refactor: rename compute_degrees and mark start nodes

Renames `compute_degrees` to `compute_degrees_and_mark_starts` across the De Bruijn graph and partitioner layers to consolidate degree calculation and start-node flagging. Introduces safe neighbor iteration methods and a debug validation block to verify graph consistency. Refactors unitig extraction to use sequential execution with a `Mutex` for safe error propagation. Fixes malformed and duplicated method calls, adds auto-generation of missing `meta.json` files, and ensures persistent matrix builders are explicitly closed to finalize metadata.

src/obikpartitionner/src/rebuild_layer.rs

@@ -2,15 +2,15 @@ use std::fs;
 use std::io;
 use std::path::{Path, PathBuf};
 
-use obicompactvec::{PersistentBitMatrixBuilder,
-                    PersistentBitVecBuilder,
-                    PersistentCompactIntMatrixBuilder,
-                    PersistentCompactIntVecBuilder};
+use obicompactvec::{
+    PersistentBitMatrixBuilder, PersistentBitVecBuilder, PersistentCompactIntMatrixBuilder,
+    PersistentCompactIntVecBuilder,
+};
 use obidebruinj::GraphDeBruijn;
 use obikseq::CanonicalKmer;
-use obiskio::{SKError, SKResult, UnitigFileReader};
-use obilayeredmap::{IndexMode, Layer, MphfLayer, OLMError};
 use obilayeredmap::meta::PartitionMeta;
+use obilayeredmap::{IndexMode, Layer, MphfLayer, OLMError};
+use obiskio::{SKError, SKResult, UnitigFileReader};
 
 use crate::filter::{KmerFilter, passes_all};
 use crate::merge_layer::{MergeMode, SrcLayerData};
@@ -21,7 +21,10 @@ const INDEX_SUBDIR: &str = "index";
 fn olm_to_sk(e: OLMError) -> SKError {
     match e {
         OLMError::Io(e) => SKError::Io(e),
-        other => SKError::InvalidData { context: "rebuild", detail: other.to_string() },
+        other => SKError::InvalidData {
+            context: "rebuild",
+            detail: other.to_string(),
+        },
     }
 }
 
@@ -34,7 +37,10 @@ fn col_path_int(dir: &Path, col: usize) -> PathBuf {
 }
 
 fn write_matrix_meta(dir: &Path, n: usize, n_cols: usize) -> io::Result<()> {
-    fs::write(dir.join("meta.json"), format!("{{\"n\":{n},\"n_cols\":{n_cols}}}\n"))
+    fs::write(
+        dir.join("meta.json"),
+        format!("{{\"n\":{n},\"n_cols\":{n_cols}}}\n"),
+    )
 }
 
 // ── ColBuilder ────────────────────────────────────────────────────────────────
@@ -54,8 +60,8 @@ impl ColBuilder {
 
     fn close(self) -> SKResult<()> {
         match self {
-            ColBuilder::Bit(b)  => b.close().map_err(SKError::Io),
-            ColBuilder::Int(b)  => b.close().map_err(SKError::Io),
+            ColBuilder::Bit(b) => b.close().map_err(SKError::Io),
+            ColBuilder::Int(b) => b.close().map_err(SKError::Io),
         }
     }
 }
@@ -65,10 +71,16 @@ impl ColBuilder {
 fn load_meta(dir: &Path) -> SKResult<PartitionMeta> {
     match PartitionMeta::load(dir) {
         Ok(m) => Ok(m),
-        Err(e) if matches!(e, OLMError::Io(ref io_e) if io_e.kind() == std::io::ErrorKind::NotFound) => {
+        Err(e) if matches!(e, OLMError::Io(ref io_e) if io_e.kind() == std::io::ErrorKind::NotFound) =>
+        {
             let mut n = 0usize;
-            while dir.join(format!("layer_{n}")).exists() { n += 1; }
-            let m = PartitionMeta { n_layers: n, mode: IndexMode::default() };
+            while dir.join(format!("layer_{n}")).exists() {
+                n += 1;
+            }
+            let m = PartitionMeta {
+                n_layers: n,
+                mode: IndexMode::default(),
+            };
             m.save(dir).map_err(olm_to_sk)?;
             Ok(m)
         }
@@ -90,10 +102,12 @@ fn iter_src_layers(
     let src_meta = load_meta(src_index_dir)?;
     for l in 0..src_meta.n_layers {
         let src_layer_dir = src_index_dir.join(format!("layer_{l}"));
-        let unitigs_path  = src_layer_dir.join("unitigs.bin");
-        if !unitigs_path.exists() { continue; }
+        let unitigs_path = src_layer_dir.join("unitigs.bin");
+        if !unitigs_path.exists() {
+            continue;
+        }
 
-        let reader   = UnitigFileReader::open_sequential(&unitigs_path)?;
+        let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
         let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
 
         for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
@@ -146,7 +160,7 @@ impl KmerPartition {
         }
 
         let n_new = g.len();
-        g.compute_degrees();
+        g.compute_degrees_and_mark_starts();
 
         // ── Build MPHF in dst layer_0 ─────────────────────────────────────────
         let dst_index_dir = self.part_dir(i).join(INDEX_SUBDIR);
@@ -167,26 +181,37 @@ impl KmerPartition {
         // ── Prepare matrix builders (one column per genome) ───────────────────
         let data_dir = match mode {
             MergeMode::Presence => dst_layer_dir.join("presence"),
-            MergeMode::Count    => dst_layer_dir.join("counts"),
+            MergeMode::Count => dst_layer_dir.join("counts"),
         };
         fs::create_dir_all(&data_dir)?;
 
         let mut builders: Vec<ColBuilder> = match mode {
             MergeMode::Presence => {
                 PersistentBitMatrixBuilder::new(n_new, &data_dir)
-                    .map_err(SKError::Io)?.close().map_err(SKError::Io)?;
-                (0..n_genomes).map(|g| -> SKResult<ColBuilder> {
-                    let b = PersistentBitVecBuilder::new(n_new, &col_path_bit(&data_dir, g))?;
-                    Ok(ColBuilder::Bit(b))
-                }).collect::<SKResult<_>>()?
+                    .map_err(SKError::Io)?
+                    .close()
+                    .map_err(SKError::Io)?;
+                (0..n_genomes)
+                    .map(|g| -> SKResult<ColBuilder> {
+                        let b = PersistentBitVecBuilder::new(n_new, &col_path_bit(&data_dir, g))?;
+                        Ok(ColBuilder::Bit(b))
+                    })
+                    .collect::<SKResult<_>>()?
             }
             MergeMode::Count => {
                 PersistentCompactIntMatrixBuilder::new(n_new, &data_dir)
-                    .map_err(SKError::Io)?.close().map_err(SKError::Io)?;
-                (0..n_genomes).map(|g| -> SKResult<ColBuilder> {
-                    let b = PersistentCompactIntVecBuilder::new(n_new, &col_path_int(&data_dir, g))?;
-                    Ok(ColBuilder::Int(b))
-                }).collect::<SKResult<_>>()?
+                    .map_err(SKError::Io)?
+                    .close()
+                    .map_err(SKError::Io)?;
+                (0..n_genomes)
+                    .map(|g| -> SKResult<ColBuilder> {
+                        let b = PersistentCompactIntVecBuilder::new(
+                            n_new,
+                            &col_path_int(&data_dir, g),
+                        )?;
+                        Ok(ColBuilder::Int(b))
+                    })
+                    .collect::<SKResult<_>>()?
             }
         };
 
@@ -200,10 +225,17 @@ impl KmerPartition {
         })?;
 
         // ── Close builders, write metadata ────────────────────────────────────
-        for b in builders { b.close()?; }
+        for b in builders {
+            b.close()?;
+        }
         write_matrix_meta(&data_dir, n_new, n_genomes).map_err(SKError::Io)?;
 
-        PartitionMeta { n_layers: 1, mode: IndexMode::Exact }.save(&dst_index_dir).map_err(olm_to_sk)?;
+        PartitionMeta {
+            n_layers: 1,
+            mode: IndexMode::Exact,
+        }
+        .save(&dst_index_dir)
+        .map_err(olm_to_sk)?;
 
         Ok(())
     }