refactor: migrate pipeline stages and improve graph processing

Refactored neighbor resolution to explicitly track unvisited indices for degree-1 nodes, updated display formatting, and added timing and debug logging to the degree computation routine. Migrated pipeline stages from eager vector returns to explicit flat implementations, enabling backpressure-aware streaming, configurable batch processing, incremental yielding, and progress tracking via a delta channel.

src/obidebruinj/src/debruijn.rs

@@ -6,6 +6,7 @@ use rayon::iter::{IntoParallelRefIterator, ParallelIterator};
 use std::fmt;
 use std::sync::atomic::{AtomicU8, Ordering};
 use xxhash_rust::xxh3::Xxh3Builder;
+use std::time::Instant;
 use tracing::{debug, info};
 
 // ── Types ─────────────────────────────────────────────────────────────────────
@@ -96,25 +97,6 @@ impl Node {
         (self.0 >> 5) & 0b11
     }
 
-    /// Number of left neighbours.
-    pub fn n_left_neighbours(self) -> u8 {
-        if self.can_extend_left() {
-            1
-        } else {
-            let v = (self.0 >> 5) & 0b11;
-            v + (v != 0) as u8
-        }
-    }
-
-    /// Number of right neighbours.
-    pub fn n_right_neighbours(self) -> u8 {
-        if self.can_extend_right() {
-            1
-        } else {
-            let v = (self.0 >> 3) & 0b11;
-            v + (v != 0) as u8
-        }
-    }
 
     /// Marks the node as visited.
     #[inline]
@@ -162,13 +144,17 @@ impl fmt::Display for Node {
         const NUC: [char; 4] = ['A', 'C', 'G', 'T'];
         let r = if self.can_extend_right() {
             format!("→{}", NUC[self.right_nuc() as usize])
+        } else if (self.0 >> 3) & 0b11 == 0 {
+            "→0".to_string()
         } else {
-            format!("→{}", self.n_right_neighbours())
+            "→≥2".to_string()
         };
         let l = if self.can_extend_left() {
             format!("←{}", NUC[self.left_nuc() as usize])
+        } else if (self.0 >> 5) & 0b11 == 0 {
+            "←0".to_string()
         } else {
-            format!("←{}", self.n_left_neighbours())
+            "←≥2".to_string()
         };
         let v = if self.is_visited() { "V" } else { "." };
         write!(f, "Node({r} {l} {v})")
@@ -272,6 +258,7 @@ impl GraphDeBruijn {
     pub fn compute_degrees_and_mark_starts(&self) {
         // Pass 1: count right/left neighbors for each node
 
+        let t1 = Instant::now();
         self.for_each_node(|kmer, atomic| {
             let mut old = Node(atomic.load(Ordering::Relaxed));
             if old.is_visited() {
@@ -286,9 +273,11 @@ impl GraphDeBruijn {
             node.set_left(lc, ln);
             atomic.store(node.0, Ordering::Relaxed);
         });
+        debug!("[compute_degrees] pass 1 (degrees): {:?} — {} nodes", t1.elapsed(), self.nodes.len());
 
         // Pass 2: mark start nodes
 
+        let t2 = Instant::now();
         self.for_each_node(|kmer, atomic| {
             let mut node = Node(atomic.load(Ordering::Relaxed));
             if node.is_visited() {
@@ -299,6 +288,7 @@ impl GraphDeBruijn {
                 atomic.store(node.0, Ordering::Relaxed);
             }
         });
+        debug!("[compute_degrees] pass 2 (starts):  {:?} — {} nodes", t2.elapsed(), self.nodes.len());
     }
 
     pub fn is_visited(&self, kmer: &CanonicalKmer) -> Option<bool> {
@@ -527,23 +517,18 @@ fn count_neighbors(
     nodes: &FastHashMap<CanonicalKmer, AtomicU8>,
 ) -> (u8, Option<u8>) {
     let mut count = 0u8;
-    let mut first = None;
+    let mut nuc = 0u8;
     for (i, neighbour) in neighbors.iter().enumerate() {
         if let Some(a) = nodes.get(neighbour) {
             if Node(a.load(Ordering::Relaxed)).is_visited() {
                 continue;
             }
+            nuc = i as u8;
             count += 1;
-            if first.is_none() {
-                first = Some(i as u8);
-            }
+            if count >= 2 { return (2, None); }
         }
     }
-    if count == 1 {
-        (1, first)
-    } else {
-        (count, None)
-    }
+    if count == 1 { (1, Some(nuc)) } else { (0, None) }
 }
 
 // ── tests ─────────────────────────────────────────────────────────────────────