feat: add CLI command to export indexed k-mers to CSV

This change introduces a new `dump` subcommand that exports all indexed k-mers to a CSV stream. The implementation spans multiple crates, adding core export logic to `obikindex` and partition iteration to `obikpartitionner`. The command supports a `--force-presence` flag to output binary presence/absence data instead of stored counts, and includes necessary module registrations and structural updates across the codebase.

src/obikpartitionner/src/dump_layer.rs

@@ -0,0 +1,77 @@
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
+use obikseq::CanonicalKmer;
+use obiskio::{SKError, SKResult, UnitigFileReader};
+use obilayeredmap::OLMError;
+use obilayeredmap::meta::PartitionMeta;
+use obilayeredmap::MphfLayer;
+
+use crate::partition::KmerPartition;
+
+const INDEX_SUBDIR: &str = "index";
+
+fn olm_to_sk(e: OLMError) -> SKError {
+    match e {
+        OLMError::Io(e) => SKError::Io(e),
+        other => SKError::InvalidData { context: "dump", detail: other.to_string() },
+    }
+}
+
+impl KmerPartition {
+    /// Iterate all indexed kmers in partition `part`, calling `cb(kmer, row)` for each.
+    ///
+    /// `use_counts = true`  → reads count columns (u32 values per genome).
+    /// `use_counts = false` → reads presence columns, converted to 0/1 u32.
+    ///
+    /// If no data matrix exists for a layer (pure set-membership, single genome),
+    /// a row of `n_genomes` ones is emitted for every kmer in that layer.
+    pub fn iter_partition_kmers(
+        &self,
+        part: usize,
+        use_counts: bool,
+        n_genomes: usize,
+        mut cb: impl FnMut(CanonicalKmer, Box<[u32]>),
+    ) -> SKResult<()> {
+        let index_dir = self.part_dir(part).join(INDEX_SUBDIR);
+        if !index_dir.exists() {
+            return Ok(());
+        }
+
+        let meta = PartitionMeta::load(&index_dir).map_err(olm_to_sk)?;
+
+        for l in 0..meta.n_layers {
+            let layer_dir = index_dir.join(format!("layer_{l}"));
+            let mphf = MphfLayer::open(&layer_dir).map_err(olm_to_sk)?;
+            let reader = UnitigFileReader::open(&layer_dir.join("unitigs.bin"))?;
+
+            let counts_dir  = layer_dir.join("counts");
+            let presence_dir = layer_dir.join("presence");
+
+            if use_counts && counts_dir.exists() {
+                let mat = PersistentCompactIntMatrix::open(&counts_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)?;
+                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();
+                        cb(kmer, row);
+                    }
+                }
+            } else {
+                // No data matrix: pure set-membership layer, all kmers belong to every genome.
+                let all_present: Box<[u32]> = vec![1u32; n_genomes].into();
+                for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
+                    if mphf.find(kmer).is_some() {
+                        cb(kmer, all_present.clone());
+                    }
+                }
+            }
+        }
+
+        Ok(())
+    }
+}

src/obikpartitionner/src/lib.rs

@@ -1,3 +1,4 @@
+mod dump_layer;
 mod index_layer;
 mod kmer_sort;
 mod merge_layer;