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feat: add kmer filtering and refactor layer iteration

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Introduce a `passes_all` utility to validate kmer rows against multiple filters using short-circuit logic. Integrate a `filters` parameter into the iteration functions to conditionally emit kmers based on filter results. Extract repetitive layer traversal and filtering into an `iter_src_layers` helper, refactoring Pass 1 and Pass 2 to eliminate duplication. Additionally, add a debug conditional to the dump output to include partition and layer metadata alongside kmer sequences.
This commit is contained in:
Eric Coissac
2026-06-04 20:43:22 +02:00
parent 476c7a6394
commit a1499e6153
5 changed files with 86 additions and 57 deletions
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src/obikpartitionner/src/rebuild_layer.rs
+38 -35
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@@ -7,11 +7,12 @@ use obicompactvec::{PersistentBitMatrixBuilder,
PersistentCompactIntMatrixBuilder,
PersistentCompactIntVecBuilder};
use obidebruinj::GraphDeBruijn;
use obikseq::CanonicalKmer;
use obiskio::{SKError, SKResult, UnitigFileReader};
use obilayeredmap::{IndexMode, Layer, MphfLayer, OLMError};
use obilayeredmap::meta::PartitionMeta;
use crate::filter::KmerFilter;
use crate::filter::{KmerFilter, passes_all};
use crate::merge_layer::{MergeMode, SrcLayerData};
use crate::partition::KmerPartition;
@@ -75,8 +76,34 @@ fn load_meta(dir: &Path) -> SKResult<PartitionMeta> {
}
}
fn passes_all(filters: &[Box<dyn KmerFilter>], row: &[u32], n_genomes: usize) -> bool {
filters.iter().all(|f| f.passes(row, n_genomes))
/// Iterate all kmers in `src_index_dir` that pass `filters`, yielding `(kmer, row)`.
///
/// Uses [`SrcLayerData`] semantics: counts take priority over presence when
/// `mode = Count`; presence (or implicit all-ones) is used for `Presence`.
fn iter_src_layers(
src_index_dir: &Path,
mode: MergeMode,
n_genomes: usize,
filters: &[Box<dyn KmerFilter>],
mut cb: impl FnMut(CanonicalKmer, Box<[u32]>),
) -> SKResult<()> {
let src_meta = load_meta(src_index_dir)?;
for l in 0..src_meta.n_layers {
let src_layer_dir = src_index_dir.join(format!("layer_{l}"));
let unitigs_path = src_layer_dir.join("unitigs.bin");
if !unitigs_path.exists() { continue; }
let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
let row = src_data.lookup(kmer, n_genomes);
if passes_all(filters, &row, n_genomes) {
cb(kmer, row.into_boxed_slice());
}
}
}
Ok(())
}
// ── KmerPartition::rebuild_partition ─────────────────────────────────────────
@@ -110,22 +137,9 @@ impl KmerPartition {
// ── Pass 1: collect filtered kmers into de Bruijn graph ───────────────
let mut g = GraphDeBruijn::new();
for l in 0..src_meta.n_layers {
let src_layer_dir = src_index_dir.join(format!("layer_{l}"));
let unitigs_path = src_layer_dir.join("unitigs.bin");
if !unitigs_path.exists() { continue; }
let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
let row = src_data.lookup(kmer, n_genomes);
if passes_all(filters, &row, n_genomes) {
g.push(kmer);
}
}
}
iter_src_layers(&src_index_dir, mode, n_genomes, filters, |kmer, _row| {
g.push(kmer);
})?;
if g.len() == 0 {
return Ok(());
@@ -176,24 +190,13 @@ impl KmerPartition {
};
// ── Pass 2: fill builders ─────────────────────────────────────────────
for l in 0..src_meta.n_layers {
let src_layer_dir = src_index_dir.join(format!("layer_{l}"));
let unitigs_path = src_layer_dir.join("unitigs.bin");
if !unitigs_path.exists() { continue; }
let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
let row = src_data.lookup(kmer, n_genomes);
if !passes_all(filters, &row, n_genomes) { continue; }
if let Some(slot) = dst_mphf.find(kmer) {
for (col, &value) in row.iter().enumerate() {
builders[col].set_val(slot, value);
}
iter_src_layers(&src_index_dir, mode, n_genomes, filters, |kmer, row| {
if let Some(slot) = dst_mphf.find(kmer) {
for (col, &value) in row.iter().enumerate() {
builders[col].set_val(slot, value);
}
}
}
})?;
// ── Close builders, write metadata ────────────────────────────────────
for b in builders { b.close()?; }