refactor: rename rebuild subcommand to filter

Rename the `rebuild` CLI subcommand to `filter` to better reflect its primary purpose of row-level selection and k-mer filtering. Update all associated CLI arguments, logging, error messages, and module registrations accordingly. Introduce a dedicated `Rebuild` subcommand for index compaction, fully decoupling it from the filtering logic. Also refine related documentation to align with the new naming and semantics.

src/obikmer/src/cmd/filter.rs

@@ -6,10 +6,10 @@ use obikpartitionner::filter::{MaxTotalCount, MinTotalCount};
 use obisys::Reporter;
 use tracing::info;
 
-use super::predicate::FilterArgs;
+use super::predicate::FilterArgs as KmerFilterArgs;
 
 #[derive(Args)]
-pub struct RebuildArgs {
+pub struct FilterArgs {
     /// Source index directory
     pub source: PathBuf,
 
@@ -18,7 +18,7 @@ pub struct RebuildArgs {
     pub output: PathBuf,
 
     #[command(flatten)]
-    pub filter: FilterArgs,
+    pub filter: KmerFilterArgs,
 
     /// Minimum total count across all genomes (count index only)
     #[arg(long)]
@@ -37,7 +37,7 @@ pub struct RebuildArgs {
     pub force: bool,
 }
 
-pub fn run(args: RebuildArgs) {
+pub fn run(args: FilterArgs) {
     let src = KmerIndex::open(&args.source).unwrap_or_else(|e| {
         eprintln!("error opening source index: {e}");
         std::process::exit(1);
@@ -50,7 +50,7 @@ pub fn run(args: RebuildArgs) {
     };
 
     info!(
-        "rebuild: {} genome(s), mode={:?}, source={}",
+        "filter: {} genome(s), mode={:?}, source={}",
         &src.meta().genomes.len(), mode, args.source.display()
     );
 
@@ -66,10 +66,10 @@ pub fn run(args: RebuildArgs) {
     let mut rep = Reporter::new();
     KmerIndex::rebuild(&args.output, &src, &filters, mode, args.force, &mut rep)
         .unwrap_or_else(|e| {
-            eprintln!("error rebuilding index: {e}");
+            eprintln!("error filtering index: {e}");
             std::process::exit(1);
         });
 
     rep.print();
-    info!("rebuilt index → {}", args.output.display());
+    info!("filtered index → {}", args.output.display());
 }

src/obikmer/src/cmd/mod.rs

@@ -1,4 +1,5 @@
 pub mod annotate;
+pub mod filter;
 pub mod pack;
 pub(crate) mod predicate;
 pub mod select;
@@ -9,7 +10,6 @@ pub mod estimate;
 pub mod index;
 pub mod merge;
 pub mod query;
-pub mod rebuild;
 pub mod reindex;
 pub mod superkmer;
 pub mod unitig;

src/obikmer/src/main.rs

@@ -20,10 +20,8 @@ enum Commands {
     Index(cmd::index::IndexArgs),
     /// Merge multiple built indexes into one
     Merge(cmd::merge::MergeArgs),
-    /// Filter and compact an existing index into a new single-layer index
-    Rebuild(cmd::rebuild::RebuildArgs),
-    /// Alias for rebuild
-    Filter(cmd::rebuild::RebuildArgs),
+    /// Apply row-level selection (σ) to an index: retain only k-mers matching the predicates
+    Filter(cmd::filter::FilterArgs),
     /// Project and/or aggregate genome columns into a new or in-place index
     Select(cmd::select::SelectArgs),
     /// Query an index with sequences and annotate matches
@@ -69,8 +67,7 @@ fn main() {
         Commands::Index(args)     => cmd::index::run(args),
         Commands::Merge(args)     => cmd::merge::run(args),
         Commands::Dump(args)      => cmd::dump::run(args),
-        Commands::Rebuild(args)   => cmd::rebuild::run(args),
-        Commands::Filter(args)    => cmd::rebuild::run(args),
+        Commands::Filter(args)    => cmd::filter::run(args),
         Commands::Select(args)    => cmd::select::run(args),
         Commands::Query(args)     => cmd::query::run(args),
         Commands::Annotate(args)  => cmd::annotate::run(args),