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;