

    pub fn to_opt_field<S: ToString, K>(
        data: &[Self],
        sep: &str,
        opt: impl Fn(&Self) -> Option<&K>,
        f: impl Fn(&Self, &K) -> S,
    ) -> String {
        data.iter()
            .map(|d| opt(d).map(|k| f(d, k).to_string()).unwrap_or_default())
            .join(sep)
    }
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::common::contig::ContigName;

    fn ts_data(er: Option<EqualCostRange>) -> TSData {
        let pos = GenomePosition::new_0(ContigName::new(b"chr1"), 100);
        TSData {
            inner_len: 10,
            jump_1_2: -20,
            er,
            inner_aln: Alignment::new(),
            apg: 5,
            pos_1: pos.clone(),
            pos_4: pos,
        }
    }

    /// `to_opt_field` must behave like `to_field` for valid ranges, and yield
    /// empty entries (but keep the separators) for missing ones.
    #[test]
    fn to_opt_field_skips_missing_equal_cost_ranges() {
        let valid = EqualCostRange {
            min_start: -1,
            max_start: 2,
            min_end: -3,
            max_end: 4,
        };
        assert!(valid.is_valid());
        assert!(!EqualCostRange::new_invalid().is_valid());

        let data = [ts_data(Some(valid)), ts_data(None), ts_data(Some(valid))];
        let field =
            |d: &[TSData]| TSData::to_opt_field(d, ",", |d| d.er.as_ref(), |_, er| er.max_end);

        // No regression: with all ranges present the output matches `to_field`.
        let all_valid = [ts_data(Some(valid)), ts_data(Some(valid))];
        assert_eq!(
            field(&all_valid),
            TSData::to_field(&all_valid, ",", |d| d.er.unwrap().max_end)
        );

        // Missing range yields a null string in its slot.
        assert_eq!(field(&data), "4,,4");
        assert_eq!(field(&[ts_data(None)]), "");

        // Same for the derived min/max columns.
        assert_eq!(
            TSData::to_opt_field(
                &data,
                ",",
                |d| d.er.as_ref(),
                |d, er| d.inner_len
                    - usize::try_from(er.max_start).unwrap_or_default()
                    - usize::try_from(-er.min_end).unwrap_or_default()
            ),
            "5,,5"
        );
    }
}