From c8e591fc78e2a9148f331e273e7aab3062f69fb6 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Thu, 21 May 2026 12:17:32 +0200
Subject: [PATCH] feat: add superkmer CLI setup and partition bit handling

This commit introduces CLI argument parsing for the `superkmer` command via a new `SuperkmerArgs` struct. It also adds a `partitions_to_bits` utility to compute the minimum bit width for partition encoding, enforcing a 1-bit floor. Finally, the index configuration automatically rounds the partition count up to the nearest power of two to ensure compatibility with bitmask-based indexing operations.
---
 src/obikmer/src/cli.rs           | 12 +++++++++---
 src/obikmer/src/cmd/index.rs     |  9 +++++++--
 src/obikmer/src/cmd/superkmer.rs |  4 ++--
 3 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/src/obikmer/src/cli.rs b/src/obikmer/src/cli.rs
index 76ed52f..1b79fa0 100644
--- a/src/obikmer/src/cli.rs
+++ b/src/obikmer/src/cli.rs
@@ -29,9 +29,9 @@ pub struct CommonArgs {
     #[arg(long, default_value_t = 6)]
     pub level_max: usize,
 
-    /// Number of bits to encode partitions (allows up to 2^partition_bits partitions)
-    #[arg(short, long, default_value_t = 8)]
-    pub partition_bits: usize,
+    /// Number of partitions (rounded up to the next power of 2)
+    #[arg(short, long, default_value_t = 256)]
+    pub partitions: usize,
 
     /// Number of worker threads
     #[arg(
@@ -44,6 +44,12 @@ pub struct CommonArgs {
     pub threads: usize,
 }
 
+/// Smallest `b` such that `2^b >= n` (i.e. `n.next_power_of_two().ilog2()`).
+/// Minimum 1 (degenerate n=0 or n=1 → 1 partition).
+pub fn partitions_to_bits(n: usize) -> usize {
+    n.max(1).next_power_of_two().trailing_zeros() as usize
+}
+
 impl CommonArgs {
     pub fn seqfile_paths(&self) -> obiread::PathIter {
         let paths = self.inputs.iter().map(PathBuf::from).collect();
diff --git a/src/obikmer/src/cmd/index.rs b/src/obikmer/src/cmd/index.rs
index ccfa487..38bc722 100644
--- a/src/obikmer/src/cmd/index.rs
+++ b/src/obikmer/src/cmd/index.rs
@@ -6,7 +6,7 @@ use obikseq::{set_k, set_m};
 use obisys::Reporter;
 use tracing::info;
 
-use crate::cli::CommonArgs;
+use crate::cli::{CommonArgs, partitions_to_bits};
 use crate::steps::scatter;
 
 #[derive(Args)]
@@ -62,10 +62,15 @@ pub fn run(args: IndexArgs) {
                 std::process::exit(1);
             });
         }
+        let n_bits = partitions_to_bits(args.common.partitions);
+        let effective = 1usize << n_bits;
+        if effective != args.common.partitions {
+            info!("partitions: {} → {} (next power of 2)", args.common.partitions, effective);
+        }
         let config = IndexConfig {
             kmer_size:      args.common.kmer_size,
             minimizer_size: args.common.minimizer_size,
-            n_bits:         args.common.partition_bits,
+            n_bits,
             with_counts:    args.with_counts,
         };
         KmerIndex::create(&output, config, args.label.clone(), false).unwrap_or_else(|e| {
diff --git a/src/obikmer/src/cmd/superkmer.rs b/src/obikmer/src/cmd/superkmer.rs
index 2ea1060..881d4a6 100644
--- a/src/obikmer/src/cmd/superkmer.rs
+++ b/src/obikmer/src/cmd/superkmer.rs
@@ -5,7 +5,7 @@ use clap::Args;
 use obifastwrite::write_scatter;
 use obikseq::{RoutableSuperKmer, set_k, set_m};
 
-use crate::cli::{CommonArgs, PipelineData, open_chunks};
+use crate::cli::{CommonArgs, PipelineData, open_chunks, partitions_to_bits};
 
 #[derive(Args)]
 pub struct SuperkmerArgs {
@@ -38,7 +38,7 @@ pub fn run(args: SuperkmerArgs) {
     let m = args.common.minimizer_size;
     let theta = args.common.theta;
     let level_max = args.common.level_max;
-    let partition_bits = args.common.partition_bits;
+    let partition_bits = partitions_to_bits(args.common.partitions);
     let n_workers = args.common.threads.max(1);
 
     set_k(k);