data-beans 0.6.13

use super::run_squeeze_if_needed;
use crate::hdf5_io::*;
use crate::sparse_io::*;
use crate::zarr_io::*;

use clap::Args;
use legume_numeric::matrix::common_io::*;
use log::info;

#[derive(Args, Debug)]
pub struct FromFragmentsArgs {
    #[arg(
        help = "Fragments TSV file (plain, .gz, or bgzipped .gz/.bgz)",
        long_help = "Per-fragment records, one per line, tab-separated:\n\
                     chr<TAB>start<TAB>end<TAB>barcode[<TAB>count]\n\
                     \n\
                     Lines starting with '#' are skipped.\n\
                     The cellranger-arc header block is the usual case.\n\
                     Plain gzip and bgzip-compressed files are both supported;\n\
                     MultiGzDecoder reads concatenated blocks."
    )]
    pub fragments: Box<str>,

    #[arg(long, value_enum, default_value = "zarr")]
    pub backend: SparseIoBackend,

    #[arg(
        short,
        long,
        help = "Output file header or name",
        long_help = "Specify the output file header.\n\
                     The zarr backend produces {output}.zarr.zip by default;\n\
                     pass --no-zip to keep a {output}.zarr directory instead."
    )]
    pub output: Box<str>,

    /// keep a `.zarr` directory instead of producing a `.zarr.zip` archive
    #[arg(long = "no-zip", default_value_t = true, action = clap::ArgAction::SetFalse)]
    pub zip: bool,

    #[arg(
        long,
        help = "BED file of peaks (chr<TAB>start<TAB>end[...])",
        long_help = "When provided, fragments aggregate into these regions.\n\
                     Fixed-width genome tiles are then not used. Lines starting with '#',\n\
                     'track' or 'browser' are skipped. Row names are formatted `chr:start-end`.\n\
                     Peaks may overlap."
    )]
    pub peaks: Option<Box<str>>,

    #[arg(
        long,
        default_value_t = 5000,
        help = "Tile width in bp when --peaks is not provided",
        long_help = "Tile the genome into fixed-width bins on the fly.\n\
                     Bin i spans [i*bin_size, (i+1)*bin_size).\n\
                     Each fragment contributes to every bin it overlaps.\n\
                     Set 0 to disable tiling; --peaks is then required."
    )]
    pub bin_size: u64,

    #[arg(
        long,
        help = "Barcode whitelist file (one barcode per line, plain or .gz)",
        long_help = "When provided, this list acts as a whitelist.\n\
                     Fragments whose barcode is absent are skipped.\n\
                     Column order then matches the whitelist."
    )]
    pub barcodes: Option<Box<str>>,

    #[arg(
        long,
        default_value_t = false,
        help = "Use the count column (col 5) instead of contributing 1 per fragment",
        long_help = "By default each fragment adds 1 to the (feature, cell) entry.\n\
                     With this flag,\n\
                     the Tn5 insertion count in column 5 is used (missing/unparsable counts fall back to 1)."
    )]
    pub use_count: bool,

    #[arg(
        long,
        default_value_t = false,
        help = "Decompress the fragments file in-memory and parse in parallel",
        long_help = "By default the file is streamed line-by-line, single-threaded.\n\
                     \n\
                     With this flag the whole file is decompressed into memory,\n\
                     as one byte buffer.\n\
                     Parsing and aggregation then split across rayon workers.\n\
                     \n\
                     This is recommended for fast SSDs.\n\
                     It also suits large inputs on machines with enough RAM,\n\
                     roughly 3-10x the compressed file size.\n\
                     Output is identical to the serial path."
    )]
    pub preload_data: bool,

    #[arg(long, default_value_t = false)]
    pub do_squeeze: bool,

    #[arg(long, default_value_t = 1)]
    pub row_nnz_cutoff: usize,

    #[arg(long, default_value_t = 1)]
    pub column_nnz_cutoff: usize,

    #[arg(long)]
    pub block_size: Option<usize>,
}

/// Build backend from a (sc)ATAC/histone fragments TSV file.
///
/// Streams the (potentially bgzipped) fragments file once. Each line is
/// `chr<TAB>start<TAB>end<TAB>barcode[<TAB>count]`. Fragments are
/// aggregated into a (feature x cell) sparse matrix where features are
/// either user-supplied peaks (`--peaks`) or fixed-width genome tiles
/// (`--bin-size`).
pub fn run_build_from_fragments(args: &FromFragmentsArgs) -> anyhow::Result<()> {
    use rustc_hash::FxHashMap as HashMap;
    use std::io::BufRead;

    if args.peaks.is_none() && args.bin_size == 0 {
        anyhow::bail!("must provide either --peaks <bed> or --bin-size > 0");
    }

    let effective_output = apply_zip_flag(&args.output, args.zip, &args.backend);
    let (backend, backend_file) =
        resolve_backend_file(&effective_output, Some(args.backend.clone()))?;

    if std::path::Path::new(backend_file.as_ref()).exists() {
        info!("Removing existing backend file: {}", &backend_file);
        remove_file(&backend_file)?;
    }

    //////////////////////////////////
    // 1. Build the feature catalog //
    //////////////////////////////////
    //
    // Peaks mode: load all peaks up front, sort per-chromosome.
    // Bin mode: discover bins lazily as fragments stream in.
    //
    // Both modes key on the normalized chromosome name (no `chr` prefix) so
    // that a BED using `1` and a fragments file using `chr1` still match.
    // Display row names preserve the input's original convention — for peaks
    // mode that's whatever the BED gave us; for bin mode, the first chr
    // string seen for each canonical key wins.
    let use_peaks = args.peaks.is_some();
    let bin_size = args.bin_size as i64;

    let mut row_names: Vec<Box<str>> = Vec::new();

    // peaks mode lookup state (key: stripped chr)
    let mut peak_chr_idx: HashMap<Box<str>, usize> = Default::default();
    let mut peaks_by_chr: Vec<Vec<(i64, i64, u64)>> = Vec::new();
    let mut peak_max_width: Vec<i64> = Vec::new();

    // bin mode lookup state: stripped_chr -> (bin_index -> row_idx)
    let mut bin_row_idx: HashMap<Box<str>, HashMap<i64, u64>> = Default::default();
    // stripped_chr -> the first display string we saw for it
    let mut bin_display_chr: HashMap<Box<str>, Box<str>> = Default::default();

    if let Some(peaks_file) = args.peaks.as_ref() {
        info!("Loading peaks from {}", peaks_file);
        let buf = open_buf_reader(peaks_file.as_ref())?;
        let mut tmp: HashMap<Box<str>, Vec<(i64, i64, u64)>> = Default::default();
        for line in buf.lines() {
            let line = line?;
            let s = line.trim();
            if s.is_empty()
                || s.starts_with('#')
                || s.starts_with("track")
                || s.starts_with("browser")
            {
                continue;
            }
            let mut it = s.split('\t');
            let chr = match it.next() {
                Some(c) if !c.is_empty() => c,
                _ => continue,
            };
            let start: i64 = match it.next().and_then(|x| x.parse().ok()) {
                Some(v) => v,
                None => continue,
            };
            let end: i64 = match it.next().and_then(|x| x.parse().ok()) {
                Some(v) => v,
                None => continue,
            };
            if end <= start {
                continue;
            }
            let row_idx = row_names.len() as u64;
            row_names.push(format!("{}:{}-{}", chr, start, end).into_boxed_str());
            tmp.entry(chr_key(chr).into())
                .or_default()
                .push((start, end, row_idx));
        }
        let total_peaks = row_names.len();
        for (chr, mut v) in tmp.into_iter() {
            v.sort_unstable_by_key(|&(s, _, _)| s);
            let max_width = v.iter().map(|&(s, e, _)| e - s).max().unwrap_or(0);
            peak_chr_idx.insert(chr, peaks_by_chr.len());
            peaks_by_chr.push(v);
            peak_max_width.push(max_width);
        }
        info!(
            "Loaded {} peaks across {} chromosomes",
            total_peaks,
            peaks_by_chr.len()
        );
    }

    ///////////////////////////////////
    // 2. Optional barcode whitelist //
    ///////////////////////////////////
    let mut barcode_idx: HashMap<Box<str>, u64> = Default::default();
    let mut col_names: Vec<Box<str>> = Vec::new();
    let whitelist_only = args.barcodes.is_some();
    if let Some(bc_file) = args.barcodes.as_ref() {
        info!("Loading barcode whitelist from {}", bc_file);
        let buf = open_buf_reader(bc_file.as_ref())?;
        for line in buf.lines() {
            let line = line?;
            let s = line.trim();
            if s.is_empty() || s.starts_with('#') {
                continue;
            }
            // 10x barcodes.tsv may have a "-1" suffix; keep as-is to match the
            // fragments file convention.
            let bc: Box<str> = s.into();
            if !barcode_idx.contains_key(bc.as_ref()) {
                let id = col_names.len() as u64;
                col_names.push(bc.clone());
                barcode_idx.insert(bc, id);
            }
        }
        info!("Loaded {} whitelist barcodes", col_names.len());
        if col_names.is_empty() {
            anyhow::bail!("barcode whitelist is empty: {}", bc_file);
        }
    }

    /////////////////////////////////////////////////
    // 3. Stream fragments and accumulate triplets //
    /////////////////////////////////////////////////
    let mut triplet_map: HashMap<(u64, u64), f32> = Default::default();
    let mut n_total: u64 = 0;
    let mut n_skipped_bc: u64 = 0;
    let mut n_no_overlap: u64 = 0;
    let mut n_malformed: u64 = 0;

    if args.preload_data {
        run_fragments_preload_parallel(
            args,
            use_peaks,
            bin_size,
            whitelist_only,
            &peak_chr_idx,
            &peaks_by_chr,
            &peak_max_width,
            &mut barcode_idx,
            &mut col_names,
            &mut bin_row_idx,
            &mut bin_display_chr,
            &mut row_names,
            &mut triplet_map,
            &mut n_total,
            &mut n_skipped_bc,
            &mut n_no_overlap,
            &mut n_malformed,
        )?;
    } else {
        info!("Streaming fragments from {}", args.fragments);
        let reader = open_fragments_reader(args.fragments.as_ref())?;
        let prog_bar = streaming_fragments_progress();

        for line in reader.lines() {
            let line = line?;
            // skip headers / blanks
            if line.is_empty() || line.starts_with('#') {
                continue;
            }

            let mut it = line.splitn(6, '\t');
            let chr = match it.next() {
                Some(c) if !c.is_empty() => c,
                _ => {
                    n_malformed += 1;
                    continue;
                }
            };
            let start: i64 = match it.next().and_then(|s| s.parse().ok()) {
                Some(v) => v,
                None => {
                    n_malformed += 1;
                    continue;
                }
            };
            let end: i64 = match it.next().and_then(|s| s.parse().ok()) {
                Some(v) => v,
                None => {
                    n_malformed += 1;
                    continue;
                }
            };
            let barcode = match it.next() {
                Some(b) if !b.is_empty() => b,
                _ => {
                    n_malformed += 1;
                    continue;
                }
            };
            if end <= start {
                n_malformed += 1;
                continue;
            }
            let cnt: f32 = if args.use_count {
                it.next().and_then(|s| s.parse::<f32>().ok()).unwrap_or(1.0)
            } else {
                1.0
            };

            n_total += 1;
            if n_total.is_multiple_of(1_000_000) {
                prog_bar.set_position(n_total);
            }

            // resolve barcode -> column index
            let col_idx = if let Some(&i) = barcode_idx.get(barcode) {
                i
            } else if whitelist_only {
                n_skipped_bc += 1;
                continue;
            } else {
                let i = col_names.len() as u64;
                let bc: Box<str> = barcode.into();
                col_names.push(bc.clone());
                barcode_idx.insert(bc, i);
                i
            };

            // resolve overlapping feature row(s) — match on the stripped chr key
            let ckey = chr_key(chr);
            if start < 0 {
                n_malformed += 1;
                continue;
            }
            if use_peaks {
                let mut hit = false;
                if let Some(&chr_i) = peak_chr_idx.get(ckey) {
                    let peaks = &peaks_by_chr[chr_i];
                    let max_w = peak_max_width[chr_i];
                    // peaks at idx < lower cannot overlap because their full
                    // [start, start+max_w] fits before frag.start
                    let lower = peaks.partition_point(|p| p.0 + max_w <= start);
                    // peaks at idx >= upper have p.start >= end → cannot overlap
                    let upper = peaks.partition_point(|p| p.0 < end);
                    for &(_, pe, ridx) in &peaks[lower..upper] {
                        if pe > start {
                            *triplet_map.entry((ridx, col_idx)).or_insert(0.0) += cnt;
                            hit = true;
                        }
                    }
                }
                if !hit {
                    n_no_overlap += 1;
                }
            } else {
                // bin mode: lookup-or-insert (stripped_chr, bin_idx) → row_idx
                let chr_map = if bin_row_idx.contains_key(ckey) {
                    bin_row_idx.get_mut(ckey).unwrap()
                } else {
                    bin_row_idx.insert(ckey.into(), Default::default());
                    bin_display_chr.insert(ckey.into(), chr.into());
                    bin_row_idx.get_mut(ckey).unwrap()
                };
                let display = bin_display_chr.get(ckey).map(|s| s.as_ref()).unwrap_or(chr);
                let first = start / bin_size;
                let last = (end - 1) / bin_size;
                for b in first..=last {
                    let ridx = if let Some(&r) = chr_map.get(&b) {
                        r
                    } else {
                        let r = row_names.len() as u64;
                        let bs = b * bin_size;
                        let be = (b + 1) * bin_size;
                        row_names.push(format!("{}:{}-{}", display, bs, be).into_boxed_str());
                        chr_map.insert(b, r);
                        r
                    };
                    *triplet_map.entry((ridx, col_idx)).or_insert(0.0) += cnt;
                }
            }
        }
        prog_bar.finish_with_message(format!("{} fragments", n_total));
    }

    info!(
        "Streamed {} fragments — {} cells, {} features, {} skipped (barcode), {} no peak overlap, {} malformed",
        n_total,
        col_names.len(),
        row_names.len(),
        n_skipped_bc,
        n_no_overlap,
        n_malformed
    );

    let nrows = row_names.len();
    let ncols = col_names.len();
    if nrows == 0 {
        anyhow::bail!("no features produced; check --peaks / --bin-size and the fragments file");
    }
    if ncols == 0 {
        anyhow::bail!("no cells produced; check the barcode whitelist or input file");
    }

    let triplets: Vec<(u64, u64, f32)> = triplet_map
        .into_iter()
        .map(|((r, c), v)| (r, c, v))
        .collect();
    let nnz = triplets.len();
    info!("Built {} triplets in {} x {} matrix", nnz, nrows, ncols);

    let mut out = create_sparse_from_triplets_owned(
        triplets,
        (nrows, ncols, nnz),
        Some(&backend_file),
        Some(&backend),
    )?;
    info!("Created sparse matrix: {}", backend_file);

    out.register_row_names_vec(&row_names);
    out.register_column_names_vec(&col_names);

    run_squeeze_if_needed(
        args.do_squeeze,
        args.row_nnz_cutoff,
        args.column_nnz_cutoff,
        args.block_size,
        &backend_file,
    )?;
    finalize_zarr_output(&backend_file, &effective_output)?;
    info!("done");
    Ok(())
}

///////////////////////////////////////////////////////////////////////
// Parallel fragments path: preload entire (decompressed) TSV into   //
// memory, split at newline boundaries, parse + aggregate per-thread //
// with rayon, then merge into the global triplet/row/col state.     //
// Output is identical to the serial path. First-appearance ordering //
// of barcodes (and bin rows) is preserved by iterating threads in   //
// chunk order during the merge phase.                               //
///////////////////////////////////////////////////////////////////////

/// Per-thread parse/accumulate state. Triplet keys are interpreted as:
/// - peaks + whitelist: (global_peak_row, global_col_idx)
/// - peaks + open:      (global_peak_row, local_col_idx)
/// - bin   + whitelist: (local_bin_row, global_col_idx)
/// - bin   + open:      (local_bin_row, local_col_idx)
///
/// Local indices are remapped to global indices during the merge phase.
#[derive(Default)]
struct FragLocalAccum {
    bc_map: rustc_hash::FxHashMap<Box<str>, u32>,
    bc_names: Vec<Box<str>>,
    bin_map: rustc_hash::FxHashMap<Box<str>, rustc_hash::FxHashMap<i64, u32>>,
    chr_display: rustc_hash::FxHashMap<Box<str>, Box<str>>,
    bin_keys: Vec<(Box<str>, i64)>,
    triplets: rustc_hash::FxHashMap<(u64, u64), f32>,
    n_total: u64,
    n_skipped_bc: u64,
    n_no_overlap: u64,
    n_malformed: u64,
}

/// Split `bytes` into approximately `n_chunks` slices, with each cut
/// placed at the first '\n' boundary at or after the target byte
/// position. The newline character itself ends up in the *preceding*
/// chunk, so each chunk (except possibly the last) ends with '\n'.
fn fragment_chunk_ranges(bytes: &[u8], n_chunks: usize) -> Vec<(usize, usize)> {
    if bytes.is_empty() || n_chunks <= 1 {
        return vec![(0, bytes.len())];
    }
    let target = bytes.len() / n_chunks;
    let mut cuts = vec![0usize];
    for i in 1..n_chunks {
        let probe = i * target;
        if probe >= bytes.len() {
            break;
        }
        match bytes[probe..].iter().position(|&b| b == b'\n') {
            Some(off) => {
                let cut = probe + off + 1;
                if cut > *cuts.last().unwrap() && cut < bytes.len() {
                    cuts.push(cut);
                }
            }
            None => break,
        }
    }
    cuts.push(bytes.len());
    cuts.windows(2).map(|w| (w[0], w[1])).collect()
}

/// Parse a single fragments line (no trailing newline).
#[allow(clippy::type_complexity)]
fn parse_fragments_line(
    line: &[u8],
    use_count: bool,
) -> Result<Option<(&str, i64, i64, &str, f32)>, ()> {
    if line.is_empty() || line[0] == b'#' {
        return Ok(None);
    }
    // strip trailing '\r' (CRLF inputs)
    let line = if let Some(&b'\r') = line.last() {
        &line[..line.len() - 1]
    } else {
        line
    };
    if line.is_empty() {
        return Ok(None);
    }
    let mut it = line.split(|&b| b == b'\t');
    let chr_b = it.next().ok_or(())?;
    let start_b = it.next().ok_or(())?;
    let end_b = it.next().ok_or(())?;
    let barcode_b = it.next().ok_or(())?;
    let count_b = it.next();

    if chr_b.is_empty() || barcode_b.is_empty() {
        return Err(());
    }
    let chr = std::str::from_utf8(chr_b).map_err(|_| ())?;
    let barcode = std::str::from_utf8(barcode_b).map_err(|_| ())?;
    let start: i64 = std::str::from_utf8(start_b)
        .map_err(|_| ())?
        .parse()
        .map_err(|_| ())?;
    let end: i64 = std::str::from_utf8(end_b)
        .map_err(|_| ())?
        .parse()
        .map_err(|_| ())?;
    if end <= start || start < 0 {
        return Err(());
    }
    let cnt: f32 = if use_count {
        count_b
            .and_then(|s| std::str::from_utf8(s).ok())
            .and_then(|s| s.parse::<f32>().ok())
            .unwrap_or(1.0)
    } else {
        1.0
    };
    Ok(Some((chr, start, end, barcode, cnt)))
}

/// Drive one rayon chunk: parse and accumulate triplets locally.
#[allow(clippy::too_many_arguments)]
fn process_fragments_chunk(
    chunk: &[u8],
    use_peaks: bool,
    bin_size: i64,
    use_count: bool,
    whitelist_only: bool,
    peak_chr_idx: &rustc_hash::FxHashMap<Box<str>, usize>,
    peaks_by_chr: &[Vec<(i64, i64, u64)>],
    peak_max_width: &[i64],
    global_bc_idx: &rustc_hash::FxHashMap<Box<str>, u64>,
) -> FragLocalAccum {
    let mut acc = FragLocalAccum::default();

    for raw in chunk.split(|&b| b == b'\n') {
        let parsed = match parse_fragments_line(raw, use_count) {
            Ok(Some(t)) => t,
            Ok(None) => continue,
            Err(()) => {
                // empty/header lines were handled by the Ok(None) branch;
                // anything else that fails parsing counts as malformed,
                // but skip purely-empty bytes (a trailing \n leaves an
                // empty slice in the iterator).
                if !raw.is_empty() && raw != b"\r" {
                    acc.n_malformed += 1;
                }
                continue;
            }
        };
        let (chr, start, end, barcode, cnt) = parsed;

        acc.n_total += 1;

        // resolve barcode -> column index (global if whitelist, else local)
        let col_idx: u64 = if whitelist_only {
            match global_bc_idx.get(barcode) {
                Some(&i) => i,
                None => {
                    acc.n_skipped_bc += 1;
                    continue;
                }
            }
        } else {
            match acc.bc_map.get(barcode) {
                Some(&i) => i as u64,
                None => {
                    let i = acc.bc_names.len() as u32;
                    let owned: Box<str> = barcode.into();
                    acc.bc_names.push(owned.clone());
                    acc.bc_map.insert(owned, i);
                    i as u64
                }
            }
        };

        let ckey = chr_key(chr);

        if use_peaks {
            let mut hit = false;
            if let Some(&chr_i) = peak_chr_idx.get(ckey) {
                let peaks = &peaks_by_chr[chr_i];
                let max_w = peak_max_width[chr_i];
                let lower = peaks.partition_point(|p| p.0 + max_w <= start);
                let upper = peaks.partition_point(|p| p.0 < end);
                for &(_, pe, ridx) in &peaks[lower..upper] {
                    if pe > start {
                        *acc.triplets.entry((ridx, col_idx)).or_insert(0.0) += cnt;
                        hit = true;
                    }
                }
            }
            if !hit {
                acc.n_no_overlap += 1;
            }
        } else {
            // bin mode: per-thread bin dict with local row indices
            let chr_map = if acc.bin_map.contains_key(ckey) {
                acc.bin_map.get_mut(ckey).unwrap()
            } else {
                let ck: Box<str> = ckey.into();
                acc.chr_display
                    .entry(ck.clone())
                    .or_insert_with(|| chr.into());
                acc.bin_map.entry(ck).or_default()
            };
            let first = start / bin_size;
            let last = (end - 1) / bin_size;
            for b in first..=last {
                let local_row: u32 = match chr_map.get(&b) {
                    Some(&r) => r,
                    None => {
                        let r = acc.bin_keys.len() as u32;
                        acc.bin_keys.push((ckey.into(), b));
                        chr_map.insert(b, r);
                        r
                    }
                };
                *acc.triplets
                    .entry((local_row as u64, col_idx))
                    .or_insert(0.0) += cnt;
            }
        }
    }

    acc
}

/// Build a progress bar matching the workspace style for the serial
/// streaming path (unknown total → spinner with fragment count).
fn streaming_fragments_progress() -> indicatif::ProgressBar {
    legume_numeric::matrix::progress::new_spinner("{spinner} streamed {pos} fragments ({per_sec})")
}

/// Preload-and-parse path: read decompressed bytes into memory, split
/// at newline boundaries, parse/aggregate per chunk with rayon, then
/// merge results into the caller's global state.
#[allow(clippy::too_many_arguments)]
fn run_fragments_preload_parallel(
    args: &FromFragmentsArgs,
    use_peaks: bool,
    bin_size: i64,
    whitelist_only: bool,
    peak_chr_idx: &rustc_hash::FxHashMap<Box<str>, usize>,
    peaks_by_chr: &[Vec<(i64, i64, u64)>],
    peak_max_width: &[i64],
    barcode_idx: &mut rustc_hash::FxHashMap<Box<str>, u64>,
    col_names: &mut Vec<Box<str>>,
    bin_row_idx: &mut rustc_hash::FxHashMap<Box<str>, rustc_hash::FxHashMap<i64, u64>>,
    bin_display_chr: &mut rustc_hash::FxHashMap<Box<str>, Box<str>>,
    row_names: &mut Vec<Box<str>>,
    triplet_map: &mut rustc_hash::FxHashMap<(u64, u64), f32>,
    n_total: &mut u64,
    n_skipped_bc: &mut u64,
    n_no_overlap: &mut u64,
    n_malformed: &mut u64,
) -> anyhow::Result<()> {
    use crate::sparse_data_visitors::styled_progress_bar;
    use indicatif::ParallelProgressIterator;
    use rayon::prelude::*;
    use std::io::Read;

    /////////////////////////////////////
    // Decompress entire file to bytes //
    /////////////////////////////////////
    info!("Preloading fragments from {}", args.fragments);
    let dec_pb = legume_numeric::matrix::progress::new_spinner(
        "{spinner} decompressing... {bytes} ({bytes_per_sec})",
    );
    let mut reader = open_fragments_reader(args.fragments.as_ref())?;
    let mut buf: Vec<u8> = Vec::with_capacity(1 << 24);
    // small read loop so the progress bar advances during long decompress
    let mut tmp = [0u8; 1 << 20];
    loop {
        let n = reader.read(&mut tmp)?;
        if n == 0 {
            break;
        }
        buf.extend_from_slice(&tmp[..n]);
        dec_pb.set_position(buf.len() as u64);
    }
    dec_pb.finish_and_clear();
    info!("Decompressed {} bytes", buf.len());

    ///////////////////////////////////////
    // Chunk & parallel parse+accumulate //
    ///////////////////////////////////////
    let n_threads = rayon::current_num_threads().max(1);
    let ranges = fragment_chunk_ranges(&buf, n_threads);
    info!(
        "Parsing with {} chunks across {} rayon threads",
        ranges.len(),
        n_threads
    );
    let prog_bar = styled_progress_bar(ranges.len() as u64, "chunks");
    let locals: Vec<FragLocalAccum> = ranges
        .par_iter()
        .progress_with(prog_bar.clone())
        .map(|&(lo, hi)| {
            process_fragments_chunk(
                &buf[lo..hi],
                use_peaks,
                bin_size,
                args.use_count,
                whitelist_only,
                peak_chr_idx,
                peaks_by_chr,
                peak_max_width,
                barcode_idx,
            )
        })
        .collect();
    prog_bar.finish_and_clear();
    drop(buf);

    ///////////////////////////////
    // Merge: barcodes (col idx) //
    ///////////////////////////////
    let mut col_remaps: Vec<Vec<u64>> = Vec::with_capacity(locals.len());
    if whitelist_only {
        // Local triplet keys already use global col idx; no remap.
        for _ in &locals {
            col_remaps.push(Vec::new());
        }
    } else {
        for local in &locals {
            let mut remap = Vec::with_capacity(local.bc_names.len());
            for bc in &local.bc_names {
                let gid = if let Some(&i) = barcode_idx.get(bc.as_ref()) {
                    i
                } else {
                    let i = col_names.len() as u64;
                    col_names.push(bc.clone());
                    barcode_idx.insert(bc.clone(), i);
                    i
                };
                remap.push(gid);
            }
            col_remaps.push(remap);
        }
    }

    ///////////////////////////
    // Merge: bins (row idx) //
    ///////////////////////////
    let mut row_remaps: Vec<Vec<u64>> = Vec::with_capacity(locals.len());
    if use_peaks {
        for _ in &locals {
            row_remaps.push(Vec::new());
        }
    } else {
        for local in &locals {
            let mut remap = Vec::with_capacity(local.bin_keys.len());
            for (ckey, bin_idx) in &local.bin_keys {
                // bin_display_chr keeps the first-seen display name across
                // threads, matching the serial path's behavior.
                bin_display_chr.entry(ckey.clone()).or_insert_with(|| {
                    local
                        .chr_display
                        .get(ckey.as_ref())
                        .cloned()
                        .unwrap_or_else(|| ckey.clone())
                });
                let chr_map = bin_row_idx.entry(ckey.clone()).or_default();
                let gid = if let Some(&r) = chr_map.get(bin_idx) {
                    r
                } else {
                    let r = row_names.len() as u64;
                    let display = bin_display_chr
                        .get(ckey.as_ref())
                        .map(|s| s.as_ref())
                        .unwrap_or_else(|| ckey.as_ref());
                    let bs = bin_idx * bin_size;
                    let be = (bin_idx + 1) * bin_size;
                    row_names.push(format!("{}:{}-{}", display, bs, be).into_boxed_str());
                    chr_map.insert(*bin_idx, r);
                    r
                };
                remap.push(gid);
            }
            row_remaps.push(remap);
        }
    }

    /////////////////////////////
    // Merge: triplets + stats //
    /////////////////////////////
    for (t, local) in locals.iter().enumerate() {
        *n_total += local.n_total;
        *n_skipped_bc += local.n_skipped_bc;
        *n_no_overlap += local.n_no_overlap;
        *n_malformed += local.n_malformed;

        let col_remap = &col_remaps[t];
        let row_remap = &row_remaps[t];
        for (&(r_or_local, c_or_local), &v) in local.triplets.iter() {
            let global_col = if whitelist_only {
                c_or_local
            } else {
                col_remap[c_or_local as usize]
            };
            let global_row = if use_peaks {
                r_or_local
            } else {
                row_remap[r_or_local as usize]
            };
            *triplet_map.entry((global_row, global_col)).or_insert(0.0) += v;
        }
    }

    Ok(())
}

/// Strip an optional `chr` / `Chr` / `CHR` prefix to get the canonical
/// chromosome key. This matches `genomic_data::coordinates::chr_stripped`
/// behavior so a peaks BED using `1` and a fragments file using `chr1`
/// (or vice versa) resolve to the same internal key.
fn chr_key(s: &str) -> &str {
    if s.len() >= 3 && s.as_bytes()[..3].eq_ignore_ascii_case(b"chr") {
        &s[3..]
    } else {
        s
    }
}

/// Open a fragments-like text file with bgzip-safe gzip support.
///
/// bgzip stores data as a series of concatenated gzip blocks, so the
/// standard `GzDecoder` would stop after the first block. `MultiGzDecoder`
/// reads all blocks and also handles ordinary single-block .gz files.
fn open_fragments_reader(path: &str) -> anyhow::Result<Box<dyn std::io::BufRead>> {
    use std::io::BufReader;
    let ext = std::path::Path::new(path)
        .extension()
        .and_then(|x| x.to_str());
    match ext {
        Some("gz") | Some("bgz") => {
            let f = std::fs::File::open(path)?;
            let dec = flate2::read::MultiGzDecoder::new(f);
            Ok(Box::new(BufReader::new(dec)))
        }
        _ => {
            let f = std::fs::File::open(path)?;
            Ok(Box::new(BufReader::new(f)))
        }
    }
}

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

    //////////////////////////////////////
    // chr_key prefix-stripping (units) //
    //////////////////////////////////////

    #[test]
    fn chr_key_strips_lowercase_prefix() {
        assert_eq!(chr_key("chr1"), "1");
        assert_eq!(chr_key("chr10"), "10");
        assert_eq!(chr_key("chrX"), "X");
        assert_eq!(chr_key("chrMT"), "MT");
    }

    #[test]
    fn chr_key_strips_mixed_case_prefix() {
        assert_eq!(chr_key("Chr1"), "1");
        assert_eq!(chr_key("CHR1"), "1");
        assert_eq!(chr_key("ChR21"), "21");
    }

    #[test]
    fn chr_key_passes_through_bare_names() {
        assert_eq!(chr_key("1"), "1");
        assert_eq!(chr_key("X"), "X");
        assert_eq!(chr_key("MT"), "MT");
    }

    #[test]
    fn chr_key_leaves_non_chr_prefixes_alone() {
        // "ch" is not the prefix we strip
        assert_eq!(chr_key("ch1"), "ch1");
        // contigs whose names happen to contain "chr" later on
        assert_eq!(chr_key("scaffold_1"), "scaffold_1");
        assert_eq!(chr_key("HLA-DRB1"), "HLA-DRB1");
        // short strings (<3 chars) can't have the prefix
        assert_eq!(chr_key("c"), "c");
        assert_eq!(chr_key("ch"), "ch");
        assert_eq!(chr_key(""), "");
    }

    ///////////////////////////////////////////////////
    // End-to-end: peaks with mixed chr/no-chr names //
    ///////////////////////////////////////////////////

    /// Peaks BED uses bare `1`/`2`, fragments file uses `chr1`/`chr2`.
    /// Without normalization, zero fragments would overlap any peak.
    #[test]
    fn from_fragments_normalizes_chr_prefix_across_peaks_and_fragments() {
        use std::io::Write;

        let tmp = tempfile::tempdir().unwrap();
        let frags_path = tmp.path().join("frags.tsv");
        let peaks_path = tmp.path().join("peaks.bed");
        let output_stem = tmp.path().join("out");
        let output_stem_str = output_stem.to_str().unwrap().to_string();

        // Fragments use UCSC naming.
        {
            let mut f = std::fs::File::create(&frags_path).unwrap();
            writeln!(f, "# header line should be skipped").unwrap();
            writeln!(f, "chr1\t100\t250\tBC_A\t1").unwrap();
            writeln!(f, "chr1\t200\t450\tBC_A\t1").unwrap();
            writeln!(f, "chr1\t5100\t5300\tBC_B\t2").unwrap();
            writeln!(f, "chr2\t7000\t7400\tBC_A\t1").unwrap();
            writeln!(f, "chr2\t7000\t7400\tBC_C\t1").unwrap();
        }

        // Peaks use Ensembl-style bare chromosome names.
        {
            let mut f = std::fs::File::create(&peaks_path).unwrap();
            writeln!(f, "1\t0\t500").unwrap();
            writeln!(f, "1\t5000\t5500").unwrap();
            writeln!(f, "2\t7000\t8000").unwrap();
        }

        let args = FromFragmentsArgs {
            fragments: frags_path.to_str().unwrap().into(),
            backend: SparseIoBackend::Zarr,
            output: output_stem_str.clone().into(),
            zip: false,
            peaks: Some(peaks_path.to_str().unwrap().into()),
            bin_size: 0,
            barcodes: None,
            use_count: false,
            preload_data: false,
            do_squeeze: false,
            row_nnz_cutoff: 1,
            column_nnz_cutoff: 1,
            block_size: None,
        };

        run_build_from_fragments(&args).unwrap();

        // Open the backend that was just written and check shape + names.
        let backend_path = format!("{}.zarr", output_stem_str);
        let data = open_sparse_matrix(&backend_path, &SparseIoBackend::Zarr).unwrap();

        assert_eq!(data.num_rows(), Some(3));
        assert_eq!(data.num_columns(), Some(3));

        let row_names = data.row_names().unwrap();
        // Row display names come straight from the BED file (no `chr`).
        assert_eq!(row_names[0].as_ref(), "1:0-500");
        assert_eq!(row_names[1].as_ref(), "1:5000-5500");
        assert_eq!(row_names[2].as_ref(), "2:7000-8000");

        let col_names = data.column_names().unwrap();
        assert_eq!(col_names[0].as_ref(), "BC_A");
        assert_eq!(col_names[1].as_ref(), "BC_B");
        assert_eq!(col_names[2].as_ref(), "BC_C");

        // Read full matrix and verify counts. Per fragments above:
        //   peak `1:0-500`     ← BC_A: 2 (two overlapping chr1 frags)
        //   peak `1:5000-5500` ← BC_B: 1 (chr1 5100-5300)
        //   peak `2:7000-8000` ← BC_A: 1, BC_C: 1
        let mat = data.read_columns_dmatrix(vec![0, 1, 2]).unwrap();
        assert_eq!(mat[(0, 0)], 2.0); // BC_A @ 1:0-500
        assert_eq!(mat[(0, 1)], 0.0);
        assert_eq!(mat[(0, 2)], 0.0);
        assert_eq!(mat[(1, 0)], 0.0);
        assert_eq!(mat[(1, 1)], 1.0); // BC_B @ 1:5000-5500
        assert_eq!(mat[(1, 2)], 0.0);
        assert_eq!(mat[(2, 0)], 1.0); // BC_A @ 2:7000-8000
        assert_eq!(mat[(2, 1)], 0.0);
        assert_eq!(mat[(2, 2)], 1.0); // BC_C @ 2:7000-8000
    }

    /// Symmetric case: peaks BED uses `chr1`, fragments use `1` — the same
    /// counts should fall out.
    #[test]
    fn from_fragments_normalizes_chr_prefix_reverse_direction() {
        use std::io::Write;

        let tmp = tempfile::tempdir().unwrap();
        let frags_path = tmp.path().join("frags.tsv");
        let peaks_path = tmp.path().join("peaks.bed");
        let output_stem = tmp.path().join("out");
        let output_stem_str = output_stem.to_str().unwrap().to_string();

        {
            let mut f = std::fs::File::create(&frags_path).unwrap();
            writeln!(f, "1\t100\t250\tBC_A").unwrap();
            writeln!(f, "1\t200\t450\tBC_A").unwrap();
        }
        {
            let mut f = std::fs::File::create(&peaks_path).unwrap();
            writeln!(f, "chr1\t0\t500").unwrap();
        }

        let args = FromFragmentsArgs {
            fragments: frags_path.to_str().unwrap().into(),
            backend: SparseIoBackend::Zarr,
            output: output_stem_str.clone().into(),
            zip: false,
            peaks: Some(peaks_path.to_str().unwrap().into()),
            bin_size: 0,
            barcodes: None,
            use_count: false,
            preload_data: false,
            do_squeeze: false,
            row_nnz_cutoff: 1,
            column_nnz_cutoff: 1,
            block_size: None,
        };

        run_build_from_fragments(&args).unwrap();

        let backend_path = format!("{}.zarr", output_stem_str);
        let data = open_sparse_matrix(&backend_path, &SparseIoBackend::Zarr).unwrap();
        assert_eq!(data.num_rows(), Some(1));
        assert_eq!(data.num_columns(), Some(1));

        let mat = data.read_columns_dmatrix(vec![0]).unwrap();
        assert_eq!(mat[(0, 0)], 2.0);
    }

    /// Bin mode: when fragments mix `chr1` and `1`, both should land in the
    /// same bin row (because the canonical key strips the prefix).
    #[test]
    fn from_fragments_bin_mode_merges_mixed_naming() {
        use std::io::Write;

        let tmp = tempfile::tempdir().unwrap();
        let frags_path = tmp.path().join("frags.tsv");
        let output_stem = tmp.path().join("out");
        let output_stem_str = output_stem.to_str().unwrap().to_string();

        {
            let mut f = std::fs::File::create(&frags_path).unwrap();
            // Same bin (chr1, 0-1000) accessed under two naming conventions.
            writeln!(f, "chr1\t100\t200\tBC_A").unwrap();
            writeln!(f, "1\t300\t400\tBC_A").unwrap();
        }

        let args = FromFragmentsArgs {
            fragments: frags_path.to_str().unwrap().into(),
            backend: SparseIoBackend::Zarr,
            output: output_stem_str.clone().into(),
            zip: false,
            peaks: None,
            bin_size: 1000,
            barcodes: None,
            use_count: false,
            preload_data: false,
            do_squeeze: false,
            row_nnz_cutoff: 1,
            column_nnz_cutoff: 1,
            block_size: None,
        };

        run_build_from_fragments(&args).unwrap();

        let backend_path = format!("{}.zarr", output_stem_str);
        let data = open_sparse_matrix(&backend_path, &SparseIoBackend::Zarr).unwrap();
        // Single canonical bin, regardless of mixed naming.
        assert_eq!(data.num_rows(), Some(1));
        assert_eq!(data.num_columns(), Some(1));

        // Display name uses the first chr string we saw (chr1).
        let row_names = data.row_names().unwrap();
        assert_eq!(row_names[0].as_ref(), "chr1:0-1000");

        let mat = data.read_columns_dmatrix(vec![0]).unwrap();
        assert_eq!(mat[(0, 0)], 2.0);
    }

    ///////////////////////////////////////////////////////////////
    // --preload-data parity: parallel path must produce exactly //
    // the same row names, column names, and matrix entries as   //
    // the serial path.                                          //
    ///////////////////////////////////////////////////////////////

    fn run_pair_and_compare(args_serial: FromFragmentsArgs, args_parallel: FromFragmentsArgs) {
        let out_serial = format!("{}.zarr", &args_serial.output);
        let out_parallel = format!("{}.zarr", &args_parallel.output);
        run_build_from_fragments(&args_serial).unwrap();
        run_build_from_fragments(&args_parallel).unwrap();
        let a = open_sparse_matrix(&out_serial, &SparseIoBackend::Zarr).unwrap();
        let b = open_sparse_matrix(&out_parallel, &SparseIoBackend::Zarr).unwrap();
        assert_eq!(a.num_rows(), b.num_rows());
        assert_eq!(a.num_columns(), b.num_columns());
        assert_eq!(a.row_names().unwrap(), b.row_names().unwrap());
        assert_eq!(a.column_names().unwrap(), b.column_names().unwrap());
        let ncols = a.num_columns().unwrap();
        let cols: Vec<usize> = (0..ncols).collect();
        let ma = a.read_columns_dmatrix(cols.clone()).unwrap();
        let mb = b.read_columns_dmatrix(cols).unwrap();
        assert_eq!(ma, mb);
    }

    #[test]
    fn from_fragments_preload_matches_serial_peaks_mode() {
        use std::io::Write;
        let tmp = tempfile::tempdir().unwrap();
        let frags_path = tmp.path().join("frags.tsv");
        let peaks_path = tmp.path().join("peaks.bed");
        let out_s = tmp.path().join("serial").to_str().unwrap().to_string();
        let out_p = tmp.path().join("parallel").to_str().unwrap().to_string();

        // Enough rows to exercise multiple rayon chunks.
        {
            let mut f = std::fs::File::create(&frags_path).unwrap();
            writeln!(f, "# header line").unwrap();
            let barcodes = ["BC_A", "BC_B", "BC_C", "BC_D", "BC_E"];
            for i in 0..2000 {
                let chr = if i % 2 == 0 { "chr1" } else { "chr2" };
                let s = (i as i64) * 37;
                let e = s + 150;
                let bc = barcodes[i % barcodes.len()];
                writeln!(f, "{}\t{}\t{}\t{}", chr, s, e, bc).unwrap();
            }
        }
        {
            let mut f = std::fs::File::create(&peaks_path).unwrap();
            writeln!(f, "1\t0\t10000").unwrap();
            writeln!(f, "1\t10000\t20000").unwrap();
            writeln!(f, "2\t0\t10000").unwrap();
            writeln!(f, "2\t10000\t20000").unwrap();
        }

        let base = FromFragmentsArgs {
            fragments: frags_path.to_str().unwrap().into(),
            backend: SparseIoBackend::Zarr,
            output: out_s.clone().into(),
            zip: false,
            peaks: Some(peaks_path.to_str().unwrap().into()),
            bin_size: 0,
            barcodes: None,
            use_count: false,
            preload_data: false,
            do_squeeze: false,
            row_nnz_cutoff: 1,
            column_nnz_cutoff: 1,
            block_size: None,
        };
        let par = FromFragmentsArgs {
            output: out_p.into(),
            preload_data: true,
            fragments: base.fragments.clone(),
            backend: base.backend.clone(),
            zip: base.zip,
            peaks: base.peaks.clone(),
            bin_size: base.bin_size,
            barcodes: base.barcodes.clone(),
            use_count: base.use_count,
            do_squeeze: base.do_squeeze,
            row_nnz_cutoff: base.row_nnz_cutoff,
            column_nnz_cutoff: base.column_nnz_cutoff,
            block_size: base.block_size,
        };
        run_pair_and_compare(base, par);
    }

    #[test]
    fn from_fragments_preload_matches_serial_bin_mode() {
        use std::io::Write;
        let tmp = tempfile::tempdir().unwrap();
        let frags_path = tmp.path().join("frags.tsv");
        let out_s = tmp.path().join("serial").to_str().unwrap().to_string();
        let out_p = tmp.path().join("parallel").to_str().unwrap().to_string();

        {
            let mut f = std::fs::File::create(&frags_path).unwrap();
            let barcodes = ["BC_A", "BC_B", "BC_C"];
            for i in 0..1500 {
                let chr = if i % 3 == 0 { "chr1" } else { "chr2" };
                let s = (i as i64) * 100;
                let e = s + 200;
                let bc = barcodes[i % barcodes.len()];
                writeln!(f, "{}\t{}\t{}\t{}", chr, s, e, bc).unwrap();
            }
        }

        let base = FromFragmentsArgs {
            fragments: frags_path.to_str().unwrap().into(),
            backend: SparseIoBackend::Zarr,
            output: out_s.clone().into(),
            zip: false,
            peaks: None,
            bin_size: 1000,
            barcodes: None,
            use_count: false,
            preload_data: false,
            do_squeeze: false,
            row_nnz_cutoff: 1,
            column_nnz_cutoff: 1,
            block_size: None,
        };
        let par = FromFragmentsArgs {
            output: out_p.into(),
            preload_data: true,
            fragments: base.fragments.clone(),
            backend: base.backend.clone(),
            zip: base.zip,
            peaks: base.peaks.clone(),
            bin_size: base.bin_size,
            barcodes: base.barcodes.clone(),
            use_count: base.use_count,
            do_squeeze: base.do_squeeze,
            row_nnz_cutoff: base.row_nnz_cutoff,
            column_nnz_cutoff: base.column_nnz_cutoff,
            block_size: base.block_size,
        };
        run_pair_and_compare(base, par);
    }
}