caps-sa 0.7.0

//! In-memory CaPS-SA-style suffix array construction.
//!
//! Phase 1 of the port: a parallel merge-sort with LCP-enhanced two-way merge,
//! exactly the inner sorting kernel of upstream CaPS-SA's `Suffix_Array::merge`
//! and `Suffix_Array::merge_sort` (see `include/Suffix_Array.hpp` and
//! `src/Suffix_Array.cpp`). The sample-sort partitioning around this kernel
//! (`select_pivots` → `distribute_sub_subarrays` → `merge_sub_subarrays`) is
//! Phase 2 / 3 work; the kernel here already produces a correct LCP-annotated
//! suffix array, and `rayon::join` gives parallel divide for free.
//!
//! The LCP-enhanced merge maintains:
//!
//! * `m` — the LCP between the last-output element and the current top of the
//!   *other* stream.
//! * `l_a` = `lcp_a[i_a]` — the LCP between the current top of the
//!   last-output stream and its immediate predecessor (which is the
//!   last-output element).
//!
//! Three cases per step:
//!
//! * `l_a > m`: the next candidate from the last-output stream agrees with the
//!   last-output element past where the other stream diverged — it lies on the
//!   same side of the other stream's top as the last-output element did, so it
//!   wins. No symbol comparison needed.
//! * `l_a < m`: the next candidate diverges from the last-output element
//!   *inside* the prefix shared with the other stream's top. Since the stream
//!   is sorted, the new candidate is larger than its predecessor; at the
//!   divergence offset it therefore exceeds the other stream's top — the
//!   other stream wins. No symbol comparison needed.
//! * `l_a == m`: undetermined; extend the LCP from offset `m` by an actual
//!   symbol scan and compare.

use crate::Index;
use crate::lcp::{LcpDispatch, Symbol};
use crate::lcp_memo::GeometricMemo;
use crate::limits::{LimitProvider, PlainText};
use rayon::join;

/// How many merge steps ahead the text prefetch runs. Large enough to cover a
/// DRAM round trip at the merge's step rate, small enough that the prefetched
/// line is still resident when the step that needs it arrives.
const PREFETCH_DISTANCE: usize = 8;

/// Hint the CPU to start pulling `text[at]` into cache.
///
/// A no-op on targets without a stable prefetch intrinsic, and harmless when
/// `at` is out of bounds: the address is never dereferenced, only used as a
/// prefetch operand, and prefetch instructions on both supported targets
/// ignore faulting addresses.
#[inline(always)]
fn prefetch_symbol<S>(text: &[S], at: usize) {
    let _ = (text, at);
    #[cfg(target_arch = "x86_64")]
    unsafe {
        std::arch::x86_64::_mm_prefetch(
            text.as_ptr().add(at.min(text.len())) as *const i8,
            std::arch::x86_64::_MM_HINT_T0,
        );
    }
    #[cfg(target_arch = "aarch64")]
    unsafe {
        // `core::arch::aarch64::_prefetch` is still unstable, so emit the
        // instruction directly. `prfm` never faults.
        let p = text.as_ptr().add(at.min(text.len()));
        std::arch::asm!("prfm pldl1keep, [{p}]", p = in(reg) p, options(nostack, readonly, preserves_flags));
    }
}

/// Tunable options for SA construction.
#[derive(Clone, Debug)]
pub struct Opts {
    /// Bound on extension comparisons inside the merge. `usize::MAX` (default)
    /// is unbounded — required for full lexicographic correctness when the
    /// caller's text doesn't guarantee comparisons terminate via sentinels
    /// within a known window.
    pub max_context: usize,
}

impl Default for Opts {
    fn default() -> Self {
        Self {
            max_context: usize::MAX,
        }
    }
}

/// Build the suffix array of `text` in memory and return it.
///
/// Generic over the symbol type `S` (`Ord + Copy`, e.g. `u8`, `u16`, `u32`)
/// and the index type `I` (`u32`, `u64`, `usize`). Pick the narrowest `I`
/// that can hold `text.len()`.
///
/// Produces a *standard lexicographic* suffix array. The "shorter suffix is
/// smaller when one runs off the end of `text`" tie-break is applied — i.e.
/// the algorithm behaves as if `text` is followed by an implicit symbol
/// smaller than all of `S`.
pub fn build_in_memory<S, I>(text: &[S]) -> Vec<I>
where
    S: Symbol,
    I: Index,
{
    build_in_memory_with_opts(text, &Opts::default())
}

/// Variant of [`build_in_memory`] that accepts tuning options.
pub fn build_in_memory_with_opts<S, I>(text: &[S], opts: &Opts) -> Vec<I>
where
    S: Symbol,
    I: Index,
{
    build_in_memory_with(text, &PlainText::new(text.len()), opts)
}

/// Variant of [`build_in_memory`] that accepts a [`LimitProvider`].
/// With [`PlainText`] this is identical to [`build_in_memory`]; with
/// [`SegmentedText`][crate::limits::SegmentedText] the LCP scans stop
/// at segment boundaries.
pub fn build_in_memory_with<S, I, L>(text: &[S], lp: &L, opts: &Opts) -> Vec<I>
where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    let n = text.len();
    let positions: Vec<I> = (0..n).map(I::from_usize).collect();
    build_in_memory_for_positions_with(text, positions, lp, opts)
}

/// Sort the caller-supplied `positions` by the lexicographic order of
/// their suffixes in `text`. Returns the positions reordered so that
/// `text[output[i]..]` is the i-th smallest suffix among the input set.
///
/// Equivalent to [`build_in_memory`] for the special case
/// `positions = (0..text.len()).collect()`; the explicit-positions form
/// lets callers skip suffixes they don't want included in the sort —
/// e.g. STAR-style genome indexing where only ACGT-starting positions
/// participate in the SA, avoiding the O(n) work of sorting and then
/// discarding the spacer-starting positions inside bin-padding.
///
/// The suffix at each position is still the slice `text[position..]`;
/// no positions are dropped from the input. To filter, the caller
/// constructs `positions` with only the indices they want.
pub fn build_in_memory_for_positions<S, I>(text: &[S], positions: Vec<I>) -> Vec<I>
where
    S: Symbol,
    I: Index,
{
    build_in_memory_for_positions_with_opts(text, positions, &Opts::default())
}

/// Variant of [`build_in_memory_for_positions`] that accepts tuning options.
pub fn build_in_memory_for_positions_with_opts<S, I>(
    text: &[S],
    positions: Vec<I>,
    opts: &Opts,
) -> Vec<I>
where
    S: Symbol,
    I: Index,
{
    build_in_memory_for_positions_with(text, positions, &PlainText::new(text.len()), opts)
}

/// Variant of [`build_in_memory_for_positions`] that accepts both a
/// [`LimitProvider`] (for segmented LCP truncation) and tuning options.
/// With [`PlainText`] this is identical to
/// [`build_in_memory_for_positions_with_opts`].
pub fn build_in_memory_for_positions_with<S, I, L>(
    text: &[S],
    positions: Vec<I>,
    lp: &L,
    opts: &Opts,
) -> Vec<I>
where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    let n = positions.len();
    if n == 0 {
        return Vec::new();
    }

    let mut sa: Vec<I> = positions;
    let mut sa_w: Vec<I> = vec![I::zero(); n];
    let mut lcp_arr: Vec<I> = vec![I::zero(); n];
    let mut lcp_w: Vec<I> = vec![I::zero(); n];

    // Choose the LCP implementation once for the whole build; the captured
    // function pointer travels through the recursion in a register, so the
    // inner merge loop pays no atomic load or feature-detection branch.
    let dispatch = LcpDispatch::detect();

    merge_sort(
        text,
        lp,
        &mut sa,
        &mut sa_w,
        &mut lcp_arr,
        &mut lcp_w,
        opts.max_context,
        dispatch,
    );

    sa
}

/// Recursive merge-sort with LCP maintenance.
///
/// Pre: `sa.len() == sa_w.len() == lcp_arr.len() == lcp_w.len()`. The contents
/// of `sa` are the suffix positions to sort (typically an identity
/// permutation at the top level). All other buffers are scratch / output.
///
/// Post: `sa` is sorted in ascending lexicographic order on
/// `text[sa[i]..]`; `lcp_arr[0] = 0` and `lcp_arr[i] = lcp(text[sa[i-1]..],
/// text[sa[i]..])` for `i >= 1`.
///
/// Visible to the rest of the crate so the external-memory path can sort
/// individual subarrays of positions using the same kernel.
#[allow(clippy::too_many_arguments)] // 4 buffers + text + lp + ctx + dispatch
pub(crate) fn merge_sort<S, I, L>(
    text: &[S],
    lp: &L,
    sa: &mut [I],
    sa_w: &mut [I],
    lcp_arr: &mut [I],
    lcp_w: &mut [I],
    max_ctx: usize,
    dispatch: LcpDispatch,
) where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    let n = sa.len();
    debug_assert_eq!(sa_w.len(), n);
    debug_assert_eq!(lcp_arr.len(), n);
    debug_assert_eq!(lcp_w.len(), n);

    if n <= 1 {
        if n == 1 {
            lcp_arr[0] = I::zero();
        }
        return;
    }

    let mid = n / 2;
    let (sa_l, sa_r) = sa.split_at_mut(mid);
    let (sa_w_l, sa_w_r) = sa_w.split_at_mut(mid);
    let (lcp_l, lcp_r) = lcp_arr.split_at_mut(mid);
    let (lcp_w_l, lcp_w_r) = lcp_w.split_at_mut(mid);

    join(
        || merge_sort(text, lp, sa_l, sa_w_l, lcp_l, lcp_w_l, max_ctx, dispatch),
        || merge_sort(text, lp, sa_r, sa_w_r, lcp_r, lcp_w_r, max_ctx, dispatch),
    );

    // Merge the two sorted halves (still living in `sa`) into the workspace,
    // then copy the workspace back into the destination so the caller's
    // postcondition holds on `sa` / `lcp_arr`.
    merge(
        text, lp, sa_l, sa_r, lcp_l, lcp_r, sa_w, lcp_w, max_ctx, dispatch,
    );
    sa.copy_from_slice(sa_w);
    lcp_arr.copy_from_slice(lcp_w);
}

/// Sort one subarray that is already owned by an outer Rayon task.
///
/// Spawning recursive Rayon joins here oversubscribes phase 1's thousands of
/// independent tasks and performs scheduler bookkeeping at every merge-tree
/// node. Keeping the recursion local still leaves ample outer parallelism.
#[allow(clippy::too_many_arguments)]
pub(crate) fn merge_sort_task_local<S, I, L>(
    text: &[S],
    lp: &L,
    sa: &mut [I],
    sa_w: &mut [I],
    lcp_arr: &mut [I],
    lcp_w: &mut [I],
    max_ctx: usize,
    dispatch: LcpDispatch,
) where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    debug_assert_eq!(sa.len(), sa_w.len());
    debug_assert_eq!(sa.len(), lcp_arr.len());
    debug_assert_eq!(sa.len(), lcp_w.len());
    if sa.is_empty() {
        return;
    }

    // Both sides begin with the same unsorted positions. Recursive calls swap
    // source and destination roles, so every merge level writes directly into
    // the side consumed by its parent and no level needs a copy-back pass.
    sa_w.copy_from_slice(sa);
    merge_sort_ping_pong(text, lp, sa_w, lcp_w, sa, lcp_arr, max_ctx, dispatch);
}

#[allow(clippy::too_many_arguments)]
fn merge_sort_ping_pong<S, I, L>(
    text: &[S],
    lp: &L,
    src_sa: &mut [I],
    src_lcp: &mut [I],
    dst_sa: &mut [I],
    dst_lcp: &mut [I],
    max_ctx: usize,
    dispatch: LcpDispatch,
) where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    let n = src_sa.len();
    debug_assert_eq!(src_lcp.len(), n);
    debug_assert_eq!(dst_sa.len(), n);
    debug_assert_eq!(dst_lcp.len(), n);
    if n <= 1 {
        if n == 1 {
            dst_sa[0] = src_sa[0];
            dst_lcp[0] = I::zero();
        }
        return;
    }

    let mid = n / 2;
    {
        let (src_sa_l, src_sa_r) = src_sa.split_at_mut(mid);
        let (src_lcp_l, src_lcp_r) = src_lcp.split_at_mut(mid);
        let (dst_sa_l, dst_sa_r) = dst_sa.split_at_mut(mid);
        let (dst_lcp_l, dst_lcp_r) = dst_lcp.split_at_mut(mid);
        merge_sort_ping_pong(
            text, lp, dst_sa_l, dst_lcp_l, src_sa_l, src_lcp_l, max_ctx, dispatch,
        );
        merge_sort_ping_pong(
            text, lp, dst_sa_r, dst_lcp_r, src_sa_r, src_lcp_r, max_ctx, dispatch,
        );
    }

    let (src_sa_l, src_sa_r) = src_sa.split_at(mid);
    let (src_lcp_l, src_lcp_r) = src_lcp.split_at(mid);
    merge(
        text, lp, src_sa_l, src_sa_r, src_lcp_l, src_lcp_r, dst_sa, dst_lcp, max_ctx, dispatch,
    );
}

/// LCP-enhanced two-way merge of two sorted suffix arrays.
///
/// `x` / `lcp_x` and `y` / `lcp_y` must each be sorted with `lcp_*[0] == 0`
/// and `lcp_*[i] = lcp(arr[i-1], arr[i])` for `i >= 1`. The result is written
/// into `z` / `lcp_z` (length `x.len() + y.len()`).
///
/// Visible to the rest of the crate so the external-memory path can cascade
/// 2-way merges across each partition's sub-subarrays during Phase 4.
macro_rules! merge_extension {
    (direct, $text:expr, $dispatch:expr, $p:expr, $q:expr, $known:expr, $max_ext:expr) => {
        $dispatch.lcp($text, $p + $known, $q + $known, $max_ext)
    };
    ((memo $memo:ident), $text:expr, $dispatch:expr, $p:expr, $q:expr, $known:expr, $max_ext:expr) => {{
        let probe = $memo.probe($max_ext);
        let got = $dispatch.lcp($text, $p + $known, $q + $known, probe);
        if got < probe || probe == $max_ext {
            got
        } else {
            $memo.lcp_after_probe($text, $dispatch, $p, $q, $known, probe, $max_ext)
        }
    }};
    ((memo_profiled $memo:ident), $text:expr, $dispatch:expr, $p:expr, $q:expr, $known:expr, $max_ext:expr) => {{
        let probe = $memo.probe($max_ext);
        let got = $dispatch.lcp($text, $p + $known, $q + $known, probe);
        $memo.record_probe_profiled(got, probe, $max_ext);
        if got < probe || probe == $max_ext {
            got
        } else {
            $memo.lcp_after_probe_profiled($text, $dispatch, $p, $q, $known, probe, $max_ext)
        }
    }};
    ((training $memo:ident), $text:expr, $dispatch:expr, $p:expr, $q:expr, $known:expr, $max_ext:expr) => {{
        let got = $dispatch.lcp($text, $p + $known, $q + $known, $max_ext);
        $memo.observe_training($p, $q, $known, got, $max_ext);
        got
    }};
    ((training_profiled $memo:ident), $text:expr, $dispatch:expr, $p:expr, $q:expr, $known:expr, $max_ext:expr) => {{
        let got = $dispatch.lcp($text, $p + $known, $q + $known, $max_ext);
        $memo.observe_training_profiled($p, $q, $known, got, $max_ext);
        got
    }};
}

// Keep the direct and memoized kernels as separate monomorphized functions.
// A trait/wrapper abstraction measurably perturbed code generation in the
// original hot loop even when memoization was disabled.  This macro retains a
// single source of truth while changing only the LCP-extension expression.
macro_rules! merge_body {
    ($lookup:tt; $text:ident, $lp:ident, $x:ident, $y:ident, $lcp_x:ident, $lcp_y:ident, $z:ident, $lcp_z:ident, $max_ctx:ident, $dispatch:ident) => {{
        let len_x = $x.len();
        let len_y = $y.len();
        debug_assert_eq!($z.len(), len_x + len_y);
        debug_assert_eq!($lcp_z.len(), len_x + len_y);

        if len_x == 0 {
            $z.copy_from_slice($y);
            $lcp_z.copy_from_slice($lcp_y);
            return;
        }
        if len_y == 0 {
            $z.copy_from_slice($x);
            $lcp_z.copy_from_slice($lcp_x);
            return;
        }

        // The "swap-on-output-from-B" trick from upstream CaPS-SA: we always
        // label the stream we last output from as `A`, and the other as `B`.
        let mut arr_a: &[I] = $x;
        let mut arr_b: &[I] = $y;
        let mut lcp_a: &[I] = $lcp_x;
        let mut lcp_b: &[I] = $lcp_y;
        let mut len_a = len_x;
        let mut len_b = len_y;
        let mut i_a: usize = 0;
        let mut i_b: usize = 0;
        let mut m: usize = 0;
        let mut k: usize = 0;
        let mut lim_a_cache: Option<(usize, usize)> = None;
        let mut lim_b_cache: Option<(usize, usize)> = None;

        while i_a < len_a && i_b < len_b {
            if i_a + PREFETCH_DISTANCE < len_a {
                prefetch_symbol($text, arr_a[i_a + PREFETCH_DISTANCE].to_usize() + m);
            }
            if i_b + PREFETCH_DISTANCE < len_b {
                prefetch_symbol($text, arr_b[i_b + PREFETCH_DISTANCE].to_usize() + m);
            }

            let l_a = lcp_a[i_a].to_usize();
            let (output_a, lcp_for_output, new_m) = if l_a > m {
                (true, l_a, m)
            } else if l_a < m {
                (false, m, l_a)
            } else {
                let p_a = arr_a[i_a].to_usize();
                let p_b = arr_b[i_b].to_usize();
                let lim_a = match lim_a_cache {
                    Some((idx, lim)) if idx == i_a => lim,
                    _ => {
                        let lim = $lp.lim_at(p_a);
                        lim_a_cache = Some((i_a, lim));
                        lim
                    }
                };
                let lim_b = match lim_b_cache {
                    Some((idx, lim)) if idx == i_b => lim,
                    _ => {
                        let lim = $lp.lim_at(p_b);
                        lim_b_cache = Some((i_b, lim));
                        lim
                    }
                };
                let cap = lim_a.min(lim_b).min($max_ctx);
                let remaining_ctx = cap.saturating_sub(m);
                let ext = merge_extension!($lookup, $text, $dispatch, p_a, p_b, m, remaining_ctx);
                let total = m + ext;
                // `cap` includes max_ctx as well as both suffix limits.  If
                // the scan exhausts max_ctx, comparison is deliberately
                // truncated and must use the configured boundary tie-break;
                // reading one more symbol here would disagree with
                // LcpDispatch::suffix_cmp_with and phase-2 pivot ordering.
                let a_smaller = if total < cap {
                    $text[p_a + total] < $text[p_b + total]
                } else {
                    $lp.boundary_order(p_a, lim_a, p_b, lim_b).is_lt()
                };
                (a_smaller, m, total)
            };

            if output_a {
                $z[k] = arr_a[i_a];
                $lcp_z[k] = I::from_usize(lcp_for_output);
                i_a += 1;
                lim_a_cache = None;
            } else {
                $z[k] = arr_b[i_b];
                $lcp_z[k] = I::from_usize(lcp_for_output);
                i_b += 1;
                lim_b_cache = None;
                std::mem::swap(&mut arr_a, &mut arr_b);
                std::mem::swap(&mut lcp_a, &mut lcp_b);
                std::mem::swap(&mut len_a, &mut len_b);
                std::mem::swap(&mut i_a, &mut i_b);
                std::mem::swap(&mut lim_a_cache, &mut lim_b_cache);
            }
            m = new_m;
            k += 1;
        }

        drain(arr_a, lcp_a, i_a, len_a, $z, $lcp_z, &mut k, m);
        drain(arr_b, lcp_b, i_b, len_b, $z, $lcp_z, &mut k, m);
    }};
}

#[allow(clippy::too_many_arguments)] // CaPS-SA's merge takes 5 buffers + text + lp + ctx + dispatch
pub(crate) fn merge<S, I, L>(
    text: &[S],
    lp: &L,
    x: &[I],
    y: &[I],
    lcp_x: &[I],
    lcp_y: &[I],
    z: &mut [I],
    lcp_z: &mut [I],
    max_ctx: usize,
    dispatch: LcpDispatch,
) where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    merge_body!(direct; text, lp, x, y, lcp_x, lcp_y, z, lcp_z, max_ctx, dispatch);
}

/// Phase-4 variant of [`merge`] that reuses exact LCP intervals discovered by
/// earlier levels of the same partition cascade.
#[allow(clippy::too_many_arguments)]
pub(crate) fn merge_memoized<S, I, L>(
    text: &[S],
    lp: &L,
    x: &[I],
    y: &[I],
    lcp_x: &[I],
    lcp_y: &[I],
    z: &mut [I],
    lcp_z: &mut [I],
    max_ctx: usize,
    dispatch: LcpDispatch,
    memo: &mut GeometricMemo,
) where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    merge_body!((memo memo); text, lp, x, y, lcp_x, lcp_y, z, lcp_z, max_ctx, dispatch);
}

/// Instrumented counterpart of [`merge_memoized`]. Selected once per
/// partition so normal memoized comparisons contain no counter branches.
#[allow(clippy::too_many_arguments)]
pub(crate) fn merge_memoized_profiled<S, I, L>(
    text: &[S],
    lp: &L,
    x: &[I],
    y: &[I],
    lcp_x: &[I],
    lcp_y: &[I],
    z: &mut [I],
    lcp_z: &mut [I],
    max_ctx: usize,
    dispatch: LcpDispatch,
    memo: &mut GeometricMemo,
) where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    merge_body!((memo_profiled memo); text, lp, x, y, lcp_x, lcp_y, z, lcp_z, max_ctx, dispatch);
}

#[allow(clippy::too_many_arguments)]
pub(crate) fn merge_memoized_training<S, I, L>(
    text: &[S],
    lp: &L,
    x: &[I],
    y: &[I],
    lcp_x: &[I],
    lcp_y: &[I],
    z: &mut [I],
    lcp_z: &mut [I],
    max_ctx: usize,
    dispatch: LcpDispatch,
    memo: &mut GeometricMemo,
) where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    merge_body!((training memo); text, lp, x, y, lcp_x, lcp_y, z, lcp_z, max_ctx, dispatch);
}

#[allow(clippy::too_many_arguments)]
pub(crate) fn merge_memoized_training_profiled<S, I, L>(
    text: &[S],
    lp: &L,
    x: &[I],
    y: &[I],
    lcp_x: &[I],
    lcp_y: &[I],
    z: &mut [I],
    lcp_z: &mut [I],
    max_ctx: usize,
    dispatch: LcpDispatch,
    memo: &mut GeometricMemo,
) where
    S: Symbol,
    I: Index,
    L: LimitProvider,
{
    merge_body!((training_profiled memo); text, lp, x, y, lcp_x, lcp_y, z, lcp_z, max_ctx, dispatch);
}

#[inline]
#[allow(clippy::too_many_arguments)] // drain handles both source streams via labelled args
fn drain<I: Index>(
    arr: &[I],
    lcp_src: &[I],
    mut i: usize,
    len: usize,
    z: &mut [I],
    lcp_z: &mut [I],
    k: &mut usize,
    boundary_m: usize,
) {
    let mut first = true;
    while i < len {
        z[*k] = arr[i];
        lcp_z[*k] = if first {
            I::from_usize(boundary_m)
        } else {
            lcp_src[i]
        };
        first = false;
        i += 1;
        *k += 1;
    }
}

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

    /// Brute-force reference suffix array via `sort_by` over byte slices.
    fn brute_force_sa(text: &[u8]) -> Vec<u32> {
        let mut sa: Vec<u32> = (0..text.len() as u32).collect();
        sa.sort_by(|&a, &b| text[a as usize..].cmp(&text[b as usize..]));
        sa
    }

    fn assert_matches_brute(text: &[u8]) {
        let got: Vec<u32> = build_in_memory(text);
        let want = brute_force_sa(text);
        assert_eq!(got, want, "mismatch on text {text:?}");
    }

    /// Run the production kernel and return **both** the suffix array and
    /// the LCP array it computes as a byproduct.
    ///
    /// The public entry points discard the LCP array, but it is not an
    /// incidental artefact: the next merge level *consumes* it in the
    /// three-case decision, so a single wrong LCP entry silently reorders
    /// suffixes at the level above. It therefore needs direct coverage.
    fn build_sa_and_lcp(text: &[u8], max_ctx: usize) -> (Vec<u32>, Vec<u32>) {
        let n = text.len();
        let mut sa: Vec<u32> = (0..n as u32).collect();
        let mut sa_w = vec![0u32; n];
        let mut lcp_arr = vec![0u32; n];
        let mut lcp_w = vec![0u32; n];
        merge_sort(
            text,
            &PlainText::new(n),
            &mut sa,
            &mut sa_w,
            &mut lcp_arr,
            &mut lcp_w,
            max_ctx,
            LcpDispatch::detect(),
        );
        (sa, lcp_arr)
    }

    /// Byte-at-a-time LCP of `text[a..]` and `text[b..]`, capped at `max_ctx`.
    fn naive_lcp(text: &[u8], a: usize, b: usize, max_ctx: usize) -> usize {
        let lim = (text.len() - a).min(text.len() - b).min(max_ctx);
        (0..lim).take_while(|&i| text[a + i] == text[b + i]).count()
    }

    /// Assert the LCP-array postcondition stated on [`merge_sort`]:
    /// `lcp[0] == 0` and `lcp[i] == lcp(text[sa[i-1]..], text[sa[i]..])`.
    fn assert_lcp_valid(text: &[u8], max_ctx: usize) {
        let (sa, lcp) = build_sa_and_lcp(text, max_ctx);
        if sa.is_empty() {
            return;
        }
        assert_eq!(lcp[0], 0, "lcp[0] must be 0 (text {text:?})");
        for i in 1..sa.len() {
            let want = naive_lcp(text, sa[i - 1] as usize, sa[i] as usize, max_ctx);
            assert_eq!(
                lcp[i] as usize,
                want,
                "lcp[{i}] wrong for sa[{}]={} vs sa[{i}]={} (text {text:?})",
                i - 1,
                sa[i - 1],
                sa[i],
            );
        }
    }

    #[test]
    fn lcp_array_matches_naive_on_fixtures() {
        for text in [
            b"banana".as_slice(),
            b"mississippi",
            b"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
            b"abababababababababababababab",
            b"a",
            b"",
        ] {
            assert_lcp_valid(text, usize::MAX);
        }
    }

    #[test]
    fn lcp_array_matches_naive_on_random() {
        use rand::{RngExt, SeedableRng};
        let mut rng = rand::rngs::StdRng::seed_from_u64(0x1CB0);
        for &sigma in &[2u8, 4, 6, 255] {
            for &n in &[2usize, 3, 7, 16, 17, 63, 64, 65, 200, 1000, 5000] {
                let text: Vec<u8> = (0..n).map(|_| rng.random_range(0..sigma)).collect();
                assert_lcp_valid(&text, usize::MAX);
            }
        }
    }

    /// Long runs of one symbol are the worst case for the LCP invariant:
    /// adjacent suffixes share almost everything, so every `lcp[i]` is
    /// large and an off-by-one is easy to miss.
    #[test]
    fn lcp_array_on_long_runs_and_periodic_text() {
        assert_lcp_valid(&vec![7u8; 2000], usize::MAX);
        let periodic: Vec<u8> = (0..2000).map(|i| (i % 3) as u8).collect();
        assert_lcp_valid(&periodic, usize::MAX);
        // A run embedded in noise, the shape a poly-N genome block has.
        let mut mixed: Vec<u8> = (0..500).map(|i| (i % 4) as u8).collect();
        mixed.extend(std::iter::repeat_n(4u8, 1500));
        mixed.extend((0..500).map(|i| (i % 4) as u8));
        assert_lcp_valid(&mixed, usize::MAX);
    }

    #[test]
    fn lcp_array_respects_max_context() {
        use rand::{RngExt, SeedableRng};
        let mut rng = rand::rngs::StdRng::seed_from_u64(0xC7A);
        for &max_ctx in &[1usize, 2, 4, 16] {
            for &n in &[64usize, 500] {
                let text: Vec<u8> = (0..n).map(|_| rng.random_range(0..3u8)).collect();
                let (sa, lcp) = build_sa_and_lcp(&text, max_ctx);
                for i in 1..sa.len() {
                    let want = naive_lcp(&text, sa[i - 1] as usize, sa[i] as usize, max_ctx);
                    assert_eq!(
                        lcp[i] as usize, want,
                        "lcp[{i}] wrong with max_ctx={max_ctx}"
                    );
                }
            }
        }
    }

    #[test]
    fn suffix_array_respects_finite_max_context() {
        use rand::{RngExt, SeedableRng};

        let dispatch = LcpDispatch::detect();
        let mut rng = rand::rngs::StdRng::seed_from_u64(0x0F11_7EC7);
        for &max_ctx in &[0usize, 1, 2, 4, 16] {
            for &n in &[2usize, 3, 7, 64, 500] {
                let text: Vec<u8> = (0..n).map(|_| rng.random_range(0..3u8)).collect();
                let opts = Opts {
                    max_context: max_ctx,
                };
                let got: Vec<u32> = build_in_memory_with_opts(&text, &opts);
                let mut want: Vec<u32> = (0..n as u32).collect();
                want.sort_by(|&a, &b| dispatch.suffix_cmp(&text, a as usize, b as usize, max_ctx));
                assert_eq!(
                    got, want,
                    "finite-context SA mismatch (n={n}, max_ctx={max_ctx})"
                );
            }
        }
    }

    #[test]
    fn empty_text() {
        let sa: Vec<u32> = build_in_memory::<u8, u32>(&[]);
        assert!(sa.is_empty());
    }

    #[test]
    fn single_symbol() {
        let sa: Vec<u32> = build_in_memory(&[7u8]);
        assert_eq!(sa, vec![0]);
    }

    #[test]
    fn banana() {
        assert_matches_brute(b"banana");
    }

    #[test]
    fn mississippi() {
        assert_matches_brute(b"mississippi");
    }

    #[test]
    fn small_distinct_sentinel() {
        // Alphabet 0..=5 with a unique terminator. Models the
        // sentinel-transformed STAR text on a tiny example.
        let text: Vec<u8> = vec![0, 1, 2, 0, 1, 5, 0, 2, 1, 6];
        let got: Vec<u32> = build_in_memory(&text);
        let want = brute_force_sa(&text);
        assert_eq!(got, want);
    }

    #[test]
    fn random_byte_texts() {
        use rand::{RngExt, SeedableRng};
        let mut rng = rand::rngs::StdRng::seed_from_u64(0xC0FFEE);
        for &n in &[1usize, 2, 3, 7, 33, 200, 1000] {
            let text: Vec<u8> = (0..n).map(|_| rng.random_range(0..6u8)).collect();
            let got: Vec<u32> = build_in_memory(&text);
            let want = brute_force_sa(&text);
            assert_eq!(got, want, "mismatch on random text len={n}");
        }
    }

    #[test]
    fn for_positions_full_set_matches_build_in_memory() {
        // Same output as build_in_memory when positions is the identity.
        let text = b"banana";
        let want: Vec<u32> = build_in_memory(text);
        let positions: Vec<u32> = (0..text.len() as u32).collect();
        let got = build_in_memory_for_positions(text, positions);
        assert_eq!(got, want);
    }

    #[test]
    fn for_positions_subset_matches_brute_force() {
        // Sort only the even positions of "mississippi" by their
        // suffixes; verify against brute force.
        let text = b"mississippi";
        let positions: Vec<u32> = (0..text.len() as u32).step_by(2).collect();
        let mut want = positions.clone();
        want.sort_by(|&a, &b| text[a as usize..].cmp(&text[b as usize..]));
        let got = build_in_memory_for_positions(text, positions);
        assert_eq!(got, want);
    }

    #[test]
    fn for_positions_random_subsets() {
        use rand::{RngExt, SeedableRng};
        let mut rng = rand::rngs::StdRng::seed_from_u64(0xFEED);
        for &n in &[33usize, 200, 1000] {
            let text: Vec<u8> = (0..n).map(|_| rng.random_range(0..6u8)).collect();
            // Random subset of positions.
            let mut positions: Vec<u32> = (0..n as u32).collect();
            // Drop a random ~30%.
            positions.retain(|_| rng.random_range(0..10) < 7);
            let mut want = positions.clone();
            want.sort_by(|&a, &b| text[a as usize..].cmp(&text[b as usize..]));
            let got = build_in_memory_for_positions(&text, positions);
            assert_eq!(got, want, "subset sort mismatch n={n}");
        }
    }

    #[test]
    fn random_with_unique_terminator() {
        // Distinct large terminator at the end — mimics the transform we'll
        // apply for STAR.
        use rand::{RngExt, SeedableRng};
        let mut rng = rand::rngs::StdRng::seed_from_u64(0xBEEF);
        for &n in &[1usize, 50, 500] {
            let mut text: Vec<u8> = (0..n).map(|_| rng.random_range(0..5u8)).collect();
            text.push(250); // unique max
            let got: Vec<u32> = build_in_memory(&text);
            let want = brute_force_sa(&text);
            assert_eq!(got, want);
        }
    }

    // ---- segmented SA tests ----

    use crate::limits::SegmentedText;

    /// Compare two suffixes under the segmented comparator (LCP
    /// truncated at the boundary, "shorter-is-smaller" tie-break).
    fn segmented_cmp(text: &[u8], lp: &SegmentedText, a: usize, b: usize) -> std::cmp::Ordering {
        use crate::limits::LimitProvider;
        let lim_a = lp.lim_at(a);
        let lim_b = lp.lim_at(b);
        let lim = lim_a.min(lim_b);
        for i in 0..lim {
            if text[a + i] != text[b + i] {
                return text[a + i].cmp(&text[b + i]);
            }
        }
        lim_a.cmp(&lim_b)
    }

    /// Assert that `sa` is a valid segmented SA over `text` partitioned
    /// by `lengths`:
    ///
    /// 1. it's a permutation of the positions in `positions`, and
    /// 2. every adjacent pair is in non-decreasing comparator order.
    ///
    /// Comparator-equivalent suffixes can appear in any relative order —
    /// caps-sa's merge isn't a stable sort, so we don't pin a canonical
    /// permutation.
    fn assert_segmented_sa_valid(text: &[u8], lengths: &[usize], positions: &[u32], sa: &[u32]) {
        let lp = SegmentedText::from_lengths(text.len(), lengths);
        let mut expected = positions.to_vec();
        expected.sort();
        let mut got_sorted = sa.to_vec();
        got_sorted.sort();
        assert_eq!(got_sorted, expected, "sa is not a permutation of positions");
        for w in sa.windows(2) {
            let a = w[0] as usize;
            let b = w[1] as usize;
            let ord = segmented_cmp(text, &lp, a, b);
            assert_ne!(
                ord,
                std::cmp::Ordering::Greater,
                "out of order: pos {a} > pos {b} under segmented comparator",
            );
        }
    }

    #[test]
    fn segmented_in_memory_matches_brute_force_small() {
        // 4 segments: "hello" | "world" | "banana" | "mississippi"
        let text: Vec<u8> = b"helloworldbananamississippi".to_vec();
        let lengths = &[5usize, 5, 6, 11];
        let lp = SegmentedText::from_lengths(text.len(), lengths);
        let sa: Vec<u32> = build_in_memory_with(&text, &lp, &Opts::default());
        let all_positions: Vec<u32> = (0..text.len() as u32).collect();
        assert_segmented_sa_valid(&text, lengths, &all_positions, &sa);
    }

    #[test]
    fn segmented_single_segment_equals_unsegmented() {
        // A single segment covering the whole text is the same as the
        // non-segmented SA — confirms the LimitProvider path doesn't
        // perturb the standard order when there's nothing to truncate.
        let text = b"mississippi";
        let lp = SegmentedText::from_lengths(text.len(), &[text.len()]);
        let got_segmented: Vec<u32> = build_in_memory_with(text, &lp, &Opts::default());
        let got_plain: Vec<u32> = build_in_memory(text);
        assert_eq!(got_segmented, got_plain);
    }

    #[test]
    fn segmented_random_validity() {
        use rand::{RngExt, SeedableRng};
        let mut rng = rand::rngs::StdRng::seed_from_u64(0x5E6);
        for _ in 0..20 {
            let n_segments = rng.random_range(1..10usize);
            let lengths: Vec<usize> = (0..n_segments)
                .map(|_| rng.random_range(5..50usize))
                .collect();
            let n: usize = lengths.iter().sum();
            // Small alphabet so the LCP-truncation case actually fires.
            let text: Vec<u8> = (0..n).map(|_| rng.random_range(0..3u8)).collect();
            let lp = SegmentedText::from_lengths(n, &lengths);
            let sa: Vec<u32> = build_in_memory_with(&text, &lp, &Opts::default());
            let all_positions: Vec<u32> = (0..n as u32).collect();
            assert_segmented_sa_valid(&text, &lengths, &all_positions, &sa);
        }
    }

    #[test]
    fn segmented_for_positions_subset_validity() {
        // Filter to even positions only, sort with segmentation.
        let text: Vec<u8> = b"helloworldbananamississippi".to_vec();
        let lengths = &[5usize, 5, 6, 11];
        let positions: Vec<u32> = (0..text.len() as u32).step_by(2).collect();
        let lp = SegmentedText::from_lengths(text.len(), lengths);
        let sa =
            build_in_memory_for_positions_with(&text, positions.clone(), &lp, &Opts::default());
        assert_segmented_sa_valid(&text, lengths, &positions, &sa);
    }

    // ---- STAR-convention boundary_order tests ----

    /// A `LimitProvider` wrapping [`SegmentedText`] with STAR's
    /// `spacer-as-largest` boundary semantics: the suffix that hits
    /// its limit first is *larger*, equivalently the longer-`lim`
    /// suffix is smaller, with an ascending-position tie-break when
    /// `lim_a == lim_b`. Used by rustar-aligner's `sa_build` to keep
    /// byte-for-byte STAR compatibility on the segmented arm.
    struct StarConvention {
        inner: SegmentedText,
    }

    impl crate::limits::LimitProvider for StarConvention {
        fn lim_at(&self, p: usize) -> usize {
            self.inner.lim_at(p)
        }
        fn boundary_order(
            &self,
            p_a: usize,
            lim_a: usize,
            p_b: usize,
            lim_b: usize,
        ) -> std::cmp::Ordering {
            lim_b.cmp(&lim_a).then(p_a.cmp(&p_b))
        }
    }

    /// Brute-force SA under STAR's convention (longer-lim is smaller,
    /// position tie-break). Used as the oracle for the differential
    /// test. With a position tie-break the SA is uniquely determined,
    /// so this can be compared with `assert_eq!`.
    fn star_brute_force_sa(text: &[u8], lengths: &[usize]) -> Vec<u32> {
        use crate::limits::LimitProvider;
        let lp = SegmentedText::from_lengths(text.len(), lengths);
        let mut sa: Vec<u32> = (0..text.len() as u32).collect();
        sa.sort_by(|&a, &b| {
            let pa = a as usize;
            let pb = b as usize;
            let lim_a = lp.lim_at(pa);
            let lim_b = lp.lim_at(pb);
            let lim = lim_a.min(lim_b);
            for i in 0..lim {
                if text[pa + i] != text[pb + i] {
                    return text[pa + i].cmp(&text[pb + i]);
                }
            }
            // STAR convention: longer-lim is smaller, then position.
            lim_b.cmp(&lim_a).then(pa.cmp(&pb))
        });
        sa
    }

    #[test]
    fn star_convention_matches_brute_force_small() {
        // 4 segments: "hello" | "world" | "banana" | "mississippi"
        let text: Vec<u8> = b"helloworldbananamississippi".to_vec();
        let lengths = &[5usize, 5, 6, 11];
        let lp = StarConvention {
            inner: SegmentedText::from_lengths(text.len(), lengths),
        };
        let got: Vec<u32> = build_in_memory_with(&text, &lp, &Opts::default());
        let want = star_brute_force_sa(&text, lengths);
        assert_eq!(got, want, "STAR-convention SA mismatch");
    }

    /// Exercises the STAR-specific within-segment longer-is-smaller
    /// case: in "AAAA" with one segment, STAR orders the longest
    /// suffix first (`AAAA < AAA < AA < A`) — opposite of the
    /// standard SA's `A < AA < AAA < AAAA`.
    #[test]
    fn star_convention_within_segment_longer_first() {
        let text = b"AAAA";
        let lp = StarConvention {
            inner: SegmentedText::from_lengths(text.len(), &[text.len()]),
        };
        let got: Vec<u32> = build_in_memory_with(text, &lp, &Opts::default());
        // Position 0 = "AAAA" (lim 4), 1 = "AAA" (lim 3), 2 = "AA"
        // (lim 2), 3 = "A" (lim 1). Longer-lim is smaller, so 0 < 1
        // < 2 < 3.
        assert_eq!(got, vec![0u32, 1, 2, 3]);
    }

    #[test]
    fn star_convention_random_matches_brute_force() {
        use rand::{RngExt, SeedableRng};
        let mut rng = rand::rngs::StdRng::seed_from_u64(0xCAFE);
        for _ in 0..20 {
            let n_segments = rng.random_range(1..10usize);
            let lengths: Vec<usize> = (0..n_segments)
                .map(|_| rng.random_range(5..50usize))
                .collect();
            let n: usize = lengths.iter().sum();
            // Small alphabet so the boundary-tie-break case fires.
            let text: Vec<u8> = (0..n).map(|_| rng.random_range(0..3u8)).collect();
            let lp = StarConvention {
                inner: SegmentedText::from_lengths(n, &lengths),
            };
            let got: Vec<u32> = build_in_memory_with(&text, &lp, &Opts::default());
            let want = star_brute_force_sa(&text, &lengths);
            assert_eq!(
                got, want,
                "STAR-convention SA mismatch (lengths={lengths:?}, text={text:?})",
            );
        }
    }
}