refactor: pass Unitig objects directly instead of raw byte slices

Refactored `try_for_each_unitig` and related pipelines across `obidebruinj` and `obikpartitionner` to accept `Unitig` instances directly. This eliminates manual `Unitig::from_nucleotides()` conversions, simplifies the data flow, and reduces unnecessary allocation overhead.

src/obidebruinj/src/debruijn.rs

@@ -1,7 +1,7 @@
 //use ahash::RandomState;
 use hashbrown::HashMap;
 use obikseq::k;
-use obikseq::{CanonicalKmer, Sequence};
+use obikseq::{CanonicalKmer, Sequence, Unitig};
 use rayon::iter::{IntoParallelRefIterator, ParallelIterator};
 use std::cell::RefCell;
 use std::fmt;
@@ -452,17 +452,17 @@ impl GraphDeBruijn {
     pub fn try_for_each_unitig<E, F>(&self, f: F) -> Result<(), E>
     where
         E: Send,
-        F: FnMut(&[u8]) -> Result<(), E> + Send,
+        F: FnMut(&Unitig) -> Result<(), E> + Send,
     {
         thread_local! {
             static BUF: RefCell<Vec<u8>> = RefCell::new(Vec::with_capacity(4096));
         }
-        let (tx, rx) = crossbeam_channel::bounded::<Vec<u8>>(rayon::current_num_threads() * 256);
+        let (tx, rx) = crossbeam_channel::bounded::<Unitig>(rayon::current_num_threads() * 256);
         std::thread::scope(|s| {
             let writer = s.spawn(move || -> Result<(), E> {
                 let mut f = f;
-                for nucs in rx {
-                    f(&nucs)?;
+                for unitig in rx {
+                    f(&unitig)?;
                 }
                 Ok(())
             });
@@ -471,9 +471,7 @@ impl GraphDeBruijn {
                     let mut buf = buf.borrow_mut();
                     buf.clear();
                     buf.extend(iter);
-                    let to_send = buf.clone();
-                    buf.clear();
-                    tx.send(to_send).ok();
+                    tx.send(Unitig::from_nucleotides(&buf)).ok();
                 });
             });
             drop(tx);

src/obidebruinj/src/tests/debruijn.rs

@@ -24,8 +24,8 @@ fn canonical_kmers(seq: &[u8]) -> Vec<CanonicalKmer> {
 
 fn collect_unitigs(g: &GraphDeBruijn) -> Vec<Unitig> {
     let mut unitigs = Vec::new();
-    g.try_for_each_unitig(|nucs| -> Result<(), std::convert::Infallible> {
-        unitigs.push(Unitig::from_nucleotides(nucs));
+    g.try_for_each_unitig(|unitig| -> Result<(), std::convert::Infallible> {
+        unitigs.push(unitig.clone());
         Ok(())
     })
     .unwrap();

src/obikpartitionner/src/index_layer.rs

@@ -107,8 +107,8 @@ impl KmerPartition {
         fs::create_dir_all(&layer_dir)?;
 
         let mut uw = Layer::<()>::unitig_writer(&layer_dir).map_err(olm_to_sk)?;
-        g.try_for_each_unitig(|nucs| {
-            uw.write(&obikseq::unitig::Unitig::from_nucleotides(nucs))
+        g.try_for_each_unitig(|unitig| {
+            uw.write(unitig)
         })?;
         uw.close()?;
 

src/obikpartitionner/src/merge_layer.rs

@@ -307,8 +307,8 @@ impl KmerPartition {
             g.compute_degrees_and_mark_starts();
             fs::create_dir_all(&new_layer_dir)?;
             let mut uw = Layer::<()>::unitig_writer(&new_layer_dir).map_err(olm_to_sk)?;
-            g.try_for_each_unitig(|nucs| {
-                uw.write(&obikseq::unitig::Unitig::from_nucleotides(nucs))
+            g.try_for_each_unitig(|unitig| {
+                uw.write(unitig)
             })?;
             uw.close()?;
             let n = g.len();

src/obikpartitionner/src/rebuild_layer.rs

@@ -168,8 +168,8 @@ impl KmerPartition {
         fs::create_dir_all(&dst_layer_dir)?;
 
         let mut uw = Layer::<()>::unitig_writer(&dst_layer_dir).map_err(olm_to_sk)?;
-        g.try_for_each_unitig(|nucs| {
-            uw.write(&obikseq::unitig::Unitig::from_nucleotides(nucs))
+        g.try_for_each_unitig(|unitig| {
+            uw.write(unitig)
         })?;
         uw.close()?;
         drop(g);