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Push ywwwypqxrtmy #14

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coissac merged 6 commits from push-ywwwypqxrtmy into main 2026-06-03 13:18:41 +00:00
Conversation 0 Commits 6 Files Changed 34
+799 -271
20 changed files with 799 additions and 271 deletions
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Showing only changes of commit 173ac9fb42 - Show all commits
src/obicompactvec/src/bitmatrix.rs
+235 -50
View File
@@ -1,22 +1,29 @@
use std::{fs, io, path::{Path, PathBuf}};
use std::fs::{self, File};
use std::io::{self, Write as _};
use std::path::{Path, PathBuf};
use memmap2::Mmap;
use ndarray::{Array1, Array2};
use rayon::prelude::*;
use crate::bitvec::{PersistentBitVec, PersistentBitVecBuilder};
use crate::layer_meta::LayerMeta;
use crate::meta::MatrixMeta;
fn col_path(dir: &Path, col: usize) -> PathBuf {
dir.join(format!("col_{col:06}.pbiv"))
}
pub struct PersistentBitMatrix {
// ── ColumnarBitMatrix ─────────────────────────────────────────────────────────
/// Per-column file layout (original format).
pub struct ColumnarBitMatrix {
cols: Vec<PersistentBitVec>,
n: usize,
}
impl PersistentBitMatrix {
pub fn open(dir: &Path) -> io::Result<Self> {
impl ColumnarBitMatrix {
pub(crate) fn open(dir: &Path) -> io::Result<Self> {
let meta = MatrixMeta::load(dir)?;
let cols = (0..meta.n_cols)
.map(|c| PersistentBitVec::open(&col_path(dir, c)))
@@ -24,24 +31,21 @@ impl PersistentBitMatrix {
Ok(Self { cols, n: meta.n })
}
pub fn n(&self) -> usize { self.n }
pub fn n_cols(&self) -> usize { self.cols.len() }
pub fn col(&self, c: usize) -> &PersistentBitVec { &self.cols[c] }
pub(crate) fn n(&self) -> usize { self.n }
pub(crate) fn n_cols(&self) -> usize { self.cols.len() }
pub(crate) fn col(&self, c: usize) -> &PersistentBitVec { &self.cols[c] }
pub fn row(&self, slot: usize) -> Box<[bool]> {
pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
self.cols.iter().map(|c| c.get(slot)).collect()
}
/// Fill `buf[i]` with `col_i[slot]` as 0/1 u32, without allocating.
/// `buf` must have length ≥ `self.n_cols()`.
pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
for (c, col) in self.cols.iter().enumerate() {
buf[c] = col.get(slot) as u32;
}
}
/// Returns the number of set bits in each column as `Array1<u64>`.
pub fn count_ones(&self) -> Array1<u64> {
pub(crate) fn count_ones(&self) -> Array1<u64> {
let counts: Vec<u64> = (0..self.n_cols())
.into_par_iter()
.map(|c| self.col(c).count_ones())
@@ -49,21 +53,15 @@ impl PersistentBitMatrix {
Array1::from_vec(counts)
}
// ── Distance matrices ─────────────────────────────────────────────────────
pub fn jaccard_dist_matrix(&self) -> Array2<f64> {
pub(crate) fn jaccard_dist_matrix(&self) -> Array2<f64> {
self.pairwise_f64(|i, j| self.col(i).jaccard_dist(self.col(j)))
}
pub fn hamming_dist_matrix(&self) -> Array2<u64> {
pub(crate) fn hamming_dist_matrix(&self) -> Array2<u64> {
self.pairwise_u64(|i, j| self.col(i).hamming_dist(self.col(j)))
}
// ── Partial matrices (additively decomposable across layers) ──────────────
/// Returns `(inter[n×n], union[n×n])`.
/// Reduce across layers by element-wise addition before computing `1 - inter/union`.
pub fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
pub(crate) fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
let n = self.n_cols();
let results: Vec<(usize, usize, u64, u64)> = upper_pairs(n)
.into_par_iter()
@@ -72,7 +70,6 @@ impl PersistentBitMatrix {
(i, j, inter, union)
})
.collect();
let mut inter_m = Array2::zeros((n, n));
let mut union_m = Array2::zeros((n, n));
for (i, j, inter, union) in results {
@@ -82,14 +79,10 @@ impl PersistentBitMatrix {
(inter_m, union_m)
}
/// Returns `hamming[n×n]` (number of differing bits per pair).
/// Additive across layers — reduce by element-wise addition.
pub fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
pub(crate) fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
self.pairwise_u64(|i, j| self.col(i).hamming_dist(self.col(j)))
}
// ── Private helpers ───────────────────────────────────────────────────────
fn pairwise_f64(&self, f: impl Fn(usize, usize) -> f64 + Sync) -> Array2<f64> {
let n = self.n_cols();
let results: Vec<(usize, usize, f64)> = upper_pairs(n)
@@ -107,17 +100,8 @@ impl PersistentBitMatrix {
.collect();
fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
}
}
// ── Column append ─────────────────────────────────────────────────────────────
impl PersistentBitMatrix {
/// Append a new column to an existing matrix on disk.
///
/// Reads `meta.json` to obtain `n` and the current column count, writes
/// `col_{n_cols:06}.pbiv` filled by `value_of(slot)`, then increments
/// `n_cols` in `meta.json`.
pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
pub(crate) fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
let mut meta = MatrixMeta::load(dir)?;
let mut b = PersistentBitVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
for slot in 0..meta.n {
@@ -129,20 +113,208 @@ impl PersistentBitMatrix {
}
}
fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
(0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
// ── PackedBitMatrix ───────────────────────────────────────────────────────────
const PBMX_MAGIC: [u8; 4] = *b"PBMX";
const PBMX_HEADER: usize = 24; // magic(4) + pad(4) + n_rows(8) + n_cols(8)
const PBIV_HEADER: usize = 16; // magic(4) + pad(4) + n(8)
/// Single-file packed layout: all columns concatenated behind a header.
pub struct PackedBitMatrix {
mmap: Mmap,
n_rows: usize,
n_cols: usize,
/// Absolute byte offset to the start of each column's bit data
/// (= file offset of the PBIV blob + PBIV_HEADER).
data_offsets: Vec<usize>,
}
fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
where
T: Clone + Default,
{
let mut m = Array2::from_elem((n, n), T::default());
for (i, j, vij, vji) in vals {
m[[i, j]] = vij;
m[[j, i]] = vji;
impl PackedBitMatrix {
pub(crate) fn open(path: &Path) -> io::Result<Self> {
let mmap = unsafe { Mmap::map(&File::open(path)?)? };
if mmap.len() < PBMX_HEADER {
return Err(io::Error::new(io::ErrorKind::InvalidData, "PBMX file too short"));
}
if &mmap[0..4] != &PBMX_MAGIC {
return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PBMX magic"));
}
let n_rows = u64::from_le_bytes(mmap[8..16].try_into().unwrap()) as usize;
let n_cols = u64::from_le_bytes(mmap[16..24].try_into().unwrap()) as usize;
let mut data_offsets = Vec::with_capacity(n_cols);
for c in 0..n_cols {
let off_pos = PBMX_HEADER + c * 8;
let col_file_off = u64::from_le_bytes(mmap[off_pos..off_pos+8].try_into().unwrap()) as usize;
data_offsets.push(col_file_off + PBIV_HEADER);
}
Ok(Self { mmap, n_rows, n_cols, data_offsets })
}
#[inline]
pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
for (c, &data_off) in self.data_offsets.iter().enumerate() {
buf[c] = ((self.mmap[data_off + (slot >> 3)] >> (slot & 7)) & 1) as u32;
}
}
pub(crate) fn row(&self, slot: usize) -> Box<[bool]> {
(0..self.n_cols).map(|c| {
(self.mmap[self.data_offsets[c] + (slot >> 3)] >> (slot & 7)) & 1 != 0
}).collect()
}
}
/// Build `presence/matrix.pbmx` from existing `col_*.pbiv` files.
pub fn pack_bit_matrix(dir: &Path) -> io::Result<()> {
let meta = MatrixMeta::load(dir)?;
let n_cols = meta.n_cols;
let col_files: Vec<Vec<u8>> = (0..n_cols)
.map(|c| fs::read(col_path(dir, c)))
.collect::<io::Result<_>>()?;
let header_size = PBMX_HEADER + n_cols * 8;
let mut col_offset = header_size;
let mut offsets = Vec::with_capacity(n_cols);
for data in &col_files {
offsets.push(col_offset as u64);
col_offset += data.len();
}
let packed_path = dir.join("matrix.pbmx");
let mut file = File::create(&packed_path)?;
file.write_all(&PBMX_MAGIC)?;
file.write_all(&[0u8; 4])?;
file.write_all(&(meta.n as u64).to_le_bytes())?;
file.write_all(&(n_cols as u64).to_le_bytes())?;
for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
for data in &col_files { file.write_all(data)?; }
Ok(())
}
// ── PersistentBitMatrix — public enum ────────────────────────────────────────
/// Bit matrix that transparently handles columnar, packed, and implicit formats.
///
/// - `Columnar`: per-column `.pbiv` files (original format, used during build)
/// - `Packed`: single `matrix.pbmx` file (optimised for query — one `mmap`)
/// - `Implicit`: no file — all values are 1 (mono-genome presence/absence)
pub enum PersistentBitMatrix {
Columnar(ColumnarBitMatrix),
Packed(PackedBitMatrix),
Implicit { n_rows: usize, n_cols: usize },
}
impl PersistentBitMatrix {
/// Open from `layer_dir`, auto-detecting the format.
///
/// Checks (in order):
/// 1. `layer_dir/presence/matrix.pbmx` → Packed
/// 2. `layer_dir/presence/meta.json` → Columnar
/// 3. `layer_dir/layer_meta.json` → Implicit (new index)
/// 4. `layer_dir/unitigs.bin` → Implicit with warning (old index)
pub fn open(layer_dir: &Path) -> io::Result<Self> {
let presence_dir = layer_dir.join("presence");
if presence_dir.join("matrix.pbmx").exists() {
return Ok(Self::Packed(PackedBitMatrix::open(&presence_dir.join("matrix.pbmx"))?));
}
if MatrixMeta::load(&presence_dir).is_ok() {
return Ok(Self::Columnar(ColumnarBitMatrix::open(&presence_dir)?));
}
// No presence matrix → Implicit; requires layer_meta.json
let meta = LayerMeta::load(layer_dir).map_err(|_| io::Error::new(
io::ErrorKind::NotFound,
format!(
"no presence matrix and no layer_meta.json in {} — run 'obikmer upgrade'",
layer_dir.display()
),
))?;
Ok(Self::Implicit { n_rows: meta.n, n_cols: 1 })
}
pub fn n(&self) -> usize {
match self {
Self::Columnar(m) => m.n(),
Self::Packed(m) => m.n_rows,
Self::Implicit { n_rows, .. } => *n_rows,
}
}
pub fn n_cols(&self) -> usize {
match self {
Self::Columnar(m) => m.n_cols(),
Self::Packed(m) => m.n_cols,
Self::Implicit { n_cols, .. } => *n_cols,
}
}
pub fn col(&self, c: usize) -> &PersistentBitVec {
match self {
Self::Columnar(m) => m.col(c),
_ => panic!("col() only available on Columnar PersistentBitMatrix"),
}
}
pub fn row(&self, slot: usize) -> Box<[bool]> {
match self {
Self::Columnar(m) => m.row(slot),
Self::Packed(m) => m.row(slot),
Self::Implicit { n_cols, .. } => vec![true; *n_cols].into_boxed_slice(),
}
}
/// Fill `buf[i]` with `col_i[slot]` as 0/1 u32, without allocating.
pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
match self {
Self::Columnar(m) => m.fill_row(slot, buf),
Self::Packed(m) => m.fill_row(slot, buf),
Self::Implicit { n_cols, .. } => buf[..*n_cols].fill(1),
}
}
pub fn count_ones(&self) -> Array1<u64> {
match self {
Self::Columnar(m) => m.count_ones(),
_ => panic!("count_ones() only available on Columnar PersistentBitMatrix"),
}
}
pub fn jaccard_dist_matrix(&self) -> Array2<f64> {
match self {
Self::Columnar(m) => m.jaccard_dist_matrix(),
_ => panic!("jaccard_dist_matrix() only available on Columnar PersistentBitMatrix"),
}
}
pub fn hamming_dist_matrix(&self) -> Array2<u64> {
match self {
Self::Columnar(m) => m.hamming_dist_matrix(),
_ => panic!("hamming_dist_matrix() only available on Columnar PersistentBitMatrix"),
}
}
pub fn partial_jaccard_dist_matrix(&self) -> (Array2<u64>, Array2<u64>) {
match self {
Self::Columnar(m) => m.partial_jaccard_dist_matrix(),
_ => panic!("partial_jaccard_dist_matrix() only available on Columnar PersistentBitMatrix"),
}
}
pub fn partial_hamming_dist_matrix(&self) -> Array2<u64> {
match self {
Self::Columnar(m) => m.partial_hamming_dist_matrix(),
_ => panic!("partial_hamming_dist_matrix() only available on Columnar PersistentBitMatrix"),
}
}
/// Append a new column to an on-disk Columnar matrix.
pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> bool) -> io::Result<()> {
ColumnarBitMatrix::append_column(dir, value_of)
}
m
}
// ── Trait impls ───────────────────────────────────────────────────────────────
@@ -162,7 +334,7 @@ impl BitPartials for PersistentBitMatrix {
}
}
// ── Builder ───────────────────────────────────────────────────────────────────
// ── Builder (unchanged — always builds Columnar) ──────────────────────────────
pub struct PersistentBitMatrixBuilder {
dir: PathBuf,
@@ -189,3 +361,16 @@ impl PersistentBitMatrixBuilder {
MatrixMeta { n: self.n, n_cols: self.n_cols }.save(&self.dir)
}
}
// ── Helpers ───────────────────────────────────────────────────────────────────
fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
(0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
}
fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
where T: Clone + Default {
let mut m = Array2::from_elem((n, n), T::default());
for (i, j, vij, vji) in vals { m[[i, j]] = vij; m[[j, i]] = vji; }
m
}
src/obicompactvec/src/intmatrix.rs
+307 -140
View File
@@ -1,9 +1,14 @@
use std::{fs, io, path::{Path, PathBuf}};
use std::cmp::Ordering;
use std::fs::{self, File};
use std::io::{self, Write as _};
use std::path::{Path, PathBuf};
use memmap2::Mmap;
use ndarray::{Array1, Array2};
use rayon::prelude::*;
use crate::builder::PersistentCompactIntVecBuilder;
use crate::format::{HEADER_SIZE, INDEX_ENTRY_SIZE, OVERFLOW_ENTRY_SIZE};
use crate::meta::MatrixMeta;
use crate::reader::PersistentCompactIntVec;
@@ -11,13 +16,15 @@ fn col_path(dir: &Path, col: usize) -> PathBuf {
dir.join(format!("col_{col:06}.pciv"))
}
pub struct PersistentCompactIntMatrix {
// ── ColumnarCompactIntMatrix ──────────────────────────────────────────────────
pub struct ColumnarCompactIntMatrix {
cols: Vec<PersistentCompactIntVec>,
n: usize,
}
impl PersistentCompactIntMatrix {
pub fn open(dir: &Path) -> io::Result<Self> {
impl ColumnarCompactIntMatrix {
pub(crate) fn open(dir: &Path) -> io::Result<Self> {
let meta = MatrixMeta::load(dir)?;
let cols = (0..meta.n_cols)
.map(|c| PersistentCompactIntVec::open(&col_path(dir, c)))
@@ -25,25 +32,29 @@ impl PersistentCompactIntMatrix {
Ok(Self { cols, n: meta.n })
}
pub fn n(&self) -> usize { self.n }
pub fn n_cols(&self) -> usize { self.cols.len() }
pub fn col(&self, c: usize) -> &PersistentCompactIntVec { &self.cols[c] }
pub(crate) fn n(&self) -> usize { self.n }
pub(crate) fn n_cols(&self) -> usize { self.cols.len() }
pub(crate) fn col(&self, c: usize) -> &PersistentCompactIntVec { &self.cols[c] }
pub fn row(&self, slot: usize) -> Box<[u32]> {
pub(crate) fn row(&self, slot: usize) -> Box<[u32]> {
self.cols.iter().map(|c| c.get(slot)).collect()
}
/// Fill `buf[i]` with `col_i[slot]`, without allocating.
/// `buf` must have length ≥ `self.n_cols()`.
pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
for (c, col) in self.cols.iter().enumerate() {
buf[c] = col.get(slot);
}
}
// ── Distance matrices ─────────────────────────────────────────────────────
pub(crate) fn sum(&self) -> Array1<u64> {
let sums: Vec<u64> = (0..self.n_cols())
.into_par_iter()
.map(|c| self.col(c).sum())
.collect();
Array1::from_vec(sums)
}
pub fn bray_dist_matrix(&self) -> Array2<f64> {
pub(crate) fn bray_dist_matrix(&self) -> Array2<f64> {
let sum_min = self.partial_bray_dist_matrix();
let col_sums = self.sum();
let n = self.n_cols();
@@ -60,63 +71,19 @@ impl PersistentCompactIntMatrix {
m
}
pub fn relfreq_bray_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).relfreq_bray_dist(self.col(j)))
}
pub fn euclidean_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).euclidean_dist(self.col(j)))
}
pub fn relfreq_euclidean_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).relfreq_euclidean_dist(self.col(j)))
}
pub fn hellinger_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).hellinger_dist(self.col(j)))
}
pub fn jaccard_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).jaccard_dist(self.col(j)))
}
pub fn threshold_jaccard_dist_matrix(&self, threshold: u32) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).threshold_jaccard_dist(self.col(j), threshold))
}
/// Returns the sum of each column as `Array1<u64>`.
pub fn sum(&self) -> Array1<u64> {
let sums: Vec<u64> = (0..self.n_cols())
.into_par_iter()
.map(|c| self.col(c).sum())
.collect();
Array1::from_vec(sums)
}
// ── Partial matrices (additively decomposable across layers) ──────────────
/// Returns `sum_min[n×n]` where `sum_min[i,j]` = Σ_slot min(col_i[slot], col_j[slot]).
/// The denominator `col_sums[i] + col_sums[j]` is obtained from `self.sum()`.
/// Additive across layers by element-wise addition.
pub fn partial_bray_dist_matrix(&self) -> Array2<u64> {
pub(crate) fn partial_bray_dist_matrix(&self) -> Array2<u64> {
self.pairwise_u64(|i, j| self.col(i).partial_bray_dist(self.col(j)))
}
/// Returns sum of squared differences `[n×n]`.
/// Reduce across layers by element-wise addition, then take `sqrt` for the final distance.
pub fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
pub(crate) fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).partial_euclidean_dist(self.col(j)))
}
/// Returns `(inter[n×n], union[n×n])` for threshold-Jaccard.
/// Reduce across layers by element-wise addition before computing `1 - inter/union`.
pub fn partial_threshold_jaccard_dist_matrix(
&self,
threshold: u32,
pub(crate) fn partial_threshold_jaccard_dist_matrix(
&self, threshold: u32,
) -> (Array2<u64>, Array2<u64>) {
let n = self.n_cols();
let pairs = upper_pairs(n);
let results: Vec<(usize, usize, u64, u64)> = pairs
.into_par_iter()
.map(|(i, j)| {
@@ -125,7 +92,6 @@ impl PersistentCompactIntMatrix {
(i, j, inter, union)
})
.collect();
let mut inter_m = Array2::zeros((n, n));
let mut union_m = Array2::zeros((n, n));
for (i, j, inter, union) in results {
@@ -135,99 +101,299 @@ impl PersistentCompactIntMatrix {
(inter_m, union_m)
}
/// Returns matrix of `Σ_slot min(col_i[slot]/sum_i, col_j[slot]/sum_j)` per pair.
/// `col_sums` must be the GLOBAL sums across all layers/partitions.
/// Reduce across layers by element-wise addition; final distance = `1 - value`.
pub fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
pub(crate) fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
self.pairwise(|i, j| {
self.col(i).partial_relfreq_bray_dist(
self.col(j),
col_sums[i] as f64,
col_sums[j] as f64,
)
self.col(i).partial_relfreq_bray_dist(self.col(j), col_sums[i] as f64, col_sums[j] as f64)
})
}
/// Returns matrix of `Σ_slot (col_i[slot]/sum_i - col_j[slot]/sum_j)²` per pair.
/// `col_sums` must be the GLOBAL sums across all layers/partitions.
/// Reduce across layers by element-wise addition; final distance = `sqrt(value)`.
pub fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
pub(crate) fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
self.pairwise(|i, j| {
self.col(i).partial_relfreq_euclidean_dist(
self.col(j),
col_sums[i] as f64,
col_sums[j] as f64,
)
self.col(i).partial_relfreq_euclidean_dist(self.col(j), col_sums[i] as f64, col_sums[j] as f64)
})
}
/// Returns matrix of `Σ_slot (√(col_i/sum_i) - √(col_j/sum_j))²` per pair.
/// `col_sums` must be the GLOBAL sums across all layers/partitions.
/// Reduce across layers by element-wise addition; final distance = `sqrt(value) / √2`.
pub fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
pub(crate) fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
self.pairwise(|i, j| {
self.col(i).partial_hellinger_euclidean_dist(
self.col(j),
col_sums[i] as f64,
col_sums[j] as f64,
)
self.col(i).partial_hellinger_euclidean_dist(self.col(j), col_sums[i] as f64, col_sums[j] as f64)
})
}
// ── Private helpers ───────────────────────────────────────────────────────
pub(crate) fn relfreq_bray_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).relfreq_bray_dist(self.col(j)))
}
pub(crate) fn euclidean_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).euclidean_dist(self.col(j)))
}
pub(crate) fn relfreq_euclidean_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).relfreq_euclidean_dist(self.col(j)))
}
pub(crate) fn hellinger_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).hellinger_dist(self.col(j)))
}
pub(crate) fn jaccard_dist_matrix(&self) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).jaccard_dist(self.col(j)))
}
pub(crate) fn threshold_jaccard_dist_matrix(&self, threshold: u32) -> Array2<f64> {
self.pairwise(|i, j| self.col(i).threshold_jaccard_dist(self.col(j), threshold))
}
pub(crate) fn append_column(dir: &Path, value_of: impl Fn(usize) -> u32) -> io::Result<()> {
let mut meta = MatrixMeta::load(dir)?;
let mut b = PersistentCompactIntVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
for slot in 0..meta.n { b.set(slot, value_of(slot)); }
b.close()?;
meta.n_cols += 1;
meta.save(dir)
}
fn pairwise(&self, f: impl Fn(usize, usize) -> f64 + Sync) -> Array2<f64> {
let n = self.n_cols();
let results: Vec<(usize, usize, f64)> = upper_pairs(n)
.into_par_iter()
.map(|(i, j)| (i, j, f(i, j)))
.collect();
.into_par_iter().map(|(i, j)| (i, j, f(i, j))).collect();
fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
}
fn pairwise_u64(&self, f: impl Fn(usize, usize) -> u64 + Sync) -> Array2<u64> {
let n = self.n_cols();
let results: Vec<(usize, usize, u64)> = upper_pairs(n)
.into_par_iter()
.map(|(i, j)| (i, j, f(i, j)))
.collect();
.into_par_iter().map(|(i, j)| (i, j, f(i, j))).collect();
fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
}
}
fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
(0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
// ── PackedCompactIntMatrix ────────────────────────────────────────────────────
const PCMX_MAGIC: [u8; 4] = *b"PCMX";
const PCMX_HEADER: usize = 24; // magic(4) + pad(4) + n_rows(8) + n_cols(8)
/// Per-column metadata pre-parsed from the embedded PCIV header.
struct ColInfo {
primary_start: usize, // absolute mmap offset to primary array
data_offset: usize, // absolute mmap offset to overflow array
n_overflow: usize,
step: usize,
index: Vec<(usize, usize)>,
}
fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
where
T: Clone + Default,
{
let mut m = Array2::from_elem((n, n), T::default());
for (i, j, vij, vji) in vals {
m[[i, j]] = vij;
m[[j, i]] = vji;
}
m
pub struct PackedCompactIntMatrix {
mmap: Mmap,
n_rows: usize,
n_cols: usize,
columns: Vec<ColInfo>,
}
// ── Column append ─────────────────────────────────────────────────────────────
impl PackedCompactIntMatrix {
pub(crate) fn open(path: &Path) -> io::Result<Self> {
let mmap = unsafe { Mmap::map(&File::open(path)?)? };
if mmap.len() < PCMX_HEADER {
return Err(io::Error::new(io::ErrorKind::InvalidData, "PCMX file too short"));
}
if &mmap[0..4] != &PCMX_MAGIC {
return Err(io::Error::new(io::ErrorKind::InvalidData, "bad PCMX magic"));
}
let n_rows = u64::from_le_bytes(mmap[8..16].try_into().unwrap()) as usize;
let n_cols = u64::from_le_bytes(mmap[16..24].try_into().unwrap()) as usize;
let mut columns = Vec::with_capacity(n_cols);
for c in 0..n_cols {
let off_pos = PCMX_HEADER + c * 8;
let col_base = u64::from_le_bytes(mmap[off_pos..off_pos+8].try_into().unwrap()) as usize;
// Parse embedded PCIV header at col_base
let n_ov = u64::from_le_bytes(mmap[col_base+16..col_base+24].try_into().unwrap()) as usize;
let n_idx = u64::from_le_bytes(mmap[col_base+24..col_base+32].try_into().unwrap()) as usize;
let step = u64::from_le_bytes(mmap[col_base+32..col_base+40].try_into().unwrap()) as usize;
let n_pciv = u64::from_le_bytes(mmap[col_base+8..col_base+16].try_into().unwrap()) as usize;
let primary_start = col_base + HEADER_SIZE;
let data_offset = primary_start + n_pciv;
let index_offset = data_offset + n_ov * OVERFLOW_ENTRY_SIZE;
let mut index = Vec::with_capacity(n_idx);
for i in 0..n_idx {
let ioff = index_offset + i * INDEX_ENTRY_SIZE;
let slot = u64::from_le_bytes(mmap[ioff..ioff+8].try_into().unwrap()) as usize;
let pos = u64::from_le_bytes(mmap[ioff+8..ioff+16].try_into().unwrap()) as usize;
index.push((slot, pos));
}
columns.push(ColInfo { primary_start, data_offset, n_overflow: n_ov, step, index });
}
Ok(Self { mmap, n_rows, n_cols, columns })
}
#[inline]
pub(crate) fn get(&self, col: usize, slot: usize) -> u32 {
let ci = &self.columns[col];
let v = self.mmap[ci.primary_start + slot];
if v < 255 { return v as u32; }
self.overflow_get(ci, slot)
}
fn overflow_get(&self, ci: &ColInfo, slot: usize) -> u32 {
let (pos_start, pos_end) = if ci.step == 0 {
(0, ci.n_overflow)
} else {
let i = ci.index.partition_point(|&(s, _)| s <= slot).saturating_sub(1);
let start = ci.index[i].1;
let end = if i + 1 < ci.index.len() { ci.index[i+1].1 } else { ci.n_overflow };
(start, end)
};
let mut lo = pos_start;
let mut hi = pos_end;
while lo < hi {
let mid = lo + (hi - lo) / 2;
let off = ci.data_offset + mid * OVERFLOW_ENTRY_SIZE;
let stored = u64::from_le_bytes(self.mmap[off..off+8].try_into().unwrap()) as usize;
match stored.cmp(&slot) {
Ordering::Equal => return u32::from_le_bytes(self.mmap[off+8..off+12].try_into().unwrap()),
Ordering::Less => lo = mid + 1,
Ordering::Greater => hi = mid,
}
}
panic!("slot {slot} marked overflow but not found")
}
pub(crate) fn fill_row(&self, slot: usize, buf: &mut [u32]) {
for c in 0..self.n_cols { buf[c] = self.get(c, slot); }
}
pub(crate) fn row(&self, slot: usize) -> Box<[u32]> {
(0..self.n_cols).map(|c| self.get(c, slot)).collect()
}
}
/// Build `counts/matrix.pcmx` from existing `col_*.pciv` files.
pub fn pack_compact_int_matrix(dir: &Path) -> io::Result<()> {
let meta = MatrixMeta::load(dir)?;
let n_cols = meta.n_cols;
let col_files: Vec<Vec<u8>> = (0..n_cols)
.map(|c| fs::read(col_path(dir, c)))
.collect::<io::Result<_>>()?;
let header_size = PCMX_HEADER + n_cols * 8;
let mut col_offset = header_size;
let mut offsets = Vec::with_capacity(n_cols);
for data in &col_files {
offsets.push(col_offset as u64);
col_offset += data.len();
}
let packed_path = dir.join("matrix.pcmx");
let mut file = File::create(&packed_path)?;
file.write_all(&PCMX_MAGIC)?;
file.write_all(&[0u8; 4])?;
file.write_all(&(meta.n as u64).to_le_bytes())?;
file.write_all(&(n_cols as u64).to_le_bytes())?;
for &off in &offsets { file.write_all(&off.to_le_bytes())?; }
for data in &col_files { file.write_all(data)?; }
Ok(())
}
// ── PersistentCompactIntMatrix — public enum ──────────────────────────────────
pub enum PersistentCompactIntMatrix {
Columnar(ColumnarCompactIntMatrix),
Packed(PackedCompactIntMatrix),
}
impl PersistentCompactIntMatrix {
/// Append a new column to an existing matrix on disk.
///
/// Reads `meta.json` to obtain `n` and the current column count, writes
/// `col_{n_cols:06}.pciv` filled by `value_of(slot)`, then increments
/// `n_cols` in `meta.json`.
pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> u32) -> io::Result<()> {
let mut meta = MatrixMeta::load(dir)?;
let mut b = PersistentCompactIntVecBuilder::new(meta.n, &col_path(dir, meta.n_cols))?;
for slot in 0..meta.n {
b.set(slot, value_of(slot));
/// Open from `layer_dir`, auto-detecting Packed or Columnar.
pub fn open(layer_dir: &Path) -> io::Result<Self> {
let counts_dir = layer_dir.join("counts");
if counts_dir.join("matrix.pcmx").exists() {
return Ok(Self::Packed(PackedCompactIntMatrix::open(&counts_dir.join("matrix.pcmx"))?));
}
b.close()?;
meta.n_cols += 1;
meta.save(dir)
if MatrixMeta::load(&counts_dir).is_ok() {
return Ok(Self::Columnar(ColumnarCompactIntMatrix::open(&counts_dir)?));
}
Err(io::Error::new(
io::ErrorKind::NotFound,
format!("no count matrix found in {} — run 'obikmer upgrade'", layer_dir.display()),
))
}
pub fn n(&self) -> usize {
match self { Self::Columnar(m) => m.n(), Self::Packed(m) => m.n_rows }
}
pub fn n_cols(&self) -> usize {
match self { Self::Columnar(m) => m.n_cols(), Self::Packed(m) => m.n_cols }
}
pub fn col(&self, c: usize) -> &PersistentCompactIntVec {
match self {
Self::Columnar(m) => m.col(c),
_ => panic!("col() only available on Columnar PersistentCompactIntMatrix"),
}
}
pub fn row(&self, slot: usize) -> Box<[u32]> {
match self { Self::Columnar(m) => m.row(slot), Self::Packed(m) => m.row(slot) }
}
pub fn fill_row(&self, slot: usize, buf: &mut [u32]) {
match self { Self::Columnar(m) => m.fill_row(slot, buf), Self::Packed(m) => m.fill_row(slot, buf) }
}
pub fn sum(&self) -> Array1<u64> {
match self {
Self::Columnar(m) => m.sum(),
_ => panic!("sum() only available on Columnar PersistentCompactIntMatrix"),
}
}
pub fn bray_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.bray_dist_matrix(), _ => panic!("Columnar only") }
}
pub fn relfreq_bray_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.relfreq_bray_dist_matrix(), _ => panic!("Columnar only") }
}
pub fn euclidean_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.euclidean_dist_matrix(), _ => panic!("Columnar only") }
}
pub fn relfreq_euclidean_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.relfreq_euclidean_dist_matrix(), _ => panic!("Columnar only") }
}
pub fn hellinger_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.hellinger_dist_matrix(), _ => panic!("Columnar only") }
}
pub fn jaccard_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.jaccard_dist_matrix(), _ => panic!("Columnar only") }
}
pub fn threshold_jaccard_dist_matrix(&self, threshold: u32) -> Array2<f64> {
match self { Self::Columnar(m) => m.threshold_jaccard_dist_matrix(threshold), _ => panic!("Columnar only") }
}
pub fn partial_bray_dist_matrix(&self) -> Array2<u64> {
match self { Self::Columnar(m) => m.partial_bray_dist_matrix(), _ => panic!("Columnar only") }
}
pub fn partial_euclidean_dist_matrix(&self) -> Array2<f64> {
match self { Self::Columnar(m) => m.partial_euclidean_dist_matrix(), _ => panic!("Columnar only") }
}
pub fn partial_threshold_jaccard_dist_matrix(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
match self { Self::Columnar(m) => m.partial_threshold_jaccard_dist_matrix(threshold), _ => panic!("Columnar only") }
}
pub fn partial_relfreq_bray_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
match self { Self::Columnar(m) => m.partial_relfreq_bray_dist_matrix(col_sums), _ => panic!("Columnar only") }
}
pub fn partial_relfreq_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
match self { Self::Columnar(m) => m.partial_relfreq_euclidean_dist_matrix(col_sums), _ => panic!("Columnar only") }
}
pub fn partial_hellinger_euclidean_dist_matrix(&self, col_sums: &Array1<u64>) -> Array2<f64> {
match self { Self::Columnar(m) => m.partial_hellinger_euclidean_dist_matrix(col_sums), _ => panic!("Columnar only") }
}
pub fn append_column(dir: &Path, value_of: impl Fn(usize) -> u32) -> io::Result<()> {
ColumnarCompactIntMatrix::append_column(dir, value_of)
}
}
@@ -240,24 +406,12 @@ impl ColumnWeights for PersistentCompactIntMatrix {
}
impl CountPartials for PersistentCompactIntMatrix {
fn partial_bray(&self) -> Array2<u64> {
self.partial_bray_dist_matrix()
}
fn partial_euclidean(&self) -> Array2<f64> {
self.partial_euclidean_dist_matrix()
}
fn partial_threshold_jaccard(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
self.partial_threshold_jaccard_dist_matrix(threshold)
}
fn partial_relfreq_bray(&self, global: &Array1<u64>) -> Array2<f64> {
self.partial_relfreq_bray_dist_matrix(global)
}
fn partial_relfreq_euclidean(&self, global: &Array1<u64>) -> Array2<f64> {
self.partial_relfreq_euclidean_dist_matrix(global)
}
fn partial_hellinger(&self, global: &Array1<u64>) -> Array2<f64> {
self.partial_hellinger_euclidean_dist_matrix(global)
}
fn partial_bray(&self) -> Array2<u64> { self.partial_bray_dist_matrix() }
fn partial_euclidean(&self) -> Array2<f64> { self.partial_euclidean_dist_matrix() }
fn partial_threshold_jaccard(&self, t: u32) -> (Array2<u64>, Array2<u64>) { self.partial_threshold_jaccard_dist_matrix(t) }
fn partial_relfreq_bray(&self, g: &Array1<u64>) -> Array2<f64> { self.partial_relfreq_bray_dist_matrix(g) }
fn partial_relfreq_euclidean(&self, g: &Array1<u64>) -> Array2<f64> { self.partial_relfreq_euclidean_dist_matrix(g) }
fn partial_hellinger(&self, g: &Array1<u64>) -> Array2<f64> { self.partial_hellinger_euclidean_dist_matrix(g) }
}
// ── Builder ───────────────────────────────────────────────────────────────────
@@ -287,3 +441,16 @@ impl PersistentCompactIntMatrixBuilder {
MatrixMeta { n: self.n, n_cols: self.n_cols }.save(&self.dir)
}
}
// ── Helpers ───────────────────────────────────────────────────────────────────
fn upper_pairs(n: usize) -> Vec<(usize, usize)> {
(0..n).flat_map(|i| (i + 1..n).map(move |j| (i, j))).collect()
}
fn fill_symmetric<T>(n: usize, vals: impl Iterator<Item = (usize, usize, T, T)>) -> Array2<T>
where T: Clone + Default {
let mut m = Array2::from_elem((n, n), T::default());
for (i, j, vij, vji) in vals { m[[i, j]] = vij; m[[j, i]] = vji; }
m
}
src/obicompactvec/src/layer_meta.rs
+33
View File
@@ -0,0 +1,33 @@
use std::{fs, io, path::Path};
/// Lightweight metadata stored at the layer level (`layer_meta.json`).
///
/// Written by `obilayeredmap::MphfLayer::build` alongside `mphf.bin`.
/// Read by `PersistentBitMatrix::open` to determine `n_rows` for the
/// implicit (mono-genome presence/absence) case.
pub struct LayerMeta {
pub n: usize,
}
impl LayerMeta {
pub const FILENAME: &'static str = "layer_meta.json";
pub fn save(layer_dir: &Path, n: usize) -> io::Result<()> {
fs::write(layer_dir.join(Self::FILENAME), format!("{{\"n\":{n}}}\n"))
}
pub fn load(layer_dir: &Path) -> io::Result<Self> {
let s = fs::read_to_string(layer_dir.join(Self::FILENAME))?;
Self::parse(&s)
.ok_or_else(|| io::Error::new(io::ErrorKind::InvalidData, "bad layer_meta.json"))
}
fn parse(s: &str) -> Option<Self> {
let key = "\"n\":";
let pos = s.find(key)? + key.len();
let rest = s[pos..].trim_start();
let end = rest.find(|c: char| !c.is_ascii_digit()).unwrap_or(rest.len());
let n = rest[..end].parse().ok()?;
Some(Self { n })
}
}
src/obicompactvec/src/lib.rs
+4 -2
View File
@@ -3,14 +3,16 @@ mod bitmatrix;
mod builder;
mod format;
mod intmatrix;
mod layer_meta;
mod meta;
mod reader;
pub mod traits;
pub use bitvec::{BitIter, PersistentBitVec, PersistentBitVecBuilder};
pub use bitmatrix::{PersistentBitMatrix, PersistentBitMatrixBuilder};
pub use bitmatrix::{PersistentBitMatrix, PersistentBitMatrixBuilder, pack_bit_matrix};
pub use builder::PersistentCompactIntVecBuilder;
pub use intmatrix::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder};
pub use intmatrix::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder, pack_compact_int_matrix};
pub use layer_meta::LayerMeta;
pub use reader::PersistentCompactIntVec;
pub use traits::{BitPartials, ColumnWeights, CountPartials};
src/obicompactvec/src/tests/bitmatrix.rs
+13 -8
View File
@@ -5,7 +5,8 @@ use crate::{PersistentBitMatrix, PersistentBitMatrixBuilder};
fn make_matrix(cols: &[&[bool]]) -> (tempfile::TempDir, PersistentBitMatrix) {
let n = cols.first().map_or(0, |c| c.len());
let dir = tempdir().unwrap();
let mut b = PersistentBitMatrixBuilder::new(n, dir.path()).unwrap();
let presence = dir.path().join("presence");
let mut b = PersistentBitMatrixBuilder::new(n, &presence).unwrap();
for &col in cols {
let mut cb = b.add_col().unwrap();
for (slot, &v) in col.iter().enumerate() {
@@ -21,7 +22,8 @@ fn make_matrix(cols: &[&[bool]]) -> (tempfile::TempDir, PersistentBitMatrix) {
#[test]
fn single_col_roundtrip() {
let dir = tempdir().unwrap();
let mut b = PersistentBitMatrixBuilder::new(4, dir.path()).unwrap();
let presence = dir.path().join("presence");
let mut b = PersistentBitMatrixBuilder::new(4, &presence).unwrap();
let mut col = b.add_col().unwrap();
col.set(0, true);
col.set(1, false);
@@ -42,7 +44,8 @@ fn single_col_roundtrip() {
#[test]
fn two_cols_roundtrip() {
let dir = tempdir().unwrap();
let mut b = PersistentBitMatrixBuilder::new(3, dir.path()).unwrap();
let presence = dir.path().join("presence");
let mut b = PersistentBitMatrixBuilder::new(3, &presence).unwrap();
let mut col0 = b.add_col().unwrap();
col0.set(0, true); col0.set(1, false); col0.set(2, true);
col0.close().unwrap();
@@ -61,7 +64,8 @@ fn two_cols_roundtrip() {
#[test]
fn col_accessor() {
let dir = tempdir().unwrap();
let mut b = PersistentBitMatrixBuilder::new(3, dir.path()).unwrap();
let presence = dir.path().join("presence");
let mut b = PersistentBitMatrixBuilder::new(3, &presence).unwrap();
let mut col = b.add_col().unwrap();
col.set(0, true); col.set(1, false); col.set(2, true);
col.close().unwrap();
@@ -76,7 +80,8 @@ fn col_accessor() {
#[test]
fn zero_cols_roundtrip() {
let dir = tempdir().unwrap();
let b = PersistentBitMatrixBuilder::new(8, dir.path()).unwrap();
let presence = dir.path().join("presence");
let b = PersistentBitMatrixBuilder::new(8, &presence).unwrap();
b.close().unwrap();
let m = PersistentBitMatrix::open(dir.path()).unwrap();
@@ -89,9 +94,9 @@ fn zero_cols_roundtrip() {
#[test]
fn count_ones_per_column() {
let (_d, m) = make_matrix(&[
&[true, false, true, true], // 3 ones
&[false, false, false, false], // 0 ones
&[true, true, true, false], // 3 ones
&[true, false, true, true],
&[false, false, false, false],
&[true, true, true, false],
]);
let c = m.count_ones();
assert_eq!(c[0], 3);
src/obicompactvec/src/tests/intmatrix.rs
+5 -5
View File
@@ -5,7 +5,7 @@ use crate::{PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder};
fn make_matrix(cols: &[&[u32]]) -> (tempfile::TempDir, PersistentCompactIntMatrix) {
let n = cols.first().map_or(0, |c| c.len());
let dir = tempdir().unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(n, dir.path()).unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(n, &dir.path().join("counts")).unwrap();
for &col in cols {
let mut cb = b.add_col().unwrap();
for (slot, &v) in col.iter().enumerate() {
@@ -21,7 +21,7 @@ fn make_matrix(cols: &[&[u32]]) -> (tempfile::TempDir, PersistentCompactIntMatri
#[test]
fn single_col_roundtrip() {
let dir = tempdir().unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(4, dir.path()).unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(4, &dir.path().join("counts")).unwrap();
let mut col = b.add_col().unwrap();
col.set(0, 10);
col.set(1, 200);
@@ -42,7 +42,7 @@ fn single_col_roundtrip() {
#[test]
fn two_cols_roundtrip() {
let dir = tempdir().unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(3, dir.path()).unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(3, &dir.path().join("counts")).unwrap();
let mut col0 = b.add_col().unwrap();
col0.set(0, 1); col0.set(1, 2); col0.set(2, 3);
col0.close().unwrap();
@@ -61,7 +61,7 @@ fn two_cols_roundtrip() {
#[test]
fn col_accessor() {
let dir = tempdir().unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(2, dir.path()).unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(2, &dir.path().join("counts")).unwrap();
let mut col0 = b.add_col().unwrap();
col0.set(0, 5); col0.set(1, 7);
col0.close().unwrap();
@@ -75,7 +75,7 @@ fn col_accessor() {
#[test]
fn zero_cols_roundtrip() {
let dir = tempdir().unwrap();
let b = PersistentCompactIntMatrixBuilder::new(10, dir.path()).unwrap();
let b = PersistentCompactIntMatrixBuilder::new(10, &dir.path().join("counts")).unwrap();
b.close().unwrap();
let m = PersistentCompactIntMatrix::open(dir.path()).unwrap();
src/obikindex/src/index.rs
+82
View File
@@ -6,6 +6,7 @@ use std::sync::{Arc, Mutex};
use indicatif::{ProgressBar, ProgressStyle};
use obikpartitionner::{KmerPartition, KmerSpectrum};
use obilayeredmap;
use obisys::{Reporter, Stage};
use rayon::prelude::*;
use tracing::info;
@@ -199,6 +200,87 @@ impl KmerIndex {
.join(format!("layer_{layer}"))
.join("unitigs.bin")
}
/// Pack all partition matrices into single-file format (presence → .pbmx, counts → .pcmx).
///
/// Reduces per-query file-open overhead from O(n_genomes) to O(1) per partition.
/// Column files are kept in place; packed files take priority when opening.
pub fn pack_matrices(&self) -> OKIResult<()> {
use obicompactvec::{pack_bit_matrix, pack_compact_int_matrix};
use obilayeredmap::meta::PartitionMeta;
let n = self.n_partitions();
let errors: Vec<_> = (0..n)
.into_par_iter()
.filter_map(|i| {
let index_dir = self.partition.part_dir(i).join("index");
if !index_dir.exists() { return None; }
let meta = match PartitionMeta::load(&index_dir) {
Ok(m) => m,
Err(e) => return Some(OKIError::Io(std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))),
};
for l in 0..meta.n_layers {
let layer_dir = index_dir.join(format!("layer_{l}"));
let presence_dir = layer_dir.join("presence");
let counts_dir = layer_dir.join("counts");
if presence_dir.exists() {
if let Err(e) = pack_bit_matrix(&presence_dir) {
return Some(OKIError::Io(e));
}
}
if counts_dir.exists() {
if let Err(e) = pack_compact_int_matrix(&counts_dir) {
return Some(OKIError::Io(e));
}
}
}
None
})
.collect();
if let Some(e) = errors.into_iter().next() { return Err(e); }
Ok(())
}
/// Write a `layer_meta.json` in any layer directory that is missing one.
///
/// Old indexes were built before this file was required. The number of
/// kmers is recovered from `unitigs.bin`, which is always present.
pub fn upgrade_layer_meta(&self) -> OKIResult<()> {
use obicompactvec::LayerMeta;
use obiskio::UnitigFileReader;
use obilayeredmap::meta::PartitionMeta;
let n = self.n_partitions();
let errors: Vec<_> = (0..n)
.into_par_iter()
.filter_map(|i| {
let index_dir = self.partition.part_dir(i).join("index");
if !index_dir.exists() { return None; }
let meta = match PartitionMeta::load(&index_dir) {
Ok(m) => m,
Err(e) => return Some(OKIError::Io(std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))),
};
for l in 0..meta.n_layers {
let layer_dir = index_dir.join(format!("layer_{l}"));
let meta_path = layer_dir.join(LayerMeta::FILENAME);
if meta_path.exists() { continue; }
let unitigs_path = layer_dir.join("unitigs.bin");
let n_kmers = match UnitigFileReader::open_sequential(&unitigs_path) {
Ok(r) => r.n_kmers(),
Err(e) => return Some(OKIError::Partition(e)),
};
if let Err(e) = LayerMeta::save(&layer_dir, n_kmers) {
return Some(OKIError::Io(e));
}
}
None
})
.collect();
if let Some(e) = errors.into_iter().next() { return Err(e); }
Ok(())
}
}
fn label_from_path(path: &Path) -> String {
src/obikindex/src/merge.rs
+10
View File
@@ -196,6 +196,16 @@ impl KmerIndex {
rep.push(t.stop());
}
// ── Pack matrices after merge ─────────────────────────────────────────
{
let t = Stage::start("pack");
let pb = spinner("pack — consolidating column files …");
let dst2 = KmerIndex::open(output)?;
dst2.pack_matrices()?;
pb.finish_and_clear();
rep.push(t.stop());
}
// Re-open to get the updated state.
KmerIndex::open(output)
}
src/obikmer/src/cmd/mod.rs
+1
View File
@@ -1,4 +1,5 @@
pub mod annotate;
pub mod pack;
pub mod utils;
pub mod distance;
pub mod dump;
src/obikmer/src/cmd/pack.rs
+36
View File
@@ -0,0 +1,36 @@
use std::path::PathBuf;
use clap::Args;
use obikindex::KmerIndex;
use obisys::{Reporter, Stage};
use tracing::info;
#[derive(Args)]
pub struct PackArgs {
/// Index directory to pack
pub index: PathBuf,
}
pub fn run(args: PackArgs) {
let idx = KmerIndex::open(&args.index).unwrap_or_else(|e| {
eprintln!("error opening index: {e}");
std::process::exit(1);
});
info!(
"pack: {} partition(s), {} genome(s)",
idx.n_partitions(),
idx.meta().genomes.len(),
);
let mut rep = Reporter::new();
let t = Stage::start("pack");
idx.pack_matrices().unwrap_or_else(|e| {
eprintln!("pack error: {e}");
std::process::exit(1);
});
rep.push(t.stop());
rep.print();
}
src/obikmer/src/cmd/utils.rs
+24 -1
View File
@@ -2,6 +2,7 @@ use std::path::PathBuf;
use clap::Args;
use obikindex::{validate_label, KmerIndex};
use obikseq::set_k;
use tracing::info;
#[derive(Args)]
@@ -12,6 +13,10 @@ pub struct UtilsArgs {
/// Set a new genome label: NEW_LABEL=OLD_LABEL
#[arg(long, value_name = "NEW=OLD")]
pub new_label: Option<String>,
/// Add missing layer_meta.json files to each layer (required after upgrading from old indexes)
#[arg(long)]
pub upgrade_index: bool,
}
pub fn run(args: UtilsArgs) {
@@ -22,12 +27,30 @@ pub fn run(args: UtilsArgs) {
run_rename(&args.index, spec);
}
if args.upgrade_index {
any = true;
run_upgrade_index(&args.index);
}
if !any {
eprintln!("utils: no operation specified. Available options: --new-label NEW=OLD");
eprintln!("utils: no operation specified. Available options: --new-label NEW=OLD, --upgrade-index");
std::process::exit(1);
}
}
fn run_upgrade_index(index_path: &PathBuf) {
let idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
eprintln!("error opening index: {e}");
std::process::exit(1);
});
set_k(idx.kmer_size());
idx.upgrade_layer_meta().unwrap_or_else(|e| {
eprintln!("upgrade error: {e}");
std::process::exit(1);
});
info!("upgrade-index: layer_meta.json written to all layers that were missing it");
}
fn run_rename(index_path: &PathBuf, spec: &str) {
let (old_label, new_label) = parse_rename_spec(spec);
src/obikmer/src/main.rs
+3
View File
@@ -38,6 +38,8 @@ enum Commands {
Reindex(cmd::reindex::ReindexArgs),
/// Miscellaneous index utilities (--rename, …)
Utils(cmd::utils::UtilsArgs),
/// Pack matrix column files into single-file format to reduce query I/O
Pack(cmd::pack::PackArgs),
}
fn main() {
@@ -71,6 +73,7 @@ fn main() {
Commands::Estimate(args) => cmd::estimate::run(args),
Commands::Reindex(args) => cmd::reindex::run(args),
Commands::Utils(args) => cmd::utils::run(args),
Commands::Pack(args) => cmd::pack::run(args),
}
#[cfg(feature = "profiling")]
src/obikpartitionner/src/distance.rs
+6 -4
View File
@@ -22,8 +22,9 @@ impl KmerPartition {
}
let matrices = (0..probe_n_layers(&index_dir))
.filter_map(|l| {
let dir = index_dir.join(format!("layer_{l}")).join("counts");
dir.exists().then(|| PersistentCompactIntMatrix::open(&dir).map_err(SKError::Io))
let layer_dir = index_dir.join(format!("layer_{l}"));
layer_dir.join("counts").exists()
.then(|| PersistentCompactIntMatrix::open(&layer_dir).map_err(SKError::Io))
})
.collect::<SKResult<Vec<_>>>()?;
Ok(LayeredStore::new(matrices))
@@ -38,8 +39,9 @@ impl KmerPartition {
}
let matrices = (0..probe_n_layers(&index_dir))
.filter_map(|l| {
let dir = index_dir.join(format!("layer_{l}")).join("presence");
dir.exists().then(|| PersistentBitMatrix::open(&dir).map_err(SKError::Io))
let layer_dir = index_dir.join(format!("layer_{l}"));
layer_dir.join("presence").exists()
.then(|| PersistentBitMatrix::open(&layer_dir).map_err(SKError::Io))
})
.collect::<SKResult<Vec<_>>>()?;
Ok(LayeredStore::new(matrices))
src/obikpartitionner/src/dump_layer.rs
+4 -4
View File
@@ -51,14 +51,14 @@ impl KmerPartition {
let presence_dir = layer_dir.join("presence");
if use_counts && counts_dir.exists() {
let mat = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
let mat = PersistentCompactIntMatrix::open(&layer_dir).map_err(SKError::Io)?;
for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
if let Some(slot) = mphf.find(kmer) {
cb(kmer, mat.row(slot));
}
}
} else if !use_counts && presence_dir.exists() {
let mat = PersistentBitMatrix::open(&presence_dir).map_err(SKError::Io)?;
let mat = PersistentBitMatrix::open(&layer_dir).map_err(SKError::Io)?;
for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
if let Some(slot) = mphf.find(kmer) {
let row: Box<[u32]> = mat.row(slot).iter().map(|&b| b as u32).collect();
@@ -108,14 +108,14 @@ impl KmerPartition {
let presence_dir = layer_dir.join("presence");
if use_counts && counts_dir.exists() {
let mat = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
let mat = PersistentCompactIntMatrix::open(&layer_dir).map_err(SKError::Io)?;
for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
if let Some(slot) = mphf.find(kmer) {
cb(part, layer, kmer, mat.row(slot));
}
}
} else if !use_counts && presence_dir.exists() {
let mat = PersistentBitMatrix::open(&presence_dir).map_err(SKError::Io)?;
let mat = PersistentBitMatrix::open(&layer_dir).map_err(SKError::Io)?;
for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
if let Some(slot) = mphf.find(kmer) {
let row: Box<[u32]> = mat.row(slot).iter().map(|&b| b as u32).collect();
src/obikpartitionner/src/merge_layer.rs
+15 -20
View File
@@ -45,37 +45,35 @@ impl ColBuilder {
// ── SrcLayerData — opened source matrix for pass-2 lookup ─────────────────────
pub(crate) enum SrcLayerData {
/// Pure set-membership layer (no data matrix): every kmer is present in all genomes.
SetMembership,
Presence(MphfOnly, PersistentBitMatrix),
Count(MphfOnly, PersistentCompactIntMatrix),
}
impl SrcLayerData {
pub(crate) fn open(layer_dir: &Path, merge_mode: MergeMode) -> SKResult<Self> {
let presence_dir = layer_dir.join("presence");
let counts_dir = layer_dir.join("counts");
match merge_mode {
MergeMode::Presence => {
if presence_dir.exists() {
if counts_dir.exists() && !layer_dir.join("presence").exists() {
let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
let mat = PersistentBitMatrix::open(&presence_dir).map_err(SKError::Io)?;
Ok(SrcLayerData::Presence(mphf, mat))
} else if counts_dir.exists() {
let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
let mat = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
Ok(SrcLayerData::Count(mphf, mat))
} else {
Ok(SrcLayerData::SetMembership)
// presence dir exists, or neither exists → Implicit handled by open()
let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
let mat = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
Ok(SrcLayerData::Presence(mphf, mat))
}
}
MergeMode::Count => {
if counts_dir.exists() {
let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
let mat = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
if counts_dir.exists() {
let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
Ok(SrcLayerData::Count(mphf, mat))
} else {
Ok(SrcLayerData::SetMembership)
// No counts → treat as implicit presence (all 1s)
let mat = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
Ok(SrcLayerData::Presence(mphf, mat))
}
}
}
@@ -85,15 +83,12 @@ impl SrcLayerData {
/// The caller guarantees `kmer` is in the source MPHF domain.
#[inline]
pub(crate) fn lookup(&self, kmer: CanonicalKmer, n_genomes: usize) -> Vec<u32> {
let mut buf = vec![0u32; n_genomes];
match self {
SrcLayerData::SetMembership => vec![1u32; n_genomes],
SrcLayerData::Presence(mphf, mat) => {
mat.row(mphf.index(kmer)).iter().map(|&b| b as u32).collect()
}
SrcLayerData::Count(mphf, mat) => {
mat.row(mphf.index(kmer)).iter().copied().collect()
}
SrcLayerData::Presence(mphf, mat) => mat.fill_row(mphf.index(kmer), &mut buf),
SrcLayerData::Count(mphf, mat) => mat.fill_row(mphf.index(kmer), &mut buf),
}
buf
}
}
src/obikpartitionner/src/query_layer.rs
+14 -32
View File
@@ -20,48 +20,33 @@ fn olm_to_sk(e: OLMError) -> SKError {
// ── per-layer query handle ────────────────────────────────────────────────────
enum QueryLayer {
/// Layer<()> — MPHF-only, no data matrix; all indexed kmers map to 1 per genome.
SetOnly(MphfLayer),
Presence(MphfLayer, PersistentBitMatrix),
Count(MphfLayer, PersistentCompactIntMatrix),
}
impl QueryLayer {
fn open(layer_dir: &Path, with_counts: bool, mode: &IndexMode) -> SKResult<Self> {
let presence_dir = layer_dir.join("presence");
let mphf = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
let counts_dir = layer_dir.join("counts");
let presence_dir = layer_dir.join("presence");
if with_counts && counts_dir.exists() {
let mphf = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
let mat = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
Ok(QueryLayer::Count(mphf, mat))
} else if presence_dir.exists() {
let mphf = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
let mat = PersistentBitMatrix::open(&presence_dir).map_err(SKError::Io)?;
} else if presence_dir.exists() || !counts_dir.exists() {
// presence mode, or no matrix at all → Implicit handled inside open()
let mat = PersistentBitMatrix::open(layer_dir).map_err(SKError::Io)?;
Ok(QueryLayer::Presence(mphf, mat))
} else if counts_dir.exists() {
// presence query on a count index — return counts as-is
let mphf = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
let mat = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
Ok(QueryLayer::Count(mphf, mat))
} else {
let mphf = MphfLayer::open(layer_dir, mode).map_err(olm_to_sk)?;
Ok(QueryLayer::SetOnly(mphf))
// counts exist but not presence — count layer, no presence requested
let mat = PersistentCompactIntMatrix::open(layer_dir).map_err(SKError::Io)?;
Ok(QueryLayer::Count(mphf, mat))
}
}
/// Write per-genome values into `buf` if `kmer` is indexed in this layer.
/// Returns `true` on hit; `buf` is untouched on miss.
/// Write per-genome values into `buf` if `kmer` is indexed; returns true on hit.
fn find_into(&self, kmer: CanonicalKmer, n_genomes: usize, buf: &mut [u32]) -> bool {
match self {
QueryLayer::SetOnly(mphf) => {
if mphf.find(kmer).is_some() {
buf[..n_genomes].fill(1);
true
} else {
false
}
}
QueryLayer::Presence(mphf, mat) => {
if let Some(slot) = mphf.find(kmer) {
mat.fill_row(slot, &mut buf[..n_genomes]);
@@ -87,14 +72,11 @@ impl QueryLayer {
impl KmerPartition {
/// Query a single partition, calling `on_hit(sk_idx, kmer_idx, row)` for
/// every found k-mer without allocating intermediate result vectors.
///
/// `row` is a shared scratch buffer valid only for the duration of the call;
/// the callback must copy what it needs before returning.
pub fn query_partition_with<F>(
&self,
part_idx: usize,
superkmers: &[&RoutableSuperKmer],
k: usize,
_k: usize,
n_genomes: usize,
with_counts: bool,
mut on_hit: F,
@@ -133,13 +115,13 @@ impl KmerPartition {
Ok(())
}
/// Query a single partition for a slice of (already-routed) super-kmers.
/// Query a single partition for a slice of super-kmers, returning per-kmer rows.
/// Prefer [`query_partition_with`] to avoid per-kmer heap allocations.
pub fn query_partition(
&self,
part_idx: usize,
superkmers: &[&RoutableSuperKmer],
k: usize,
_k: usize,
n_genomes: usize,
with_counts: bool,
) -> SKResult<Vec<Vec<Option<Box<[u32]>>>>> {
@@ -152,7 +134,7 @@ impl KmerPartition {
if !index_dir.exists() {
return Ok(superkmers
.iter()
.map(|rsk| vec![None; rsk.seql() - k + 1])
.map(|rsk| vec![None; rsk.seql()])
.collect());
}
src/obilayeredmap/src/layer.rs
+2 -2
View File
@@ -34,7 +34,7 @@ impl LayerData for () {
impl LayerData for PersistentCompactIntMatrix {
type Item = Box<[u32]>;
fn open(layer_dir: &Path) -> OLMResult<Self> {
PersistentCompactIntMatrix::open(&layer_dir.join(COUNTS_DIR)).map_err(OLMError::Io)
PersistentCompactIntMatrix::open(layer_dir).map_err(OLMError::Io)
}
fn read(&self, slot: usize) -> Box<[u32]> { self.row(slot) }
}
@@ -42,7 +42,7 @@ impl LayerData for PersistentCompactIntMatrix {
impl LayerData for PersistentBitMatrix {
type Item = Box<[bool]>;
fn open(layer_dir: &Path) -> OLMResult<Self> {
PersistentBitMatrix::open(&layer_dir.join(PRESENCE_DIR)).map_err(OLMError::Io)
PersistentBitMatrix::open(layer_dir).map_err(OLMError::Io)
}
fn read(&self, slot: usize) -> Box<[bool]> { self.row(slot) }
}
src/obilayeredmap/src/layered_store.rs
+2 -2
View File
@@ -107,7 +107,7 @@ mod tests {
fn make_int_matrix(cols: &[&[u32]]) -> (tempfile::TempDir, PersistentCompactIntMatrix) {
let n = cols.first().map_or(0, |c| c.len());
let dir = tempdir().unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(n, dir.path()).unwrap();
let mut b = PersistentCompactIntMatrixBuilder::new(n, &dir.path().join("counts")).unwrap();
for &col in cols {
let mut cb = b.add_col().unwrap();
for (slot, &v) in col.iter().enumerate() { cb.set(slot, v); }
@@ -121,7 +121,7 @@ mod tests {
fn make_bit_matrix(cols: &[&[bool]]) -> (tempfile::TempDir, PersistentBitMatrix) {
let n = cols.first().map_or(0, |c| c.len());
let dir = tempdir().unwrap();
let mut b = PersistentBitMatrixBuilder::new(n, dir.path()).unwrap();
let mut b = PersistentBitMatrixBuilder::new(n, &dir.path().join("presence")).unwrap();
for &col in cols {
let mut cb = b.add_col().unwrap();
for (slot, &v) in col.iter().enumerate() { cb.set(slot, v); }
src/obilayeredmap/src/mphf_layer.rs
+2
View File
@@ -3,6 +3,7 @@ use std::path::{Path, PathBuf};
use cacheline_ef::{CachelineEf, CachelineEfVec};
use epserde::prelude::*;
use obicompactvec::LayerMeta;
use obikseq::CanonicalKmer;
use obiskio::{CanonicalKmerIter, UnitigFileReader, UnitigFileWriter, build_unitig_idx};
use ptr_hash::{PtrHash, PtrHashParams, bucket_fn::CubicEps, hash::Xx64};
@@ -341,6 +342,7 @@ impl MphfLayer {
}
}
LayerMeta::save(dir, n)?;
Ok(n)
}
}