Add unified matrix builder abstraction and k-mer filtering CLI

Introduces a unified MatrixBuilder abstraction for persistent bit and integer matrices, replacing custom dispatch enums and boolean flags across consumers. Refactors index, merge, and select layers to adopt explicit merge modes and centralized lifecycle management. Adds a complete k-mer filtering implementation with partition-level processing, progress tracking, and a new CLI subcommand supporting configurable predicates and thresholds.

src/obikmerge/src/partition_merge.rs

@@ -6,8 +6,7 @@
 //! instead.
 
 use std::fs;
-use std::io;
-use std::path::{Path, PathBuf};
+use std::path::PathBuf;
 use std::sync::{Arc, Mutex};
 
 use obipipeline::{
@@ -16,66 +15,19 @@ use obipipeline::{
 };
 use tracing::debug;
 
-use obicompactvec::{PersistentBitMatrixBuilder, PersistentCompactIntMatrixBuilder};
+use obicompactvec::{ColBuilder, MatrixBuilder};
 use obikindex::layer::{IndexMode, KmerLayer, TypedLayer};
-use obikindex::{ColBuilder, KmerIndex, OKIError, OKIResult};
+use obikindex::{KmerIndex, OKIError, OKIResult};
 use obikindexer::{build_graph, materialize_layer};
 use obikseq::CanonicalKmer;
 use obiskio::UnitigFileReader;
 
 use crate::MergeMode;
 
-// ── MatrixBuilder ─────────────────────────────────────────────────────────────
-//
-// Wraps whichever matrix builder `mode` calls for, so the merge pipeline never
-// has to know the on-disk column naming (`col_NNNNNN.pbiv`/`.pciv`) or the
-// matrix `meta.json` schema itself — both stay private to obicompactvec.
-// `resume` reopens a matrix directory already closed by a previous builder
-// session (an existing destination layer), continuing from its current
-// `n_cols` instead of starting a fresh matrix at 0.
-
-enum MatrixBuilder {
-    Bit(PersistentBitMatrixBuilder),
-    Int(PersistentCompactIntMatrixBuilder),
-}
-
-impl MatrixBuilder {
-    fn new(mode: MergeMode, n: usize, dir: &Path) -> io::Result<Self> {
-        Ok(match mode {
-            MergeMode::Presence => MatrixBuilder::Bit(PersistentBitMatrixBuilder::new(n, dir)?),
-            MergeMode::Count => MatrixBuilder::Int(PersistentCompactIntMatrixBuilder::new(n, dir)?),
-        })
-    }
-
-    fn resume(mode: MergeMode, dir: &Path) -> io::Result<Self> {
-        Ok(match mode {
-            MergeMode::Presence => MatrixBuilder::Bit(PersistentBitMatrixBuilder::resume(dir)?),
-            MergeMode::Count => MatrixBuilder::Int(PersistentCompactIntMatrixBuilder::resume(dir)?),
-        })
-    }
-
-    /// Add a column with no data written (all-zero/false) — for genome
-    /// columns absent from this source (e.g. dst genomes in a new layer).
-    fn add_absent_col(&mut self) -> io::Result<()> {
-        match self {
-            MatrixBuilder::Bit(b) => b.add_col()?.close(),
-            MatrixBuilder::Int(b) => b.add_col()?.close(),
-        }
-    }
-
-    fn add_col(&mut self) -> io::Result<ColBuilder> {
-        Ok(match self {
-            MatrixBuilder::Bit(b) => ColBuilder::Bit(b.add_col()?),
-            MatrixBuilder::Int(b) => ColBuilder::Int(b.add_col()?),
-        })
-    }
-
-    fn close(self) -> io::Result<()> {
-        match self {
-            MatrixBuilder::Bit(b) => b.close(),
-            MatrixBuilder::Int(b) => b.close(),
-        }
-    }
+// `MatrixBuilder::new`/`resume` take a `presence: bool` — `MergeMode` maps
+// to it directly (`Presence` → `true`, `Count` → `false`).
+fn presence(mode: MergeMode) -> bool {
+    mode == MergeMode::Presence
 }
 
 #[cfg(test)]
@@ -84,7 +36,7 @@ mod matrix_builder_tests {
 
     use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
 
-    use super::{ColBuilder, MatrixBuilder, MergeMode};
+    use super::{ColBuilder, MatrixBuilder};
 
     /// Mirrors `merge_partition`'s "new layer" setup: absent (dst-genome)
     /// columns get no data, then source columns are filled — all through one
@@ -93,7 +45,7 @@ mod matrix_builder_tests {
     fn new_layer_absent_then_source_columns_presence() {
         let dir = tempdir().unwrap();
         let data_dir = dir.path().join("presence");
-        let mut mb = MatrixBuilder::new(MergeMode::Presence, 3, &data_dir).unwrap();
+        let mut mb = MatrixBuilder::new(true, 3, &data_dir).unwrap();
 
         // Two absent (dst-genome) columns.
         mb.add_absent_col().unwrap();
@@ -123,7 +75,7 @@ mod matrix_builder_tests {
     fn new_layer_absent_then_source_columns_count() {
         let dir = tempdir().unwrap();
         let data_dir = dir.path().join("counts");
-        let mut mb = MatrixBuilder::new(MergeMode::Count, 2, &data_dir).unwrap();
+        let mut mb = MatrixBuilder::new(false, 2, &data_dir).unwrap();
 
         mb.add_absent_col().unwrap();
 
@@ -154,12 +106,12 @@ mod matrix_builder_tests {
         let data_dir = dir.path().join("presence");
 
         // Previous merge: one dst-genome column already on disk.
-        let mut mb0 = MatrixBuilder::new(MergeMode::Presence, 3, &data_dir).unwrap();
+        let mut mb0 = MatrixBuilder::new(true, 3, &data_dir).unwrap();
         mb0.add_absent_col().unwrap();
         mb0.close().unwrap();
 
         // This merge: resume and append two more source columns.
-        let mut mb = MatrixBuilder::resume(MergeMode::Presence, &data_dir).unwrap();
+        let mut mb = MatrixBuilder::resume(true, &data_dir).unwrap();
         for vals in [[true, false, true], [false, true, false]] {
             let mut col = mb.add_col().unwrap();
             match &mut col {
@@ -368,7 +320,7 @@ pub(crate) fn merge_partition(
             MergeMode::Count => new_layer_dir.join("counts"),
         };
         fs::create_dir_all(&data_dir)?;
-        let mut mb = MatrixBuilder::new(mode, n_new, &data_dir).map_err(OKIError::Io)?;
+        let mut mb = MatrixBuilder::new(presence(mode), n_new, &data_dir).map_err(OKIError::Io)?;
         for _ in 0..n_dst_genomes {
             mb.add_absent_col().map_err(OKIError::Io)?;
         }
@@ -393,7 +345,7 @@ pub(crate) fn merge_partition(
             MergeMode::Presence => layer_dir.join("presence"),
             MergeMode::Count => layer_dir.join("counts"),
         };
-        let mut mb = MatrixBuilder::resume(mode, &data_dir).map_err(OKIError::Io)?;
+        let mut mb = MatrixBuilder::resume(presence(mode), &data_dir).map_err(OKIError::Io)?;
         let cols = (0..n_src_total)
             .map(|_| mb.add_col().map_err(OKIError::Io))
             .collect::<OKIResult<Vec<_>>>()?;