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/obikindex/src/dump.rs

@@ -0,0 +1,50 @@
+use std::io::Write;
+
+use crate::error::{OKIError, OKIResult};
+use crate::index::KmerIndex;
+
+impl KmerIndex {
+    /// Write a CSV table of all indexed kmers to `out`.
+    ///
+    /// Columns: `kmer`, then one column per genome (in index order).
+    /// Values are counts (u32) when `use_counts = true`, otherwise 0/1.
+    ///
+    /// `force_presence` overrides `with_counts`: even if the index stores counts,
+    /// the output uses 0/1 presence columns.
+    ///
+    /// The caller must have set the global kmer length (`obikseq::set_k`) before
+    /// calling this method.
+    pub fn dump<W: Write>(&self, out: &mut W, force_presence: bool) -> OKIResult<()> {
+
+        let genomes  = &self.meta.genomes;
+        let use_counts = self.meta.config.with_counts && !force_presence;
+        let n_genomes  = genomes.len().max(1);
+
+        // ── Header ────────────────────────────────────────────────────────────
+        write!(out, "kmer")?;
+        for g in genomes {
+            write!(out, ",{g}")?;
+        }
+        writeln!(out)?;
+
+        // ── Rows ──────────────────────────────────────────────────────────────
+        let n = self.n_partitions();
+        for i in 0..n {
+            self.partition
+                .iter_partition_kmers(i, use_counts, n_genomes, |kmer, row| {
+                    let seq = String::from_utf8(kmer.to_ascii())
+                        .unwrap_or_else(|_| "?".repeat(self.kmer_size()));
+                    // write is infallible inside a closure — propagate via a flag if needed
+                    let _ = write!(out, "{seq}");
+                    for &v in row.iter() {
+                        let _ = write!(out, ",{v}");
+                    }
+                    let _ = writeln!(out);
+                })
+                .map_err(OKIError::Partition)?;
+        }
+
+        out.flush()?;
+        Ok(())
+    }
+}

src/obikindex/src/lib.rs

@@ -1,6 +1,7 @@
 pub mod error;
 pub mod meta;
 pub mod state;
+mod dump;
 mod index;
 mod merge;
 

src/obikmer/src/cmd/dump.rs

@@ -0,0 +1,39 @@
+use std::io::{self, BufWriter};
+use std::path::PathBuf;
+
+use clap::Args;
+use obikindex::KmerIndex;
+use obikseq::set_k;
+use tracing::info;
+
+#[derive(Args)]
+pub struct DumpArgs {
+    /// Index directory to dump
+    pub index: PathBuf,
+
+    /// Output presence/absence (0/1) even if the index stores counts
+    #[arg(long, default_value_t = false)]
+    pub force_presence: bool,
+}
+
+pub fn run(args: DumpArgs) {
+    let idx = KmerIndex::open(&args.index).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    });
+
+    set_k(idx.kmer_size());
+    info!(
+        "dumping {} partitions, {} genome(s)",
+        idx.n_partitions(),
+        idx.meta().genomes.len()
+    );
+
+    let stdout = io::stdout();
+    let mut out = BufWriter::new(stdout.lock());
+
+    idx.dump(&mut out, args.force_presence).unwrap_or_else(|e| {
+        eprintln!("dump error: {e}");
+        std::process::exit(1);
+    });
+}

src/obikmer/src/cmd/mod.rs

@@ -1,3 +1,4 @@
+pub mod dump;
 pub mod index;
 pub mod merge;
 pub mod superkmer;

src/obikmer/src/main.rs

@@ -20,6 +20,8 @@ enum Commands {
     Index(cmd::index::IndexArgs),
     /// Merge multiple built indexes into one
     Merge(cmd::merge::MergeArgs),
+    /// Dump all indexed kmers as CSV (kmer + per-genome counts or presence)
+    Dump(cmd::dump::DumpArgs),
     /// Dump unitigs from a built index to stdout (debug)
     Unitig(cmd::unitig::UnitigArgs),
 }
@@ -46,6 +48,7 @@ fn main() {
         Commands::Superkmer(args) => cmd::superkmer::run(args),
         Commands::Index(args)     => cmd::index::run(args),
         Commands::Merge(args)     => cmd::merge::run(args),
+        Commands::Dump(args)      => cmd::dump::run(args),
         Commands::Unitig(args)    => cmd::unitig::run(args),
     }
 

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;