refactor: shift indexing algorithms to layer-centric partition APIs

Replaces manual filesystem path handling and parallel iteration with dedicated internal utilities. Introduces `par_over_layer0` and `layer0()` to abstract partition layer access, enabling partition-driven initialization and centralized progress tracking. Removes disabled or internal methods (`rewrite_config`, `open_data`) no longer part of the active interface. Updates error propagation and metadata persistence to align with the new layer-centric workflow.

src/obikindex/src/index/kmer_index.rs

@@ -5,7 +5,7 @@ use std::sync::Arc;
 use crate::layer::KmerLayer;
 use crate::partition::KmerPartition;
 use obisys::progress_bar;
-use rayon::prelude::*;
+// use rayon::prelude::*;
 
 use obikseq::{set_k, set_m};
 
@@ -112,16 +112,16 @@ impl KmerIndex {
         1usize << self.meta.config.n_bits
     }
 
-    /// Path of partition `i`'s raw directory (`partitions/part_{i:05}`) —
+    // /// Path of partition `i`'s raw directory (`partitions/part_{i:05}`) —
-    /// delegates to `crate::partition`, the Partition tier's own naming
+    // /// delegates to `crate::partition`, the Partition tier's own naming
-    /// primitive (mirrors `layer_dir` delegating to `crate::layer`).
+    // /// primitive (mirrors `layer_dir` delegating to `crate::layer`).
-    /// `obikindexer::algorithms::partitionner::PartitionRouter` reaches this
+    // /// `obikindexer::algorithms::partitionner::PartitionRouter` reaches this
-    /// same directory only indirectly, through this method — `obikindexer`
+    // /// same directory only indirectly, through this method — `obikindexer`
-    /// depends on `KmerIndex`, not the other way around — see
+    // /// depends on `KmerIndex`, not the other way around — see
-    /// `DevDocMD/implementation/partition_layer_cache.md`.
+    // /// `DevDocMD/implementation/partition_layer_cache.md`.
-    pub(crate) fn partition_dir(&self, i: usize) -> OKIResult<PathBuf> {
+    // pub(crate) fn partition_dir(&self, i: usize) -> OKIResult<PathBuf> {
-        Ok(self.partition(i)?.dir().to_path_buf())
+    //     Ok(self.partition(i)?.dir().to_path_buf())
-    }
+    // }
 
     pub fn partition(&self, i: usize) -> OKIResult<KmerPartition> {
         let n = self.n_partitions();
@@ -227,62 +227,62 @@ impl KmerIndex {
         Ok(())
     }
 
-    /// Write a `layer_meta.json` in any layer directory that is missing one.
+    // /// Write a `layer_meta.json` in any layer directory that is missing one.
-    ///
+    // ///
-    /// Old indexes were built before this file was required.  The number of
+    // /// Old indexes were built before this file was required.  The number of
-    /// kmers is recovered from `unitigs.bin`, which is always present.
+    // /// kmers is recovered from `unitigs.bin`, which is always present.
-    /// TODO: Should not exist anymore
+    // /// TODO: Should not exist anymore
-    pub(crate) fn upgrade_layer_meta(&self) -> OKIResult<()> {
+    // pub(crate) fn upgrade_layer_meta(&self) -> OKIResult<()> {
-        use obicompactvec::LayerMeta;
+    //     use obicompactvec::LayerMeta;
-        use obiskio::UnitigFileReader;
+    //     use obiskio::UnitigFileReader;
 
-        let n = self.n_partitions();
+    //     let n = self.n_partitions();
-        let errors: Vec<_> = (0..n)
+    //     let errors: Vec<_> = (0..n)
-            .into_par_iter()
+    //         .into_par_iter()
-            .filter_map(|i| {
+    //         .filter_map(|i| {
-                let index_dir = self.index_dir(i);
+    //             let index_dir = self.index_dir(i);
-                if !index_dir.exists() {
+    //             if !index_dir.exists() {
-                    return None;
+    //                 return None;
-                }
+    //             }
-                let n_layers = match self.n_layers(i) {
+    //             let n_layers = match self.n_layers(i) {
-                    Ok(n) => n,
+    //                 Ok(n) => n,
-                    Err(e) => {
+    //                 Err(e) => {
-                        return Some(OKIError::Io(std::io::Error::new(
+    //                     return Some(OKIError::Io(std::io::Error::new(
-                            std::io::ErrorKind::Other,
+    //                         std::io::ErrorKind::Other,
-                            e.to_string(),
+    //                         e.to_string(),
-                        )));
+    //                     )));
-                    }
+    //                 }
-                };
+    //             };
-                for l in 0..n_layers {
+    //             for l in 0..n_layers {
-                    let layer_dir = match self.layer_dir(i, l) {
+    //                 let layer_dir = match self.layer_dir(i, l) {
-                        Ok(d) => d,
+    //                     Ok(d) => d,
-                        Err(e) => {
+    //                     Err(e) => {
-                            return Some(OKIError::Io(std::io::Error::new(
+    //                         return Some(OKIError::Io(std::io::Error::new(
-                                std::io::ErrorKind::Other,
+    //                             std::io::ErrorKind::Other,
-                                e.to_string(),
+    //                             e.to_string(),
-                            )));
+    //                         )));
-                        }
+    //                     }
-                    };
+    //                 };
-                    let meta_path = layer_dir.join(LayerMeta::FILENAME);
+    //                 let meta_path = layer_dir.join(LayerMeta::FILENAME);
-                    if meta_path.exists() {
+    //                 if meta_path.exists() {
-                        continue;
+    //                     continue;
-                    }
+    //                 }
-                    let unitigs_path = layer_dir.join("unitigs.bin");
+    //                 let unitigs_path = layer_dir.join("unitigs.bin");
-                    let n_kmers = match UnitigFileReader::open_sequential(&unitigs_path) {
+    //                 let n_kmers = match UnitigFileReader::open_sequential(&unitigs_path) {
-                        Ok(r) => r.n_kmers(),
+    //                     Ok(r) => r.n_kmers(),
-                        Err(e) => return Some(OKIError::Partition(e)),
+    //                     Err(e) => return Some(OKIError::Partition(e)),
-                    };
+    //                 };
-                    if let Err(e) = LayerMeta::save(&layer_dir, n_kmers) {
+    //                 if let Err(e) = LayerMeta::save(&layer_dir, n_kmers) {
-                        return Some(OKIError::Io(e));
+    //                     return Some(OKIError::Io(e));
-                    }
+    //                 }
-                }
+    //             }
-                None
+    //             None
-            })
+    //         })
-            .collect();
+    //         .collect();
 
-        if let Some(e) = errors.into_iter().next() {
+    //     if let Some(e) = errors.into_iter().next() {
-            return Err(e);
+    //         return Err(e);
-        }
+    //     }
-        Ok(())
+    //     Ok(())
-    }
+    // }
 }

src/obikindex/src/index/meta.rs

@@ -218,29 +218,29 @@ impl IndexMeta {
         self.write_full(&on_disk)
     }
 
-    /// Overwrite `config` and the whole `genomes` list at once, preserving
+    // /// Overwrite `config` and the whole `genomes` list at once, preserving
-    /// `state`. `config` otherwise never changes once an index exists —
+    // /// `state`. `config` otherwise never changes once an index exists —
-    /// this is the deliberate, rare exception for construction paths that
+    // /// this is the deliberate, rare exception for construction paths that
-    /// legitimately rewrite it in place (`select_in_place`, `reindex`).
+    // /// legitimately rewrite it in place (`select_in_place`, `reindex`).
-    /// The caller must refresh its own cached `Arc<IndexMeta>` afterward
+    // /// The caller must refresh its own cached `Arc<IndexMeta>` afterward
-    /// (e.g. `self.meta = Arc::new(IndexMeta::open(self)?)`) — this method
+    // /// (e.g. `self.meta = Arc::new(IndexMeta::open(self)?)`) — this method
-    /// only updates the file, it has no way to reach back into whatever
+    // /// only updates the file, it has no way to reach back into whatever
-    /// `KmerIndex` holds it.
+    // /// `KmerIndex` holds it.
-    /// TODO: This methode is strange
+    // /// TODO: This methode is strange
-    pub(crate) fn rewrite_config(
+    // pub(crate) fn rewrite_config(
-        &self,
+    //     &self,
-        config: IndexConfig,
+    //     config: IndexConfig,
-        genomes: Vec<GenomeInfo>,
+    //     genomes: Vec<GenomeInfo>,
-    ) -> io::Result<()> {
+    // ) -> io::Result<()> {
-        let _guard = self.lock.write().unwrap();
+    //     let _guard = self.lock.write().unwrap();
-        let state = Self::read_full(&self.root_path)?.state;
+    //     let state = Self::read_full(&self.root_path)?.state;
-        self.write_full(&IndexMetadata {
+    //     self.write_full(&IndexMetadata {
-            version: self.version,
+    //         version: self.version,
-            config,
+    //         config,
-            genomes,
+    //         genomes,
-            state,
+    //         state,
-        })
+    //     })
-    }
+    // }
 
     pub fn set_state(&self, state: IndexState) -> io::Result<()> {
         let _guard = self.lock.write().unwrap();

src/obikindex/src/layer/typed_layer.rs

@@ -1,4 +1,4 @@
-use crate::layer::utils::layer_dir;
+// use crate::layer::utils::layer_dir;
 use obicompactvec::{
     BinaryMatrix, PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentCompactIntMatrix,
     PersistentCompactIntMatrixBuilder, PersistentSparseBitMatrix,
@@ -24,20 +24,20 @@ pub trait LayerData: Sized {
     fn read(&self, slot: usize) -> Self::Item;
 }
 
-/// Opens layer `i`'s data only, skipping the MPHF — for callers that only
+// /// Opens layer `i`'s data only, skipping the MPHF — for callers that only
-/// need matrix-level operations (distance traits, column weights, group
+// /// need matrix-level operations (distance traits, column weights, group
-/// filters, sub-matrix extraction) and never look up a kmer for this layer.
+// /// filters, sub-matrix extraction) and never look up a kmer for this layer.
-/// `TypedLayer<D>::open` always pays for the MPHF too (and doesn't expose `data`
+// /// `TypedLayer<D>::open` always pays for the MPHF too (and doesn't expose `data`
-/// once open), so it's the wrong tool for these; this is the other half of
+// /// once open), so it's the wrong tool for these; this is the other half of
-/// the same `D::open(layer_dir)` call, without the MPHF alongside it.
+// /// the same `D::open(layer_dir)` call, without the MPHF alongside it.
-///
+// ///
-/// Takes `(root, i)`, not a pre-built path: the caller names a layer
+// /// Takes `(root, i)`, not a pre-built path: the caller names a layer
-/// *number* within a partition it already knows the root of, the same
+// /// *number* within a partition it already knows the root of, the same
-/// vocabulary as [`layer_dir`] and `LayeredMap` — never the `layer_N`
+// /// vocabulary as [`layer_dir`] and `LayeredMap` — never the `layer_N`
-/// naming convention itself, which stays private to this crate.
+// /// naming convention itself, which stays private to this crate.
-pub(crate) fn open_data<D: LayerData>(root: &Path, i: usize) -> OKIResult<D> {
+// pub(crate) fn open_data<D: LayerData>(root: &Path, i: usize) -> OKIResult<D> {
-    D::open(&layer_dir(root, i))
+//     D::open(&layer_dir(root, i))
-}
+// }
 
 impl LayerData for () {
     type Item = ();

src/obikindexer/src/algorithms/counter/mod.rs

@@ -8,16 +8,14 @@
 mod count;
 mod kmer_sort;
 
+use crate::algorithms::{existing_layer0, par_over_layer0};
 use std::collections::BTreeMap;
 use std::fs;
 use std::io;
-use std::sync::atomic::{AtomicU64, Ordering};
 
 use obikalgorithm::Algorithm;
 use obikindex::KmerIndex;
-use obiskio::SKResult;
 use obisys::Progress;
-use rayon::prelude::*;
 use sysinfo::System;
 
 use count::count_partition;
@@ -86,7 +84,7 @@ impl Algorithm for Counter<'_> {
     fn run(&mut self) -> obikalgorithm::Result<KmerSpectrum> {
         let index = self.index;
         let n_partitions = self.n_partitions;
-        let on_progress = &self.on_progress;
+        let on_progress = self.on_progress.as_deref();
         let sys = System::new_all();
         // available_memory() can return 0 on macOS when the compressor page count exceeds
         // free+inactive+purgeable pages (sysinfo saturating_sub). Fall back to half of total.
@@ -96,40 +94,23 @@ impl Algorithm for Counter<'_> {
         };
         let n_threads = rayon::current_num_threads().max(1) as u64;
         let chunk_kmers = chunk_size_from_ram(available / n_threads);
-        let done = AtomicU64::new(0);
 
-        let results: Vec<SKResult<()>> = (0..n_partitions)
+        par_over_layer0(index, n_partitions, on_progress, |layer| {
-            .into_par_iter()
+            let dedup_path = layer.dereplicated_superkmers_path();
-            .map(|i| {
+            if dedup_path.exists() {
-                let dir = index.layer_dir(i, 0);
+                count_partition(layer.dir(), &dedup_path, chunk_kmers)
-                let dedup_path = obikindex::layer::dereplicated_superkmers_path(&dir);
-                let result = if dedup_path.exists() {
-                    count_partition(&dir, &dedup_path, chunk_kmers)
             } else {
                 Ok(())
-                };
-                if let Some(cb) = on_progress {
-                    let pos = done.fetch_add(1, Ordering::Relaxed) + 1;
-                    cb(Progress {
-                        position: pos,
-                        total: Some(n_partitions as u64),
-                    });
-                }
-                result
-            })
-            .collect();
-
-        for r in results {
-            r?;
             }
+        })?;
 
         // Aggregate per-partition spectra.
         let mut counts: BTreeMap<u32, u64> = BTreeMap::new();
         let mut f0: u64 = 0;
         let mut f1: u64 = 0;
 
-        for i in 0..n_partitions {
+        for layer in existing_layer0(index, n_partitions) {
-            let path = index.layer_dir(i, 0).join("kmer_spectrum_raw.json");
+            let path = layer.dir().join("kmer_spectrum_raw.json");
             if !path.exists() {
                 continue;
             }

src/obikindexer/src/algorithms/dereplicator/dereplicate.rs

@@ -14,7 +14,7 @@ use niffler::send::compression::Format;
 use niffler::Level;
 use obikseq::superkmer::SuperKmer;
 use obikseq::Sequence;
-use obikindex::layer::{dereplicated_superkmers_path, raw_superkmers_path};
+use obikindex::layer::KmerLayer;
 use obiskio::{SKFileMeta, SKFileReader, SKFileWriter, SKResult};
 
 /// Scratch-file extension for this algorithm's own intermediate split
@@ -72,15 +72,16 @@ fn remove_skmer_file(path: &Path) -> SKResult<()> {
 /// Maximum value that fits in the 24-bit COUNT field of a SuperKmer header.
 const MAX_SK_COUNT: u64 = (1 << 24) - 1;
 
-/// Deduplicate one partition's layer-0 directory in place (two-phase split
+/// Deduplicate one partition's layer-0 in place (two-phase split
-/// + merge): `raw_superkmers_path(dir)` -> `dereplicated_superkmers_path(dir)`.
+/// + merge): `layer.raw_superkmers_path()` -> `layer.dereplicated_superkmers_path()`.
-pub(crate) fn dereplicate_partition(dir: &Path, level: Level, n_temp: usize) -> SKResult<()> {
+pub(crate) fn dereplicate_partition(layer: &KmerLayer, level: Level, n_temp: usize) -> SKResult<()> {
-    let raw_path = raw_superkmers_path(dir);
+    let raw_path = layer.raw_superkmers_path();
     if !raw_path.exists() {
         return Ok(());
     }
+    let dir = layer.dir();
 
-    let out_path = dereplicated_superkmers_path(dir);
+    let out_path = layer.dereplicated_superkmers_path();
     let mut writer = SKFileWriter::create_with(&out_path, Format::Zstd, level)?;
 
     if n_temp == 1 {

src/obikindexer/src/algorithms/dereplicator/mod.rs

@@ -7,12 +7,9 @@
 
 mod dereplicate;
 
-use std::sync::atomic::{AtomicU64, Ordering};
+use crate::algorithms::par_over_layer0;
-
 use niffler::Level;
-use obiskio::SKResult;
 use obisys::Progress;
-use rayon::prelude::*;
 use sysinfo::System;
 
 use obikalgorithm::Algorithm;
@@ -79,7 +76,7 @@ impl Algorithm for Dereplicator<'_> {
         let level = self.level;
         let index = self.index;
         let n_partitions = self.n_partitions;
-        let on_progress = &self.on_progress;
+        let on_progress = self.on_progress.as_deref();
         let sys = System::new_all();
         // available_memory() can return 0 on macOS when the compressor page count exceeds
         // free+inactive+purgeable pages (sysinfo saturating_sub). Fall back to half of total.
@@ -89,30 +86,12 @@ impl Algorithm for Dereplicator<'_> {
         };
         let n_threads = rayon::current_num_threads().max(1) as u64;
         let available_per_thread = available / n_threads;
-        let done = AtomicU64::new(0);
 
-        let results: Vec<SKResult<()>> = (0..n_partitions)
+        par_over_layer0(index, n_partitions, on_progress, |layer| {
-            .into_par_iter()
+            let raw_path = layer.raw_superkmers_path();
-            .map(|i| {
-                let dir = index.layer_dir(i, 0);
-                let result = if dir.exists() {
-                    let raw_path = obikindex::layer::raw_superkmers_path(&dir);
             let n_buckets = optimal_buckets(&raw_path, available_per_thread);
-                    dereplicate_partition(&dir, level, n_buckets)
+            dereplicate_partition(&layer, level, n_buckets)
-                } else {
+        })?;
-                    Ok(())
-                };
-                if let Some(cb) = on_progress {
-                    let pos = done.fetch_add(1, Ordering::Relaxed) + 1;
-                    cb(Progress { position: pos, total: Some(n_partitions as u64) });
-                }
-                result
-            })
-            .collect();
-
-        for r in results {
-            r?;
-        }
         Ok(())
     }
 }

src/obikindexer/src/algorithms/layer_builder/mod.rs

@@ -5,8 +5,8 @@
 //! `DevDocMD/implementation/partition_layer_cache.md`.
 
 use obikalgorithm::Algorithm;
-use obikindex::{KmerIndex, PartitionRunner};
+use obikindex::KmerIndex;
-use obisys::Progress;
+use obisys::{PartitionRunner, Progress};
 
 use crate::extensions::PrivateBuilder;
 

src/obikindexer/src/algorithms/mod.rs

@@ -12,3 +12,66 @@ pub mod counter;
 pub mod dereplicator;
 pub mod layer_builder;
 pub mod partitionner;
+
+
+use std::sync::atomic::{AtomicU64, Ordering};
+
+use obikindex::KmerIndex;
+use obikindex::layer::KmerLayer;
+use obiskio::SKResult;
+use obisys::Progress;
+use rayon::prelude::*;
+
+use crate::extensions::PrivateBuilder;
+
+/// Runs `f` over every partition's layer 0 in parallel, skipping partitions
+/// whose layer 0 doesn't exist yet (e.g. no data routed to them) — the
+/// per-partition-in-parallel shape shared by
+/// [`dereplicator::Dereplicator::run`] and [`counter::Counter::run`]:
+/// resolve layer 0 via [`PrivateBuilder::layer0`], apply `f`, report one
+/// progress tick per partition regardless of outcome, then propagate the
+/// first error once every partition has run.
+pub(crate) fn par_over_layer0<F>(
+    index: &KmerIndex,
+    n_partitions: usize,
+    on_progress: Option<&(dyn Fn(Progress) + Sync)>,
+    f: F,
+) -> SKResult<()>
+where
+    F: Fn(KmerLayer) -> SKResult<()> + Sync,
+{
+    let done = AtomicU64::new(0);
+    let results: Vec<SKResult<()>> = (0..n_partitions)
+        .into_par_iter()
+        .map(|i| {
+            let result = match index.layer0(i) {
+                Ok(layer) => f(layer),
+                Err(_) => Ok(()),
+            };
+            if let Some(cb) = on_progress {
+                let pos = done.fetch_add(1, Ordering::Relaxed) + 1;
+                cb(Progress {
+                    position: pos,
+                    total: Some(n_partitions as u64),
+                });
+            }
+            result
+        })
+        .collect();
+    for r in results {
+        r?;
+    }
+    Ok(())
+}
+
+
+/// Sequential counterpart to [`par_over_layer0`]: every partition's layer 0
+/// that exists, in order, skipping those that don't — for callers that
+/// aggregate into shared state (e.g. [`counter::Counter::run`]'s spectrum
+/// aggregation) rather than run independent per-partition work in parallel.
+pub(crate) fn existing_layer0(
+    index: &KmerIndex,
+    n_partitions: usize,
+) -> impl Iterator<Item = KmerLayer> + '_ {
+    (0..n_partitions).filter_map(move |i| index.layer0(i).ok())
+}

src/obikindexer/src/algorithms/partitionner/router.rs

@@ -212,14 +212,6 @@ impl<'a> PartitionRouter<'a> {
 
     // ── private ───────────────────────────────────────────────────────────────
 
-    /// Directory of partition `i`'s layer 0 — every raw/dereplicated
-    /// superkmer file and provisional `mphf1.bin`/`counts1.bin` this router
-    /// produces lives here, alongside where `build_index_layer`
-    /// (`obikindex`) will later turn it into the real layer 0.
-    fn layer0_dir(&self, i: usize) -> PathBuf {
-        obikindex::layer::layer_dir(&self.index.index_dir(i), 0)
-    }
-
     fn check_not_closed(&self) -> SKResult<()> {
         if self.closed {
             Err(io::Error::new(io::ErrorKind::BrokenPipe, "write to closed PartitionRouter").into())
@@ -230,9 +222,14 @@ impl<'a> PartitionRouter<'a> {
 
     fn ensure_writer(&mut self, partition: usize) -> SKResult<&mut SKFileWriter> {
         if self.writers[partition].is_none() {
-            let dir = self.layer0_dir(partition);
+            let part = self
-            KmerLayer::create(&dir).map_err(|e| io::Error::other(e.to_string()))?;
+                .index
-            let file_path = obikindex::layer::raw_superkmers_path(&dir);
+                .partition(partition)
+                .map_err(|e| io::Error::other(e.to_string()))?;
+            let layer = KmerLayer::new(&part, 0)
+                .create()
+                .map_err(|e| io::Error::other(e.to_string()))?;
+            let file_path = layer.raw_superkmers_path();
             let writer = SKFileWriter::create_with(file_path, Format::Zstd, self.level)?;
             self.writers[partition] = Some(writer);
         }

src/obikindexer/src/extensions/mod.rs

@@ -34,7 +34,7 @@ use epserde::prelude::*;
 use obicompactvec::{PersistentCompactIntMatrix, PersistentCompactIntVec};
 use obidebruinj::GraphDeBruijn;
 use obikindex::layer::IndexMode;
-use obikindex::layer::{TypedLayer, meta::PartitionMeta};
+use obikindex::layer::{KmerLayer, TypedLayer};
 use obikindex::{KmerIndex, OKIError, OKIResult};
 use crate::graph_pipeline::{materialize_layer, write_graph_as_unitigs};
 use obiskio::{SKError, SKFileMeta, SKFileReader};
@@ -54,6 +54,12 @@ pub(crate) trait PrivateBuilder {
     /// Mark dereplicate+count as complete (`IndexState::Counted`).
     fn mark_counted(&self) -> OKIResult<()>;
 
+    /// Partition `i`'s layer 0 — the one and only layer every pipeline
+    /// algorithm in this crate (`partitionner`/`dereplicator`/`counter`/
+    /// `layer_builder`) reads from or writes to; later layers only exist
+    /// after a `merge`, which lives in `obikindex`, not here.
+    fn layer0(&self, i: usize) -> OKIResult<KmerLayer>;
+
     /// Mark layer construction as complete (`IndexState::Indexed`).
     fn mark_indexed(&self) -> OKIResult<()>;
 
@@ -98,6 +104,10 @@ impl PrivateBuilder for KmerIndex {
         self.meta().mark_counted().map_err(OKIError::Io)
     }
 
+    fn layer0(&self, i: usize) -> OKIResult<KmerLayer> {
+        self.partition(i)?.layer(0)
+    }
+
     fn mark_indexed(&self) -> OKIResult<()> {
         self.meta().mark_indexed().map_err(OKIError::Io)
     }
@@ -134,8 +144,9 @@ impl PrivateBuilder for KmerIndex {
         mode: &IndexMode,
         block_bits: u8,
     ) -> Result<usize, SKError> {
-        let layer0_dir = self.layer_dir(i, 0);
+        let layer0 = self.layer0(i).map_err(|e| io::Error::other(e.to_string()))?;
-        let dedup_path = obikindex::layer::dereplicated_superkmers_path(&layer0_dir);
+        let layer0_dir = layer0.dir();
+        let dedup_path = layer0.dereplicated_superkmers_path();
         if !dedup_path.exists() {
             return Ok(0);
         }
@@ -185,34 +196,37 @@ impl PrivateBuilder for KmerIndex {
         }
 
         let n_kmers = if with_counts {
-            let n = write_graph_as_unitigs(g, &layer0_dir)?;
+            let n = write_graph_as_unitigs(g, layer0_dir)
+                .map_err(|e| io::Error::other(e.to_string()))?;
             TypedLayer::<PersistentCompactIntMatrix>::build(
-                &layer0_dir,
+                layer0_dir,
                 block_bits,
                 mode,
                 |kmer| match (&mphf1_opt, &counts1_opt) {
                     (Some(mphf), Some(counts)) => counts.get(mphf.index(&kmer.raw())),
                     _ => 1,
                 },
-            )?;
+            )
+            .map_err(|e| io::Error::other(e.to_string()))?;
             n
         } else {
-            materialize_layer(g, &layer0_dir, block_bits, mode)?
+            materialize_layer(g, layer0_dir, block_bits, mode)
+                .map_err(|e| io::Error::other(e.to_string()))?
         };
 
-        let index_dir = layer0_dir.parent().expect("layer_dir has a parent");
-        PartitionMeta {
-            n_layers: 1,
-            mode: mode.clone(),
-        }
-        .save(index_dir)?;
-
         Ok(n_kmers)
     }
 
     fn remove_build_artifacts(&self, i: usize) {
-        let layer0_dir = self.layer_dir(i, 0);
+        let layer0 = match self.layer0(i) {
-        let dedup = obikindex::layer::dereplicated_superkmers_path(&layer0_dir);
+            Ok(layer) => layer,
+            Err(e) => {
+                eprintln!("warning: could not locate layer 0 of partition {i}: {e}");
+                return;
+            }
+        };
+        let layer0_dir = layer0.dir();
+        let dedup = layer0.dereplicated_superkmers_path();
         remove_if_exists(&SKFileMeta::sidecar_path(&dedup));
         remove_if_exists(&dedup);
         remove_if_exists(&layer0_dir.join("mphf1.bin"));