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Refactor k-mer index building to use disk-based KmerSetGroupBuilder

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Refactor k-mer index building to use the new disk-based KmerSetGroupBuilder instead of the old KmerSet and FrequencyFilter approaches. This change introduces a more efficient and scalable approach to building k-mer indices by using partitioned disk storage with streaming operations.

- Replace BuildKmerIndex and BuildFrequencyFilterIndex with KmerSetGroupBuilder
- Add support for frequency filtering via WithMinFrequency option
- Remove deprecated k-mer set persistence methods
- Update CLI to use new builder approach
- Add new disk-based k-mer operations (union, intersect, difference, quorum)
- Introduce KDI (K-mer Delta Index) file format for efficient storage
- Add K-way merge operations for combining sorted k-mer streams
- Update documentation and examples to reflect new API

This refactoring provides better memory usage, faster operations on large datasets, and more flexible k-mer set operations.
This commit is contained in:
Eric Coissac
2026-02-09 21:57:03 +01:00
parent a016ad5b8a
commit f78543ee75
33 changed files with 3291 additions and 3636 deletions
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1
.gitignore vendored
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@@ -33,3 +33,4 @@ LLM/**
entropy.html
bug_id.txt
obilowmask_ref
test_*

2
cmd/obitools/obikindex/main.go
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@@ -11,7 +11,7 @@ import (
func main() {
optionParser := obioptions.GenerateOptionParser(
"obikindex",
"builds a roaring kmer index from sequence files",
"builds a disk-based kmer index from sequence files",
obikindex.OptionSet)
_, args := optionParser(os.Args)

5
go.mod
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@@ -14,6 +14,7 @@ require (
github.com/goccy/go-json v0.10.3
github.com/klauspost/pgzip v1.2.6
github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58
github.com/pelletier/go-toml/v2 v2.2.4
github.com/rrethy/ahocorasick v1.0.0
github.com/schollz/progressbar/v3 v3.13.1
github.com/sirupsen/logrus v1.9.3
@@ -27,14 +28,10 @@ require (
)
require (
github.com/RoaringBitmap/roaring v1.9.4 // indirect
github.com/bits-and-blooms/bitset v1.12.0 // indirect
github.com/davecgh/go-spew v1.1.1 // indirect
github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419 // indirect
github.com/kr/pretty v0.3.1 // indirect
github.com/kr/text v0.2.0 // indirect
github.com/mschoch/smat v0.2.0 // indirect
github.com/pelletier/go-toml/v2 v2.2.4 // indirect
github.com/pmezard/go-difflib v1.0.0 // indirect
github.com/rogpeppe/go-internal v1.12.0 // indirect
)

6
go.sum
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@@ -4,12 +4,8 @@ github.com/PaesslerAG/gval v1.2.2 h1:Y7iBzhgE09IGTt5QgGQ2IdaYYYOU134YGHBThD+wm9E
github.com/PaesslerAG/gval v1.2.2/go.mod h1:XRFLwvmkTEdYziLdaCeCa5ImcGVrfQbeNUbVR+C6xac=
github.com/PaesslerAG/jsonpath v0.1.0 h1:gADYeifvlqK3R3i2cR5B4DGgxLXIPb3TRTH1mGi0jPI=
github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8=
github.com/RoaringBitmap/roaring v1.9.4 h1:yhEIoH4YezLYT04s1nHehNO64EKFTop/wBhxv2QzDdQ=
github.com/RoaringBitmap/roaring v1.9.4/go.mod h1:6AXUsoIEzDTFFQCe1RbGA6uFONMhvejWj5rqITANK90=
github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df h1:GSoSVRLoBaFpOOds6QyY1L8AX7uoY+Ln3BHc22W40X0=
github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df/go.mod h1:hiVxq5OP2bUGBRNS3Z/bt/reCLFNbdcST6gISi1fiOM=
github.com/bits-and-blooms/bitset v1.12.0 h1:U/q1fAF7xXRhFCrhROzIfffYnu+dlS38vCZtmFVPHmA=
github.com/bits-and-blooms/bitset v1.12.0/go.mod h1:7hO7Gc7Pp1vODcmWvKMRA9BNmbv6a/7QIWpPxHddWR8=
github.com/buger/jsonparser v1.1.1 h1:2PnMjfWD7wBILjqQbt530v576A/cAbQvEW9gGIpYMUs=
github.com/buger/jsonparser v1.1.1/go.mod h1:6RYKKt7H4d4+iWqouImQ9R2FZql3VbhNgx27UK13J/0=
github.com/chen3feng/stl4go v0.1.1 h1:0L1+mDw7pomftKDruM23f1mA7miavOj6C6MZeadzN2Q=
@@ -51,8 +47,6 @@ github.com/mattn/go-runewidth v0.0.15 h1:UNAjwbU9l54TA3KzvqLGxwWjHmMgBUVhBiTjelZ
github.com/mattn/go-runewidth v0.0.15/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db h1:62I3jR2EmQ4l5rM/4FEfDWcRD+abF5XlKShorW5LRoQ=
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db/go.mod h1:l0dey0ia/Uv7NcFFVbCLtqEBQbrT4OCwCSKTEv6enCw=
github.com/mschoch/smat v0.2.0 h1:8imxQsjDm8yFEAVBe7azKmKSgzSkZXDuKkSq9374khM=
github.com/mschoch/smat v0.2.0/go.mod h1:kc9mz7DoBKqDyiRL7VZN8KvXQMWeTaVnttLRXOlotKw=
github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58 h1:onHthvaw9LFnH4t2DcNVpwGmV9E1BkGknEliJkfwQj0=
github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58/go.mod h1:DXv8WO4yhMYhSNPKjeNKa5WY9YCIEBRbNzFFPJbWO6Y=
github.com/pelletier/go-toml/v2 v2.2.4 h1:mye9XuhQ6gvn5h28+VilKrrPoQVanw5PMw/TB0t5Ec4=

292
kmer_roaring_index/FREQUENCY_FILTER_FINAL.md
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@@ -1,292 +0,0 @@
# Filtre de Fréquence avec v Niveaux de Roaring Bitmaps
## Algorithme
```go
Pour chaque k-mer rencontré dans les données:
c = 0
tant que (k-mer ∈ index[c] ET c < v):
c++
si c < v:
index[c].insert(k-mer)
```
**Résultat** : `index[v-1]` contient les k-mers vus **≥ v fois**
---
## Exemple d'exécution (v=3)
```
Données:
Read1: kmer X
Read2: kmer X
Read3: kmer X (X vu 3 fois)
Read4: kmer Y
Read5: kmer Y (Y vu 2 fois)
Read6: kmer Z (Z vu 1 fois)
Exécution:
Read1 (X):
c=0: X ∉ index[0] → index[0].add(X)
État: index[0]={X}, index[1]={}, index[2]={}
Read2 (X):
c=0: X ∈ index[0] → c=1
c=1: X ∉ index[1] → index[1].add(X)
État: index[0]={X}, index[1]={X}, index[2]={}
Read3 (X):
c=0: X ∈ index[0] → c=1
c=1: X ∈ index[1] → c=2
c=2: X ∉ index[2] → index[2].add(X)
État: index[0]={X}, index[1]={X}, index[2]={X}
Read4 (Y):
c=0: Y ∉ index[0] → index[0].add(Y)
État: index[0]={X,Y}, index[1]={X}, index[2]={X}
Read5 (Y):
c=0: Y ∈ index[0] → c=1
c=1: Y ∉ index[1] → index[1].add(Y)
État: index[0]={X,Y}, index[1]={X,Y}, index[2]={X}
Read6 (Z):
c=0: Z ∉ index[0] → index[0].add(Z)
État: index[0]={X,Y,Z}, index[1]={X,Y}, index[2]={X}
Résultat final:
index[0] (freq≥1): {X, Y, Z}
index[1] (freq≥2): {X, Y}
index[2] (freq≥3): {X} ← K-mers filtrés ✓
```
---
## Utilisation
```go
// Créer le filtre
filter := obikmer.NewFrequencyFilter(31, 3) // k=31, minFreq=3
// Ajouter les séquences
for _, read := range reads {
filter.AddSequence(read)
}
// Récupérer les k-mers filtrés (freq ≥ 3)
filtered := filter.GetFilteredSet("filtered")
fmt.Printf("K-mers de qualité: %d\n", filtered.Cardinality())
// Statistiques
stats := filter.Stats()
fmt.Println(stats.String())
```
---
## Performance
### Complexité
**Par k-mer** :
- Lookups : Moyenne ~v/2, pire cas v
- Insertions : 1 Add
- **Pas de Remove** ✅
**Total pour n k-mers** :
- Temps : O(n × v/2)
- Mémoire : O(unique_kmers × v × 2 bytes)
### Early exit pour distribution skewed
Avec distribution typique (séquençage) :
```
80% singletons → 1 lookup (early exit)
15% freq 2-3 → 2-3 lookups
5% freq ≥4 → jusqu'à v lookups
Moyenne réelle : ~2 lookups/kmer (au lieu de v/2)
```
---
## Mémoire
### Pour 10^8 k-mers uniques
| v (minFreq) | Nombre bitmaps | Mémoire | vs map simple |
|-------------|----------------|---------|---------------|
| v=2 | 2 | ~400 MB | 6x moins |
| v=3 | 3 | ~600 MB | 4x moins |
| v=5 | 5 | ~1 GB | 2.4x moins |
| v=10 | 10 | ~2 GB | 1.2x moins |
| v=20 | 20 | ~4 GB | ~égal |
**Note** : Avec distribution skewed (beaucoup de singletons), la mémoire réelle est bien plus faible car les niveaux hauts ont peu d'éléments.
### Exemple réaliste (séquençage)
Pour 10^8 k-mers totaux, v=3 :
```
Distribution:
80% singletons → 80M dans index[0]
15% freq 2-3 → 15M dans index[1]
5% freq ≥3 → 5M dans index[2]
Mémoire:
index[0]: 80M × 2 bytes = 160 MB
index[1]: 15M × 2 bytes = 30 MB
index[2]: 5M × 2 bytes = 10 MB
Total: ~200 MB ✅
vs map simple: 80M × 24 bytes = ~2 GB
Réduction: 10x
```
---
## Comparaison des approches
| Approche | Mémoire (10^8 kmers) | Passes | Lookups/kmer | Quand utiliser |
|----------|----------------------|--------|--------------|----------------|
| **v-Bitmaps** | **200-600 MB** | **1** | **~2 (avg)** | **Standard** ✅ |
| Map simple | 2.4 GB | 1 | 1 | Si RAM illimitée |
| Multi-pass | 400 MB | v | v | Si I/O pas cher |
---
## Avantages de v-Bitmaps
✅ **Une seule passe** sur les données
✅ **Mémoire optimale** avec Roaring bitmaps
✅ **Pas de Remove** (seulement Contains + Add)
✅ **Early exit** efficace sur singletons
✅ **Scalable** jusqu'à v~10-20
✅ **Simple** à implémenter et comprendre
---
## Cas d'usage typiques
### 1. Éliminer erreurs de séquençage
```go
filter := obikmer.NewFrequencyFilter(31, 3)
// Traiter FASTQ
for read := range StreamFastq("sample.fastq") {
filter.AddSequence(read)
}
// K-mers de qualité (pas d'erreurs)
cleaned := filter.GetFilteredSet("cleaned")
```
**Résultat** : Élimine 70-80% des k-mers (erreurs)
### 2. Assemblage de génome
```go
filter := obikmer.NewFrequencyFilter(31, 2)
// Filtrer avant l'assemblage
for read := range reads {
filter.AddSequence(read)
}
solidKmers := filter.GetFilteredSet("solid")
// Utiliser solidKmers pour le graphe de Bruijn
```
### 3. Comparaison de génomes
```go
collection := obikmer.NewKmerSetCollection(31)
for _, genome := range genomes {
filter := obikmer.NewFrequencyFilter(31, 3)
filter.AddSequences(genome.Reads)
cleaned := filter.GetFilteredSet(genome.ID)
collection.Add(cleaned)
}
// Analyses comparatives sur k-mers de qualité
matrix := collection.ParallelPairwiseJaccard(8)
```
---
## Limites
**Pour v > 20** :
- Trop de lookups (v lookups/kmer)
- Mémoire importante (v × 200MB pour 10^8 kmers)
**Solutions alternatives pour v > 20** :
- Utiliser map simple (9 bytes/kmer) si RAM disponible
- Algorithme différent (sketch, probabiliste)
---
## Optimisations possibles
### 1. Parallélisation
```go
// Traiter plusieurs fichiers en parallèle
filters := make([]*FrequencyFilter, numFiles)
var wg sync.WaitGroup
for i, file := range files {
wg.Add(1)
go func(idx int, f string) {
defer wg.Done()
filters[idx] = ProcessFile(f, k, minFreq)
}(i, file)
}
wg.Wait()
// Merger les résultats
merged := MergeFilters(filters)
```
### 2. Streaming avec seuil adaptatif
```go
// Commencer avec v=5, réduire progressivement
filter := obikmer.NewFrequencyFilter(31, 5)
// ... traitement ...
// Si trop de mémoire, réduire à v=3
if filter.MemoryUsage() > threshold {
filter = ConvertToLowerThreshold(filter, 3)
}
```
---
## Récapitulatif final
**Pour filtrer les k-mers par fréquence ≥ v :**
1. **Créer** : `filter := NewFrequencyFilter(k, v)`
2. **Traiter** : `filter.AddSequence(read)` pour chaque read
3. **Résultat** : `filtered := filter.GetFilteredSet(id)`
**Mémoire** : ~2v MB par million de k-mers uniques
**Temps** : Une seule passe, ~2 lookups/kmer en moyenne
**Optimal pour** : v ≤ 20, distribution skewed (séquençage)
---
## Code fourni
1. **frequency_filter.go** - Implémentation complète
2. **examples_frequency_filter_final.go** - Exemples d'utilisation
**Tout est prêt à utiliser !** 🚀

320
kmer_roaring_index/examples_frequency_filter_final.go
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@@ -1,320 +0,0 @@
package main
import (
"fmt"
"obikmer"
)
func main() {
// ==========================================
// EXEMPLE 1 : Utilisation basique
// ==========================================
fmt.Println("=== EXEMPLE 1 : Utilisation basique ===\n")
k := 31
minFreq := 3 // Garder les k-mers vus ≥3 fois
// Créer le filtre
filter := obikmer.NewFrequencyFilter(k, minFreq)
// Simuler des séquences avec différentes fréquences
sequences := [][]byte{
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"), // Kmer X
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"), // Kmer X (freq=2)
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"), // Kmer X (freq=3) ✓
[]byte("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"), // Kmer Y
[]byte("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"), // Kmer Y (freq=2) ✗
[]byte("GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"), // Kmer Z (freq=1) ✗
}
fmt.Printf("Traitement de %d séquences...\n", len(sequences))
for _, seq := range sequences {
filter.AddSequence(seq)
}
// Récupérer les k-mers filtrés
filtered := filter.GetFilteredSet("filtered")
fmt.Printf("\nK-mers avec freq ≥ %d: %d\n", minFreq, filtered.Cardinality())
// Statistiques
stats := filter.Stats()
fmt.Println("\n" + stats.String())
// ==========================================
// EXEMPLE 2 : Vérifier les niveaux
// ==========================================
fmt.Println("\n=== EXEMPLE 2 : Inspection des niveaux ===\n")
// Vérifier chaque niveau
for level := 0; level < minFreq; level++ {
levelSet := filter.GetKmersAtLevel(level)
fmt.Printf("Niveau %d (freq≥%d): %d k-mers\n",
level+1, level+1, levelSet.Cardinality())
}
// ==========================================
// EXEMPLE 3 : Données réalistes
// ==========================================
fmt.Println("\n=== EXEMPLE 3 : Simulation données séquençage ===\n")
filter2 := obikmer.NewFrequencyFilter(31, 3)
// Simuler un dataset réaliste :
// - 1000 reads
// - 80% contiennent des erreurs (singletons)
// - 15% vrais k-mers à basse fréquence
// - 5% vrais k-mers à haute fréquence
// Vraie séquence répétée
trueSeq := []byte("ACGTACGTACGTACGTACGTACGTACGTACG")
for i := 0; i < 50; i++ {
filter2.AddSequence(trueSeq)
}
// Séquence à fréquence moyenne
mediumSeq := []byte("CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC")
for i := 0; i < 5; i++ {
filter2.AddSequence(mediumSeq)
}
// Erreurs de séquençage (singletons)
for i := 0; i < 100; i++ {
errorSeq := []byte(fmt.Sprintf("TTTTTTTTTTTTTTTTTTTTTTTTTTTT%03d", i))
filter2.AddSequence(errorSeq)
}
stats2 := filter2.Stats()
fmt.Println(stats2.String())
fmt.Println("Distribution attendue:")
fmt.Println(" - Beaucoup de singletons (erreurs)")
fmt.Println(" - Peu de k-mers à haute fréquence (signal)")
fmt.Println(" → Filtrage efficace !")
// ==========================================
// EXEMPLE 4 : Tester différents seuils
// ==========================================
fmt.Println("\n=== EXEMPLE 4 : Comparaison de seuils ===\n")
testSeqs := [][]byte{
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"), // freq=5
[]byte("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"),
[]byte("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"),
[]byte("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"), // freq=3
[]byte("GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"), // freq=1
}
for _, minFreq := range []int{2, 3, 5} {
f := obikmer.NewFrequencyFilter(31, minFreq)
f.AddSequences(testSeqs)
fmt.Printf("minFreq=%d: %d k-mers retenus (%.2f MB)\n",
minFreq,
f.Cardinality(),
float64(f.MemoryUsage())/1024/1024)
}
// ==========================================
// EXEMPLE 5 : Comparaison mémoire
// ==========================================
fmt.Println("\n=== EXEMPLE 5 : Comparaison mémoire ===\n")
filter3 := obikmer.NewFrequencyFilter(31, 3)
// Simuler 10000 séquences
for i := 0; i < 10000; i++ {
seq := make([]byte, 100)
for j := range seq {
seq[j] = "ACGT"[(i+j)%4]
}
filter3.AddSequence(seq)
}
fmt.Println(filter3.CompareWithSimpleMap())
// ==========================================
// EXEMPLE 6 : Workflow complet
// ==========================================
fmt.Println("\n=== EXEMPLE 6 : Workflow complet ===\n")
fmt.Println("1. Créer le filtre")
finalFilter := obikmer.NewFrequencyFilter(31, 3)
fmt.Println("2. Traiter les données (simulation)")
// En pratique : lire depuis FASTQ
// for read := range ReadFastq("data.fastq") {
// finalFilter.AddSequence(read)
// }
// Simulation
for i := 0; i < 1000; i++ {
seq := []byte("ACGTACGTACGTACGTACGTACGTACGTACG")
finalFilter.AddSequence(seq)
}
fmt.Println("3. Récupérer les k-mers filtrés")
result := finalFilter.GetFilteredSet("final")
fmt.Println("4. Utiliser le résultat")
fmt.Printf(" K-mers de qualité: %d\n", result.Cardinality())
fmt.Printf(" Mémoire utilisée: %.2f MB\n", float64(finalFilter.MemoryUsage())/1024/1024)
fmt.Println("5. Sauvegarder (optionnel)")
// result.Save("filtered_kmers.bin")
// ==========================================
// EXEMPLE 7 : Vérification individuelle
// ==========================================
fmt.Println("\n=== EXEMPLE 7 : Vérification de k-mers spécifiques ===\n")
checkFilter := obikmer.NewFrequencyFilter(31, 3)
testSeq := []byte("ACGTACGTACGTACGTACGTACGTACGTACG")
for i := 0; i < 5; i++ {
checkFilter.AddSequence(testSeq)
}
var kmers []uint64
kmers = obikmer.EncodeKmers(testSeq, 31, &kmers)
if len(kmers) > 0 {
testKmer := kmers[0]
fmt.Printf("K-mer test: 0x%016X\n", testKmer)
fmt.Printf(" Présent dans filtre: %v\n", checkFilter.Contains(testKmer))
fmt.Printf(" Fréquence approx: %d\n", checkFilter.GetFrequency(testKmer))
}
// ==========================================
// EXEMPLE 8 : Intégration avec collection
// ==========================================
fmt.Println("\n=== EXEMPLE 8 : Intégration avec KmerSetCollection ===\n")
// Créer une collection de génomes filtrés
collection := obikmer.NewKmerSetCollection(31)
genomes := map[string][][]byte{
"Genome1": {
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"), // Erreur
},
"Genome2": {
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("ACGTACGTACGTACGTACGTACGTACGTACG"),
[]byte("GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG"), // Erreur
},
}
for id, sequences := range genomes {
// Filtrer chaque génome
genomeFilter := obikmer.NewFrequencyFilter(31, 3)
genomeFilter.AddSequences(sequences)
// Ajouter à la collection
filteredSet := genomeFilter.GetFilteredSet(id)
collection.Add(filteredSet)
fmt.Printf("%s: %d k-mers de qualité\n", id, filteredSet.Cardinality())
}
// Analyser la collection
fmt.Println("\nAnalyse comparative:")
collectionStats := collection.ComputeStats()
fmt.Printf(" Core genome: %d k-mers\n", collectionStats.CoreSize)
fmt.Printf(" Pan genome: %d k-mers\n", collectionStats.PanGenomeSize)
// ==========================================
// RÉSUMÉ
// ==========================================
fmt.Println("\n=== RÉSUMÉ ===\n")
fmt.Println("Le FrequencyFilter permet de:")
fmt.Println(" ✓ Filtrer les k-mers par fréquence minimale")
fmt.Println(" ✓ Utiliser une mémoire optimale avec Roaring bitmaps")
fmt.Println(" ✓ Une seule passe sur les données")
fmt.Println(" ✓ Éliminer efficacement les erreurs de séquençage")
fmt.Println("")
fmt.Println("Workflow typique:")
fmt.Println(" 1. filter := NewFrequencyFilter(k, minFreq)")
fmt.Println(" 2. for each sequence: filter.AddSequence(seq)")
fmt.Println(" 3. filtered := filter.GetFilteredSet(id)")
fmt.Println(" 4. Utiliser filtered dans vos analyses")
}
// ==================================
// FONCTION HELPER POUR BENCHMARKS
// ==================================
func BenchmarkFrequencyFilter() {
k := 31
minFreq := 3
// Test avec différentes tailles
sizes := []int{1000, 10000, 100000}
fmt.Println("\n=== BENCHMARK ===\n")
for _, size := range sizes {
filter := obikmer.NewFrequencyFilter(k, minFreq)
// Générer des séquences
for i := 0; i < size; i++ {
seq := make([]byte, 100)
for j := range seq {
seq[j] = "ACGT"[(i+j)%4]
}
filter.AddSequence(seq)
}
fmt.Printf("Size=%d reads:\n", size)
fmt.Printf(" Filtered k-mers: %d\n", filter.Cardinality())
fmt.Printf(" Memory: %.2f MB\n", float64(filter.MemoryUsage())/1024/1024)
fmt.Println()
}
}
// ==================================
// FONCTION POUR DONNÉES RÉELLES
// ==================================
func ProcessRealData() {
// Exemple pour traiter de vraies données FASTQ
k := 31
minFreq := 3
filter := obikmer.NewFrequencyFilter(k, minFreq)
// Pseudo-code pour lire un FASTQ
/*
fastqFile := "sample.fastq"
reader := NewFastqReader(fastqFile)
for reader.HasNext() {
read := reader.Next()
filter.AddSequence(read.Sequence)
}
// Récupérer le résultat
filtered := filter.GetFilteredSet("sample_filtered")
filtered.Save("sample_filtered_kmers.bin")
// Stats
stats := filter.Stats()
fmt.Println(stats.String())
*/
fmt.Println("Workflow pour données réelles:")
fmt.Println(" 1. Créer le filtre avec minFreq approprié (2-5 typique)")
fmt.Println(" 2. Stream les reads depuis FASTQ")
fmt.Println(" 3. Récupérer les k-mers filtrés")
fmt.Println(" 4. Utiliser pour assemblage/comparaison/etc.")
_ = filter // unused
}

317
pkg/obikmer/frequency_filter.go
View File

@@ -1,317 +0,0 @@
package obikmer
import (
"fmt"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// FrequencyFilter filters k-mers by minimum frequency
// Specialization of KmerSetGroup where index[i] contains k-mers seen at least i+1 times
type FrequencyFilter struct {
*KmerSetGroup // Group of KmerSet (one per frequency level)
MinFreq int // v - minimum required frequency
}
// NewFrequencyFilter creates a new frequency filter
// minFreq: minimum number d'occurrences required (v)
func NewFrequencyFilter(k, minFreq int) *FrequencyFilter {
ff := &FrequencyFilter{
KmerSetGroup: NewKmerSetGroup(k, minFreq),
MinFreq: minFreq,
}
// Initialize group metadata
ff.SetAttribute("type", "FrequencyFilter")
ff.SetAttribute("min_freq", minFreq)
// Initialize metadata for each level
for i := 0; i < minFreq; i++ {
level := ff.Get(i)
level.SetAttribute("level", i)
level.SetAttribute("min_occurrences", i+1)
level.SetId(fmt.Sprintf("level_%d", i))
}
return ff
}
// AddSequence adds all k-mers from a sequence to the filter
// Uses an iterator to avoid allocating an intermediate vector
func (ff *FrequencyFilter) AddSequence(seq *obiseq.BioSequence) {
rawSeq := seq.Sequence()
for canonical := range IterCanonicalKmers(rawSeq, ff.K()) {
ff.AddKmerCode(canonical)
}
}
// AddKmerCode adds an encoded k-mer to the filter (main algorithm)
func (ff *FrequencyFilter) AddKmerCode(kmer uint64) {
// Find the current level of the k-mer
c := 0
for c < ff.MinFreq && ff.Get(c).Contains(kmer) {
c++
}
// Add to next level (if not yet at maximum)
if c < ff.MinFreq {
ff.Get(c).AddKmerCode(kmer)
}
}
// AddCanonicalKmerCode adds an encoded canonical k-mer to the filter
func (ff *FrequencyFilter) AddCanonicalKmerCode(kmer uint64) {
canonical := CanonicalKmer(kmer, ff.K())
ff.AddKmerCode(canonical)
}
// AddKmer adds a k-mer to the filter by encoding the sequence
// The sequence must have exactly k nucleotides
// Zero-allocation: encodes directly without creating an intermediate slice
func (ff *FrequencyFilter) AddKmer(seq []byte) {
kmer := EncodeKmer(seq, ff.K())
ff.AddKmerCode(kmer)
}
// AddCanonicalKmer adds a canonical k-mer to the filter by encoding the sequence
// The sequence must have exactly k nucleotides
// Zero-allocation: encodes directly in canonical form without creating an intermediate slice
func (ff *FrequencyFilter) AddCanonicalKmer(seq []byte) {
canonical := EncodeCanonicalKmer(seq, ff.K())
ff.AddKmerCode(canonical)
}
// GetFilteredSet returns a KmerSet of k-mers with frequency ≥ minFreq
func (ff *FrequencyFilter) GetFilteredSet() *KmerSet {
// Filtered k-mers are in the last level
return ff.Get(ff.MinFreq - 1).Copy()
}
// GetKmersAtLevel returns a KmerSet of k-mers seen at least (level+1) times
// level doit être dans [0, minFreq-1]
func (ff *FrequencyFilter) GetKmersAtLevel(level int) *KmerSet {
ks := ff.Get(level)
if ks == nil {
return NewKmerSet(ff.K())
}
return ks.Copy()
}
// Stats returns statistics on frequency levels
func (ff *FrequencyFilter) Stats() FrequencyFilterStats {
stats := FrequencyFilterStats{
MinFreq: ff.MinFreq,
Levels: make([]LevelStats, ff.MinFreq),
}
for i := 0; i < ff.MinFreq; i++ {
ks := ff.Get(i)
card := ks.Len()
sizeBytes := ks.MemoryUsage()
stats.Levels[i] = LevelStats{
Level: i + 1, // Level 1 = freq ≥ 1
Cardinality: card,
SizeBytes: sizeBytes,
}
stats.TotalBytes += sizeBytes
}
// The last level contains the result
stats.FilteredKmers = stats.Levels[ff.MinFreq-1].Cardinality
return stats
}
// FrequencyFilterStats contains the filter statistics
type FrequencyFilterStats struct {
MinFreq int
FilteredKmers uint64 // K-mers with freq ≥ minFreq
TotalBytes uint64 // Total memory used
Levels []LevelStats
}
// LevelStats contains the stats of a level
type LevelStats struct {
Level int // freq ≥ Level
Cardinality uint64 // Number of k-mers
SizeBytes uint64 // Size in bytes
}
func (ffs FrequencyFilterStats) String() string {
result := fmt.Sprintf(`Frequency Filter Statistics (minFreq=%d):
Filtered k-mers (freq≥%d): %d
Total memory: %.2f MB
Level breakdown:
`, ffs.MinFreq, ffs.MinFreq, ffs.FilteredKmers, float64(ffs.TotalBytes)/1024/1024)
for _, level := range ffs.Levels {
result += fmt.Sprintf(" freq≥%d: %d k-mers (%.2f MB)\n",
level.Level,
level.Cardinality,
float64(level.SizeBytes)/1024/1024)
}
return result
}
// Clear libère la mémoire de tous les niveaux
// (héritée de KmerSetGroup mais redéfinie pour clarté)
func (ff *FrequencyFilter) Clear() {
ff.KmerSetGroup.Clear()
}
// ==================================
// BATCH PROCESSING
// ==================================
// AddSequences adds multiple sequences in batch
func (ff *FrequencyFilter) AddSequences(sequences *obiseq.BioSequenceSlice) {
for _, seq := range *sequences {
ff.AddSequence(seq)
}
}
// AddSequenceSlice adds all k-mers from a slice of sequences to the filter
func (ff *FrequencyFilter) AddSequenceSlice(sequences *obiseq.BioSequenceSlice) {
for _, seq := range *sequences {
ff.AddSequence(seq)
}
}
// ==================================
// PERSISTANCE
// ==================================
// Save sauvegarde le FrequencyFilter dans un répertoire
// Utilise le format de sérialisation du KmerSetGroup sous-jacent
// Les métadonnées incluent le type "FrequencyFilter" et min_freq
//
// Format:
// - directory/metadata.{toml,yaml,json} - métadonnées du filtre
// - directory/set_0.roaring - k-mers vus ≥1 fois
// - directory/set_1.roaring - k-mers vus ≥2 fois
// - ...
// - directory/set_{minFreq-1}.roaring - k-mers vus ≥minFreq fois
//
// Parameters:
// - directory: répertoire de destination
// - format: format des métadonnées (FormatTOML, FormatYAML, FormatJSON)
//
// Example:
//
// err := ff.Save("./my_filter", obikmer.FormatTOML)
func (ff *FrequencyFilter) Save(directory string, format MetadataFormat) error {
// Déléguer à KmerSetGroup qui gère déjà tout
return ff.KmerSetGroup.Save(directory, format)
}
// LoadFrequencyFilter charge un FrequencyFilter depuis un répertoire
// Vérifie que les métadonnées correspondent à un FrequencyFilter
//
// Parameters:
// - directory: répertoire source
//
// Returns:
// - *FrequencyFilter: le filtre chargé
// - error: erreur si le chargement échoue ou si ce n'est pas un FrequencyFilter
//
// Example:
//
// ff, err := obikmer.LoadFrequencyFilter("./my_filter")
func LoadFrequencyFilter(directory string) (*FrequencyFilter, error) {
// Charger le KmerSetGroup
ksg, err := LoadKmerSetGroup(directory)
if err != nil {
return nil, err
}
// Vérifier que c'est bien un FrequencyFilter
if typeAttr, ok := ksg.GetAttribute("type"); !ok || typeAttr != "FrequencyFilter" {
return nil, fmt.Errorf("loaded data is not a FrequencyFilter (type=%v)", typeAttr)
}
// Récupérer min_freq
minFreqAttr, ok := ksg.GetIntAttribute("min_freq")
if !ok {
return nil, fmt.Errorf("FrequencyFilter missing min_freq attribute")
}
// Créer le FrequencyFilter
ff := &FrequencyFilter{
KmerSetGroup: ksg,
MinFreq: minFreqAttr,
}
return ff, nil
}
// ==================================
// UTILITAIRES
// ==================================
// Contains vérifie si un k-mer a atteint la fréquence minimale
func (ff *FrequencyFilter) Contains(kmer uint64) bool {
canonical := CanonicalKmer(kmer, ff.K())
return ff.Get(ff.MinFreq - 1).Contains(canonical)
}
// GetFrequency returns the approximate frequency of a k-mer
// Retourne le niveau maximum atteint (freq ≥ niveau)
func (ff *FrequencyFilter) GetFrequency(kmer uint64) int {
canonical := CanonicalKmer(kmer, ff.K())
freq := 0
for i := 0; i < ff.MinFreq; i++ {
if ff.Get(i).Contains(canonical) {
freq = i + 1
} else {
break
}
}
return freq
}
// Len returns the number of filtered k-mers or at a specific level
// Without argument: returns the number of k-mers with freq ≥ minFreq (last level)
// With argument level: returns the number of k-mers with freq ≥ (level+1)
// Exemple: Len() pour les k-mers filtrés, Len(2) pour freq ≥ 3
// (héritée de KmerSetGroup mais redéfinie pour la documentation)
func (ff *FrequencyFilter) Len(level ...int) uint64 {
return ff.KmerSetGroup.Len(level...)
}
// MemoryUsage returns memory usage in bytes
// (héritée de KmerSetGroup mais redéfinie pour clarté)
func (ff *FrequencyFilter) MemoryUsage() uint64 {
return ff.KmerSetGroup.MemoryUsage()
}
// ==================================
// COMPARAISON AVEC D'AUTRES APPROCHES
// ==================================
// CompareWithSimpleMap compare la mémoire avec une simple map
func (ff *FrequencyFilter) CompareWithSimpleMap() string {
totalKmers := ff.Get(0).Len()
simpleMapBytes := totalKmers * 24 // ~24 bytes par entrée
roaringBytes := ff.MemoryUsage()
reduction := float64(simpleMapBytes) / float64(roaringBytes)
return fmt.Sprintf(`Memory Comparison for %d k-mers:
Simple map[uint64]uint32: %.2f MB
Roaring filter (v=%d): %.2f MB
Reduction: %.1fx
`,
totalKmers,
float64(simpleMapBytes)/1024/1024,
ff.MinFreq,
float64(roaringBytes)/1024/1024,
reduction,
)
}

86
pkg/obikmer/kdi_merge.go Normal file
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@@ -0,0 +1,86 @@
package obikmer
import "container/heap"
// mergeItem represents an element in the min-heap for k-way merge.
type mergeItem struct {
value uint64
idx int // index of the reader that produced this value
}
// mergeHeap implements heap.Interface for k-way merge.
type mergeHeap []mergeItem
func (h mergeHeap) Len() int { return len(h) }
func (h mergeHeap) Less(i, j int) bool { return h[i].value < h[j].value }
func (h mergeHeap) Swap(i, j int) { h[i], h[j] = h[j], h[i] }
func (h *mergeHeap) Push(x interface{}) { *h = append(*h, x.(mergeItem)) }
func (h *mergeHeap) Pop() interface{} {
old := *h
n := len(old)
x := old[n-1]
*h = old[:n-1]
return x
}
// KWayMerge performs a k-way merge of multiple sorted KdiReader streams.
// For each unique k-mer value, it reports the value and the number of
// input streams that contained it (count).
type KWayMerge struct {
h mergeHeap
readers []*KdiReader
}
// NewKWayMerge creates a k-way merge from multiple KdiReaders.
// Each reader must produce values in sorted (ascending) order.
func NewKWayMerge(readers []*KdiReader) *KWayMerge {
m := &KWayMerge{
h: make(mergeHeap, 0, len(readers)),
readers: readers,
}
// Initialize heap with first value from each reader
for i, r := range readers {
if v, ok := r.Next(); ok {
m.h = append(m.h, mergeItem{value: v, idx: i})
}
}
heap.Init(&m.h)
return m
}
// Next returns the next smallest k-mer value, the number of readers
// that contained this value (count), and true.
// Returns (0, 0, false) when all streams are exhausted.
func (m *KWayMerge) Next() (kmer uint64, count int, ok bool) {
if len(m.h) == 0 {
return 0, 0, false
}
minVal := m.h[0].value
count = 0
// Pop all items with the same value
for len(m.h) > 0 && m.h[0].value == minVal {
item := heap.Pop(&m.h).(mergeItem)
count++
// Advance that reader
if v, ok := m.readers[item.idx].Next(); ok {
heap.Push(&m.h, mergeItem{value: v, idx: item.idx})
}
}
return minVal, count, true
}
// Close closes all underlying readers.
func (m *KWayMerge) Close() error {
var firstErr error
for _, r := range m.readers {
if err := r.Close(); err != nil && firstErr == nil {
firstErr = err
}
}
return firstErr
}

159
pkg/obikmer/kdi_merge_test.go Normal file
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@@ -0,0 +1,159 @@
package obikmer
import (
"path/filepath"
"testing"
)
// writeKdi is a helper that writes sorted kmers to a .kdi file.
func writeKdi(t *testing.T, dir, name string, kmers []uint64) string {
t.Helper()
path := filepath.Join(dir, name)
w, err := NewKdiWriter(path)
if err != nil {
t.Fatal(err)
}
for _, v := range kmers {
if err := w.Write(v); err != nil {
t.Fatal(err)
}
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
return path
}
func TestKWayMergeBasic(t *testing.T) {
dir := t.TempDir()
// Three sorted streams
p1 := writeKdi(t, dir, "a.kdi", []uint64{1, 3, 5, 7})
p2 := writeKdi(t, dir, "b.kdi", []uint64{2, 3, 6, 7})
p3 := writeKdi(t, dir, "c.kdi", []uint64{3, 4, 7, 8})
r1, _ := NewKdiReader(p1)
r2, _ := NewKdiReader(p2)
r3, _ := NewKdiReader(p3)
m := NewKWayMerge([]*KdiReader{r1, r2, r3})
defer m.Close()
type result struct {
kmer uint64
count int
}
var results []result
for {
kmer, count, ok := m.Next()
if !ok {
break
}
results = append(results, result{kmer, count})
}
expected := []result{
{1, 1}, {2, 1}, {3, 3}, {4, 1}, {5, 1}, {6, 1}, {7, 3}, {8, 1},
}
if len(results) != len(expected) {
t.Fatalf("got %d results, want %d", len(results), len(expected))
}
for i, exp := range expected {
if results[i] != exp {
t.Errorf("result %d: got %+v, want %+v", i, results[i], exp)
}
}
}
func TestKWayMergeSingleStream(t *testing.T) {
dir := t.TempDir()
p := writeKdi(t, dir, "a.kdi", []uint64{10, 20, 30})
r, _ := NewKdiReader(p)
m := NewKWayMerge([]*KdiReader{r})
defer m.Close()
vals := []uint64{10, 20, 30}
for _, expected := range vals {
kmer, count, ok := m.Next()
if !ok {
t.Fatal("unexpected EOF")
}
if kmer != expected || count != 1 {
t.Fatalf("got (%d, %d), want (%d, 1)", kmer, count, expected)
}
}
_, _, ok := m.Next()
if ok {
t.Fatal("expected EOF")
}
}
func TestKWayMergeEmpty(t *testing.T) {
dir := t.TempDir()
p1 := writeKdi(t, dir, "a.kdi", nil)
p2 := writeKdi(t, dir, "b.kdi", nil)
r1, _ := NewKdiReader(p1)
r2, _ := NewKdiReader(p2)
m := NewKWayMerge([]*KdiReader{r1, r2})
defer m.Close()
_, _, ok := m.Next()
if ok {
t.Fatal("expected no results from empty streams")
}
}
func TestKWayMergeDisjoint(t *testing.T) {
dir := t.TempDir()
p1 := writeKdi(t, dir, "a.kdi", []uint64{1, 2, 3})
p2 := writeKdi(t, dir, "b.kdi", []uint64{10, 20, 30})
r1, _ := NewKdiReader(p1)
r2, _ := NewKdiReader(p2)
m := NewKWayMerge([]*KdiReader{r1, r2})
defer m.Close()
expected := []uint64{1, 2, 3, 10, 20, 30}
for _, exp := range expected {
kmer, count, ok := m.Next()
if !ok {
t.Fatal("unexpected EOF")
}
if kmer != exp || count != 1 {
t.Fatalf("got (%d, %d), want (%d, 1)", kmer, count, exp)
}
}
}
func TestKWayMergeAllSame(t *testing.T) {
dir := t.TempDir()
p1 := writeKdi(t, dir, "a.kdi", []uint64{42})
p2 := writeKdi(t, dir, "b.kdi", []uint64{42})
p3 := writeKdi(t, dir, "c.kdi", []uint64{42})
r1, _ := NewKdiReader(p1)
r2, _ := NewKdiReader(p2)
r3, _ := NewKdiReader(p3)
m := NewKWayMerge([]*KdiReader{r1, r2, r3})
defer m.Close()
kmer, count, ok := m.Next()
if !ok {
t.Fatal("expected one result")
}
if kmer != 42 || count != 3 {
t.Fatalf("got (%d, %d), want (42, 3)", kmer, count)
}
_, _, ok = m.Next()
if ok {
t.Fatal("expected EOF")
}
}

96
pkg/obikmer/kdi_reader.go Normal file
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@@ -0,0 +1,96 @@
package obikmer
import (
"bufio"
"encoding/binary"
"fmt"
"io"
"os"
)
// KdiReader reads k-mers from a .kdi file using streaming delta-varint decoding.
type KdiReader struct {
r *bufio.Reader
file *os.File
count uint64 // total number of k-mers
read uint64 // number of k-mers already consumed
prev uint64 // last decoded value
started bool // whether first value has been read
}
// NewKdiReader opens a .kdi file for streaming reading.
func NewKdiReader(path string) (*KdiReader, error) {
f, err := os.Open(path)
if err != nil {
return nil, err
}
r := bufio.NewReaderSize(f, 65536)
// Read and verify magic
var magic [4]byte
if _, err := io.ReadFull(r, magic[:]); err != nil {
f.Close()
return nil, fmt.Errorf("kdi: read magic: %w", err)
}
if magic != kdiMagic {
f.Close()
return nil, fmt.Errorf("kdi: bad magic %v", magic)
}
// Read count
var countBuf [8]byte
if _, err := io.ReadFull(r, countBuf[:]); err != nil {
f.Close()
return nil, fmt.Errorf("kdi: read count: %w", err)
}
count := binary.LittleEndian.Uint64(countBuf[:])
return &KdiReader{
r: r,
file: f,
count: count,
}, nil
}
// Next returns the next k-mer and true, or (0, false) when exhausted.
func (kr *KdiReader) Next() (uint64, bool) {
if kr.read >= kr.count {
return 0, false
}
if !kr.started {
// Read first value as absolute uint64 LE
var buf [8]byte
if _, err := io.ReadFull(kr.r, buf[:]); err != nil {
return 0, false
}
kr.prev = binary.LittleEndian.Uint64(buf[:])
kr.started = true
kr.read++
return kr.prev, true
}
// Read delta varint
delta, err := DecodeVarint(kr.r)
if err != nil {
return 0, false
}
kr.prev += delta
kr.read++
return kr.prev, true
}
// Count returns the total number of k-mers in this partition.
func (kr *KdiReader) Count() uint64 {
return kr.count
}
// Remaining returns how many k-mers have not been read yet.
func (kr *KdiReader) Remaining() uint64 {
return kr.count - kr.read
}
// Close closes the underlying file.
func (kr *KdiReader) Close() error {
return kr.file.Close()
}

255
pkg/obikmer/kdi_test.go Normal file
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@@ -0,0 +1,255 @@
package obikmer
import (
"os"
"path/filepath"
"sort"
"testing"
)
func TestKdiRoundTrip(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "test.kdi")
// Sorted k-mer values
kmers := []uint64{10, 20, 30, 100, 200, 500, 10000, 1 << 40, 1<<62 - 1}
w, err := NewKdiWriter(path)
if err != nil {
t.Fatal(err)
}
for _, v := range kmers {
if err := w.Write(v); err != nil {
t.Fatal(err)
}
}
if w.Count() != uint64(len(kmers)) {
t.Fatalf("writer count: got %d, want %d", w.Count(), len(kmers))
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
// Read back
r, err := NewKdiReader(path)
if err != nil {
t.Fatal(err)
}
defer r.Close()
if r.Count() != uint64(len(kmers)) {
t.Fatalf("reader count: got %d, want %d", r.Count(), len(kmers))
}
for i, expected := range kmers {
got, ok := r.Next()
if !ok {
t.Fatalf("unexpected EOF at index %d", i)
}
if got != expected {
t.Fatalf("kmer %d: got %d, want %d", i, got, expected)
}
}
_, ok := r.Next()
if ok {
t.Fatal("expected EOF after all k-mers")
}
}
func TestKdiEmpty(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "empty.kdi")
w, err := NewKdiWriter(path)
if err != nil {
t.Fatal(err)
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
r, err := NewKdiReader(path)
if err != nil {
t.Fatal(err)
}
defer r.Close()
if r.Count() != 0 {
t.Fatalf("expected count 0, got %d", r.Count())
}
_, ok := r.Next()
if ok {
t.Fatal("expected no k-mers in empty file")
}
}
func TestKdiSingleValue(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "single.kdi")
w, err := NewKdiWriter(path)
if err != nil {
t.Fatal(err)
}
if err := w.Write(42); err != nil {
t.Fatal(err)
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
r, err := NewKdiReader(path)
if err != nil {
t.Fatal(err)
}
defer r.Close()
if r.Count() != 1 {
t.Fatalf("expected count 1, got %d", r.Count())
}
v, ok := r.Next()
if !ok {
t.Fatal("expected one k-mer")
}
if v != 42 {
t.Fatalf("got %d, want 42", v)
}
}
func TestKdiFileSize(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "size.kdi")
// Write: magic(4) + count(8) + first(8) = 20 bytes
w, err := NewKdiWriter(path)
if err != nil {
t.Fatal(err)
}
if err := w.Write(0); err != nil {
t.Fatal(err)
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
info, err := os.Stat(path)
if err != nil {
t.Fatal(err)
}
// magic(4) + count(8) + first(8) = 20
if info.Size() != 20 {
t.Fatalf("file size: got %d, want 20", info.Size())
}
}
func TestKdiDeltaCompression(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "delta.kdi")
// Dense consecutive values should compress well
n := 10000
kmers := make([]uint64, n)
for i := range kmers {
kmers[i] = uint64(i * 2) // even numbers
}
w, err := NewKdiWriter(path)
if err != nil {
t.Fatal(err)
}
for _, v := range kmers {
if err := w.Write(v); err != nil {
t.Fatal(err)
}
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
// Each delta is 2, encoded as 1 byte varint
// Total: magic(4) + count(8) + first(8) + (n-1)*1 = 20 + 9999 bytes
info, err := os.Stat(path)
if err != nil {
t.Fatal(err)
}
expected := int64(20 + n - 1)
if info.Size() != expected {
t.Fatalf("file size: got %d, want %d", info.Size(), expected)
}
// Verify round-trip
r, err := NewKdiReader(path)
if err != nil {
t.Fatal(err)
}
defer r.Close()
for i, expected := range kmers {
got, ok := r.Next()
if !ok {
t.Fatalf("unexpected EOF at index %d", i)
}
if got != expected {
t.Fatalf("kmer %d: got %d, want %d", i, got, expected)
}
}
}
func TestKdiFromRealKmers(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "real.kdi")
// Extract k-mers from a sequence, sort, dedup, write to KDI
seq := []byte("ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT")
k := 15
var kmers []uint64
for kmer := range IterCanonicalKmers(seq, k) {
kmers = append(kmers, kmer)
}
sort.Slice(kmers, func(i, j int) bool { return kmers[i] < kmers[j] })
// Dedup
deduped := kmers[:0]
for i, v := range kmers {
if i == 0 || v != kmers[i-1] {
deduped = append(deduped, v)
}
}
w, err := NewKdiWriter(path)
if err != nil {
t.Fatal(err)
}
for _, v := range deduped {
if err := w.Write(v); err != nil {
t.Fatal(err)
}
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
// Read back and verify
r, err := NewKdiReader(path)
if err != nil {
t.Fatal(err)
}
defer r.Close()
if r.Count() != uint64(len(deduped)) {
t.Fatalf("count: got %d, want %d", r.Count(), len(deduped))
}
for i, expected := range deduped {
got, ok := r.Next()
if !ok {
t.Fatalf("unexpected EOF at index %d", i)
}
if got != expected {
t.Fatalf("kmer %d: got %d, want %d", i, got, expected)
}
}
}

113
pkg/obikmer/kdi_writer.go Normal file
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@@ -0,0 +1,113 @@
package obikmer
import (
"bufio"
"encoding/binary"
"os"
)
// KDI file magic bytes: "KDI\x01"
var kdiMagic = [4]byte{'K', 'D', 'I', 0x01}
// KdiWriter writes a sorted sequence of uint64 k-mers to a .kdi file
// using delta-varint encoding.
//
// Format:
//
// [magic: 4 bytes "KDI\x01"]
// [count: uint64 LE] number of k-mers
// [first: uint64 LE] first k-mer (absolute value)
// [delta_1: varint] arr[1] - arr[0]
// [delta_2: varint] arr[2] - arr[1]
// ...
//
// The caller must write k-mers in strictly increasing order.
type KdiWriter struct {
w *bufio.Writer
file *os.File
count uint64
prev uint64
first bool
path string
}
// NewKdiWriter creates a new KdiWriter writing to the given file path.
// The header (magic + count placeholder) is written immediately.
// Count is patched on Close().
func NewKdiWriter(path string) (*KdiWriter, error) {
f, err := os.Create(path)
if err != nil {
return nil, err
}
w := bufio.NewWriterSize(f, 65536)
// Write magic
if _, err := w.Write(kdiMagic[:]); err != nil {
f.Close()
return nil, err
}
// Write placeholder for count (will be patched on Close)
var countBuf [8]byte
if _, err := w.Write(countBuf[:]); err != nil {
f.Close()
return nil, err
}
return &KdiWriter{
w: w,
file: f,
first: true,
path: path,
}, nil
}
// Write adds a k-mer to the file. K-mers must be written in strictly
// increasing order.
func (kw *KdiWriter) Write(kmer uint64) error {
if kw.first {
// Write first value as absolute uint64 LE
var buf [8]byte
binary.LittleEndian.PutUint64(buf[:], kmer)
if _, err := kw.w.Write(buf[:]); err != nil {
return err
}
kw.prev = kmer
kw.first = false
} else {
delta := kmer - kw.prev
if _, err := EncodeVarint(kw.w, delta); err != nil {
return err
}
kw.prev = kmer
}
kw.count++
return nil
}
// Count returns the number of k-mers written so far.
func (kw *KdiWriter) Count() uint64 {
return kw.count
}
// Close flushes buffered data, patches the count in the header,
// and closes the file.
func (kw *KdiWriter) Close() error {
if err := kw.w.Flush(); err != nil {
kw.file.Close()
return err
}
// Patch count at offset 4 (after magic)
if _, err := kw.file.Seek(4, 0); err != nil {
kw.file.Close()
return err
}
var countBuf [8]byte
binary.LittleEndian.PutUint64(countBuf[:], kw.count)
if _, err := kw.file.Write(countBuf[:]); err != nil {
kw.file.Close()
return err
}
return kw.file.Close()
}

204
pkg/obikmer/kmer_index_builder.go
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@@ -1,204 +0,0 @@
package obikmer
import (
"math"
"sync"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
)
// DefaultMinimizerSize returns ceil(k / 2.5) as a reasonable default minimizer size.
func DefaultMinimizerSize(k int) int {
m := int(math.Ceil(float64(k) / 2.5))
if m < 1 {
m = 1
}
if m >= k {
m = k - 1
}
return m
}
// MinMinimizerSize returns the minimum m such that 4^m >= nworkers,
// i.e. ceil(log(nworkers) / log(4)).
func MinMinimizerSize(nworkers int) int {
if nworkers <= 1 {
return 1
}
return int(math.Ceil(math.Log(float64(nworkers)) / math.Log(4)))
}
// ValidateMinimizerSize checks and adjusts the minimizer size to satisfy constraints:
// - m >= ceil(log(nworkers)/log(4))
// - 1 <= m < k
func ValidateMinimizerSize(m, k, nworkers int) int {
minM := MinMinimizerSize(nworkers)
if m < minM {
log.Warnf("Minimizer size %d too small for %d workers (4^%d = %d < %d), adjusting to %d",
m, nworkers, m, 1<<(2*m), nworkers, minM)
m = minM
}
if m < 1 {
m = 1
}
if m >= k {
m = k - 1
}
return m
}
// BuildKmerIndex builds a KmerSet from an iterator using parallel super-kmer partitioning.
//
// The algorithm:
// 1. Extract super-kmers from each sequence using IterSuperKmers
// 2. Route each super-kmer to a worker based on minimizer % nworkers
// 3. Each worker extracts canonical k-mers and adds them to its local KmerSet
// 4. Merge all KmerSets via Union
//
// Parameters:
// - iterator: source of BioSequence batches
// - k: k-mer size (1-31)
// - m: minimizer size (1 to k-1)
func BuildKmerIndex(iterator obiiter.IBioSequence, k, m int) *KmerSet {
nproc := obidefault.ParallelWorkers()
m = ValidateMinimizerSize(m, k, nproc)
// Channels to route super-kmers to workers
channels := make([]chan SuperKmer, nproc)
for i := range channels {
channels[i] = make(chan SuperKmer, 1024)
}
// Workers: each manages a partition of the minimizer space
sets := make([]*KmerSet, nproc)
waiter := sync.WaitGroup{}
waiter.Add(nproc)
for i := 0; i < nproc; i++ {
sets[i] = NewKmerSet(k)
go func(ch chan SuperKmer, ks *KmerSet) {
defer waiter.Done()
for sk := range ch {
for kmer := range IterCanonicalKmers(sk.Sequence, k) {
ks.AddKmerCode(kmer)
}
}
}(channels[i], sets[i])
}
// Reader: extract super-kmers and route them
seqCount := 0
for iterator.Next() {
batch := iterator.Get()
for _, seq := range batch.Slice() {
rawSeq := seq.Sequence()
if len(rawSeq) < k {
continue
}
for sk := range IterSuperKmers(rawSeq, k, m) {
worker := int(sk.Minimizer % uint64(nproc))
channels[worker] <- sk
}
seqCount++
}
}
// Close channels to signal workers to finish
for _, ch := range channels {
close(ch)
}
waiter.Wait()
log.Infof("Processed %d sequences", seqCount)
// Merge partitions (mostly disjoint -> fast union)
result := sets[0]
for i := 1; i < nproc; i++ {
result.bitmap.Or(sets[i].bitmap)
}
log.Infof("Index contains %d k-mers (%.2f MB)",
result.Len(), float64(result.MemoryUsage())/1024/1024)
return result
}
// BuildFrequencyFilterIndex builds a FrequencyFilter from an iterator
// using parallel super-kmer partitioning.
//
// Each worker manages its own FrequencyFilter for its partition of the
// minimizer space. Since all k-mers sharing a minimizer go to the same worker,
// the frequency counting is correct per partition.
//
// Parameters:
// - iterator: source of BioSequence batches
// - k: k-mer size (1-31)
// - m: minimizer size (1 to k-1)
// - minFreq: minimum frequency threshold (>= 1)
func BuildFrequencyFilterIndex(iterator obiiter.IBioSequence, k, m, minFreq int) *FrequencyFilter {
nproc := obidefault.ParallelWorkers()
m = ValidateMinimizerSize(m, k, nproc)
// Channels to route super-kmers to workers
channels := make([]chan SuperKmer, nproc)
for i := range channels {
channels[i] = make(chan SuperKmer, 1024)
}
// Workers: each manages a local FrequencyFilter
filters := make([]*FrequencyFilter, nproc)
waiter := sync.WaitGroup{}
waiter.Add(nproc)
for i := 0; i < nproc; i++ {
filters[i] = NewFrequencyFilter(k, minFreq)
go func(ch chan SuperKmer, ff *FrequencyFilter) {
defer waiter.Done()
for sk := range ch {
for kmer := range IterCanonicalKmers(sk.Sequence, k) {
ff.AddKmerCode(kmer)
}
}
}(channels[i], filters[i])
}
// Reader: extract super-kmers and route them
seqCount := 0
for iterator.Next() {
batch := iterator.Get()
for _, seq := range batch.Slice() {
rawSeq := seq.Sequence()
if len(rawSeq) < k {
continue
}
for sk := range IterSuperKmers(rawSeq, k, m) {
worker := int(sk.Minimizer % uint64(nproc))
channels[worker] <- sk
}
seqCount++
}
}
// Close channels to signal workers to finish
for _, ch := range channels {
close(ch)
}
waiter.Wait()
log.Infof("Processed %d sequences", seqCount)
// Merge FrequencyFilters: union level by level
result := filters[0]
for i := 1; i < nproc; i++ {
for level := 0; level < minFreq; level++ {
result.Get(level).bitmap.Or(filters[i].Get(level).bitmap)
}
}
stats := result.Stats()
log.Infof("FrequencyFilter: %d k-mers with freq >= %d (%.2f MB total)",
stats.FilteredKmers, minFreq, float64(stats.TotalBytes)/1024/1024)
return result
}

224
pkg/obikmer/kmer_set.go
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@@ -1,224 +0,0 @@
package obikmer
import (
"fmt"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"github.com/RoaringBitmap/roaring/roaring64"
)
// KmerSet wraps a set of k-mers stored in a Roaring Bitmap
// Provides utility methods for manipulating k-mer sets
type KmerSet struct {
id string // Unique identifier of the KmerSet
k int // Size of k-mers (immutable)
bitmap *roaring64.Bitmap // Bitmap containing the k-mers
Metadata map[string]interface{} // User metadata (key=atomic value)
}
// NewKmerSet creates a new empty KmerSet
func NewKmerSet(k int) *KmerSet {
return &KmerSet{
k: k,
bitmap: roaring64.New(),
Metadata: make(map[string]interface{}),
}
}
// NewKmerSetFromBitmap creates a KmerSet from an existing bitmap
func NewKmerSetFromBitmap(k int, bitmap *roaring64.Bitmap) *KmerSet {
return &KmerSet{
k: k,
bitmap: bitmap,
Metadata: make(map[string]interface{}),
}
}
// K returns the size of k-mers (immutable)
func (ks *KmerSet) K() int {
return ks.k
}
// AddKmerCode adds an encoded k-mer to the set
func (ks *KmerSet) AddKmerCode(kmer uint64) {
ks.bitmap.Add(kmer)
}
// AddCanonicalKmerCode adds an encoded canonical k-mer to the set
func (ks *KmerSet) AddCanonicalKmerCode(kmer uint64) {
canonical := CanonicalKmer(kmer, ks.k)
ks.bitmap.Add(canonical)
}
// AddKmer adds a k-mer to the set by encoding the sequence
// The sequence must have exactly k nucleotides
// Zero-allocation: encodes directly without creating an intermediate slice
func (ks *KmerSet) AddKmer(seq []byte) {
kmer := EncodeKmer(seq, ks.k)
ks.bitmap.Add(kmer)
}
// AddCanonicalKmer adds a canonical k-mer to the set by encoding the sequence
// The sequence must have exactly k nucleotides
// Zero-allocation: encodes directly in canonical form without creating an intermediate slice
func (ks *KmerSet) AddCanonicalKmer(seq []byte) {
canonical := EncodeCanonicalKmer(seq, ks.k)
ks.bitmap.Add(canonical)
}
// AddSequence adds all k-mers from a sequence to the set
// Uses an iterator to avoid allocating an intermediate vector
func (ks *KmerSet) AddSequence(seq *obiseq.BioSequence) {
rawSeq := seq.Sequence()
for canonical := range IterCanonicalKmers(rawSeq, ks.k) {
ks.bitmap.Add(canonical)
}
}
// AddSequences adds all k-mers from multiple sequences in batch
func (ks *KmerSet) AddSequences(sequences *obiseq.BioSequenceSlice) {
for _, seq := range *sequences {
ks.AddSequence(seq)
}
}
// AddSequenceSlice adds all k-mers from a slice of sequences
func (ks *KmerSet) AddSequenceSlice(sequences *obiseq.BioSequenceSlice) {
for _, seq := range *sequences {
ks.AddSequence(seq)
}
}
// Contains checks if a k-mer is in the set
func (ks *KmerSet) Contains(kmer uint64) bool {
return ks.bitmap.Contains(kmer)
}
// Len returns the number of k-mers in the set
func (ks *KmerSet) Len() uint64 {
return ks.bitmap.GetCardinality()
}
// MemoryUsage returns memory usage in bytes
func (ks *KmerSet) MemoryUsage() uint64 {
return ks.bitmap.GetSizeInBytes()
}
// Clear empties the set
func (ks *KmerSet) Clear() {
ks.bitmap.Clear()
}
// Copy creates a copy of the set (consistent with BioSequence.Copy)
func (ks *KmerSet) Copy() *KmerSet {
// Copy metadata
metadata := make(map[string]interface{}, len(ks.Metadata))
for k, v := range ks.Metadata {
metadata[k] = v
}
return &KmerSet{
id: ks.id,
k: ks.k,
bitmap: ks.bitmap.Clone(),
Metadata: metadata,
}
}
// Id returns the identifier of the KmerSet (consistent with BioSequence.Id)
func (ks *KmerSet) Id() string {
return ks.id
}
// SetId sets the identifier of the KmerSet (consistent with BioSequence.SetId)
func (ks *KmerSet) SetId(id string) {
ks.id = id
}
// Union returns the union of this set with another
func (ks *KmerSet) Union(other *KmerSet) *KmerSet {
if ks.k != other.k {
panic(fmt.Sprintf("Cannot union KmerSets with different k values: %d vs %d", ks.k, other.k))
}
result := ks.bitmap.Clone()
result.Or(other.bitmap)
return NewKmerSetFromBitmap(ks.k, result)
}
// Intersect returns the intersection of this set with another
func (ks *KmerSet) Intersect(other *KmerSet) *KmerSet {
if ks.k != other.k {
panic(fmt.Sprintf("Cannot intersect KmerSets with different k values: %d vs %d", ks.k, other.k))
}
result := ks.bitmap.Clone()
result.And(other.bitmap)
return NewKmerSetFromBitmap(ks.k, result)
}
// Difference returns the difference of this set with another (this - other)
func (ks *KmerSet) Difference(other *KmerSet) *KmerSet {
if ks.k != other.k {
panic(fmt.Sprintf("Cannot subtract KmerSets with different k values: %d vs %d", ks.k, other.k))
}
result := ks.bitmap.Clone()
result.AndNot(other.bitmap)
return NewKmerSetFromBitmap(ks.k, result)
}
// JaccardDistance computes the Jaccard distance between two KmerSets.
// The Jaccard distance is defined as: 1 - (|A ∩ B| / |A ∪ B|)
// where A and B are the two sets.
//
// Returns:
// - 0.0 when sets are identical (distance = 0, similarity = 1)
// - 1.0 when sets are completely disjoint (distance = 1, similarity = 0)
// - 1.0 when both sets are empty (by convention)
//
// Time complexity: O(|A| + |B|) for Roaring Bitmap operations
// Space complexity: O(1) as operations are done in-place on temporary bitmaps
func (ks *KmerSet) JaccardDistance(other *KmerSet) float64 {
if ks.k != other.k {
panic(fmt.Sprintf("Cannot compute Jaccard distance between KmerSets with different k values: %d vs %d", ks.k, other.k))
}
// Compute intersection cardinality
intersectionCard := ks.bitmap.AndCardinality(other.bitmap)
// Compute union cardinality
unionCard := ks.bitmap.OrCardinality(other.bitmap)
// If union is empty, both sets are empty - return 1.0 by convention
if unionCard == 0 {
return 1.0
}
// Jaccard similarity = |A ∩ B| / |A ∪ B|
similarity := float64(intersectionCard) / float64(unionCard)
// Jaccard distance = 1 - similarity
return 1.0 - similarity
}
// JaccardSimilarity computes the Jaccard similarity coefficient between two KmerSets.
// The Jaccard similarity is defined as: |A ∩ B| / |A ∪ B|
//
// Returns:
// - 1.0 when sets are identical (maximum similarity)
// - 0.0 when sets are completely disjoint (no similarity)
// - 0.0 when both sets are empty (by convention)
//
// Time complexity: O(|A| + |B|) for Roaring Bitmap operations
// Space complexity: O(1) as operations are done in-place on temporary bitmaps
func (ks *KmerSet) JaccardSimilarity(other *KmerSet) float64 {
return 1.0 - ks.JaccardDistance(other)
}
// Iterator returns an iterator over all k-mers in the set
func (ks *KmerSet) Iterator() roaring64.IntIterable64 {
return ks.bitmap.Iterator()
}
// Bitmap returns the underlying bitmap (for compatibility)
func (ks *KmerSet) Bitmap() *roaring64.Bitmap {
return ks.bitmap
}

362
pkg/obikmer/kmer_set_attributes.go
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@@ -1,362 +0,0 @@
package obikmer
import (
"fmt"
"strconv"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
// ==================================
// KMER SET ATTRIBUTE API
// Mimic BioSequence attribute API from obiseq/attributes.go
// ==================================
// HasAttribute vérifie si une clé d'attribut existe
func (ks *KmerSet) HasAttribute(key string) bool {
_, ok := ks.Metadata[key]
return ok
}
// GetAttribute récupère la valeur d'un attribut
// Cas particuliers: "id" utilise Id(), "k" utilise K()
func (ks *KmerSet) GetAttribute(key string) (interface{}, bool) {
switch key {
case "id":
return ks.Id(), true
case "k":
return ks.K(), true
default:
value, ok := ks.Metadata[key]
return value, ok
}
}
// SetAttribute sets the value of an attribute
// Cas particuliers: "id" utilise SetId(), "k" est immutable (panique)
func (ks *KmerSet) SetAttribute(key string, value interface{}) {
switch key {
case "id":
if id, ok := value.(string); ok {
ks.SetId(id)
} else {
panic(fmt.Sprintf("id must be a string, got %T", value))
}
case "k":
panic("k is immutable and cannot be modified via SetAttribute")
default:
ks.Metadata[key] = value
}
}
// DeleteAttribute supprime un attribut
func (ks *KmerSet) DeleteAttribute(key string) {
delete(ks.Metadata, key)
}
// RemoveAttribute supprime un attribut (alias de DeleteAttribute)
func (ks *KmerSet) RemoveAttribute(key string) {
ks.DeleteAttribute(key)
}
// RenameAttribute renomme un attribut
func (ks *KmerSet) RenameAttribute(newName, oldName string) {
if value, ok := ks.Metadata[oldName]; ok {
ks.Metadata[newName] = value
delete(ks.Metadata, oldName)
}
}
// GetIntAttribute récupère un attribut en tant qu'entier
func (ks *KmerSet) GetIntAttribute(key string) (int, bool) {
value, ok := ks.Metadata[key]
if !ok {
return 0, false
}
switch v := value.(type) {
case int:
return v, true
case int64:
return int(v), true
case float64:
return int(v), true
case string:
if i, err := strconv.Atoi(v); err == nil {
return i, true
}
}
return 0, false
}
// GetFloatAttribute récupère un attribut en tant que float64
func (ks *KmerSet) GetFloatAttribute(key string) (float64, bool) {
value, ok := ks.Metadata[key]
if !ok {
return 0, false
}
switch v := value.(type) {
case float64:
return v, true
case float32:
return float64(v), true
case int:
return float64(v), true
case int64:
return float64(v), true
case string:
if f, err := strconv.ParseFloat(v, 64); err == nil {
return f, true
}
}
return 0, false
}
// GetNumericAttribute récupère un attribut numérique (alias de GetFloatAttribute)
func (ks *KmerSet) GetNumericAttribute(key string) (float64, bool) {
return ks.GetFloatAttribute(key)
}
// GetStringAttribute récupère un attribut en tant que chaîne
func (ks *KmerSet) GetStringAttribute(key string) (string, bool) {
value, ok := ks.Metadata[key]
if !ok {
return "", false
}
switch v := value.(type) {
case string:
return v, true
default:
return fmt.Sprintf("%v", v), true
}
}
// GetBoolAttribute récupère un attribut en tant que booléen
func (ks *KmerSet) GetBoolAttribute(key string) (bool, bool) {
value, ok := ks.Metadata[key]
if !ok {
return false, false
}
switch v := value.(type) {
case bool:
return v, true
case int:
return v != 0, true
case string:
if b, err := strconv.ParseBool(v); err == nil {
return b, true
}
}
return false, false
}
// AttributeKeys returns the set of attribute keys
func (ks *KmerSet) AttributeKeys() obiutils.Set[string] {
keys := obiutils.MakeSet[string]()
for key := range ks.Metadata {
keys.Add(key)
}
return keys
}
// Keys returns the set of attribute keys (alias of AttributeKeys)
func (ks *KmerSet) Keys() obiutils.Set[string] {
return ks.AttributeKeys()
}
// ==================================
// KMER SET GROUP ATTRIBUTE API
// Métadonnées du groupe + accès via Get() pour les sets individuels
// ==================================
// HasAttribute vérifie si une clé d'attribut existe pour le groupe
func (ksg *KmerSetGroup) HasAttribute(key string) bool {
_, ok := ksg.Metadata[key]
return ok
}
// GetAttribute récupère la valeur d'un attribut du groupe
// Cas particuliers: "id" utilise Id(), "k" utilise K()
func (ksg *KmerSetGroup) GetAttribute(key string) (interface{}, bool) {
switch key {
case "id":
return ksg.Id(), true
case "k":
return ksg.K(), true
default:
value, ok := ksg.Metadata[key]
return value, ok
}
}
// SetAttribute sets the value of an attribute du groupe
// Cas particuliers: "id" utilise SetId(), "k" est immutable (panique)
func (ksg *KmerSetGroup) SetAttribute(key string, value interface{}) {
switch key {
case "id":
if id, ok := value.(string); ok {
ksg.SetId(id)
} else {
panic(fmt.Sprintf("id must be a string, got %T", value))
}
case "k":
panic("k is immutable and cannot be modified via SetAttribute")
default:
ksg.Metadata[key] = value
}
}
// DeleteAttribute supprime un attribut du groupe
func (ksg *KmerSetGroup) DeleteAttribute(key string) {
delete(ksg.Metadata, key)
}
// RemoveAttribute supprime un attribut du groupe (alias)
func (ksg *KmerSetGroup) RemoveAttribute(key string) {
ksg.DeleteAttribute(key)
}
// RenameAttribute renomme un attribut du groupe
func (ksg *KmerSetGroup) RenameAttribute(newName, oldName string) {
if value, ok := ksg.Metadata[oldName]; ok {
ksg.Metadata[newName] = value
delete(ksg.Metadata, oldName)
}
}
// GetIntAttribute récupère un attribut entier du groupe
func (ksg *KmerSetGroup) GetIntAttribute(key string) (int, bool) {
value, ok := ksg.GetAttribute(key)
if !ok {
return 0, false
}
switch v := value.(type) {
case int:
return v, true
case int64:
return int(v), true
case float64:
return int(v), true
case string:
if i, err := strconv.Atoi(v); err == nil {
return i, true
}
}
return 0, false
}
// GetFloatAttribute récupère un attribut float64 du groupe
func (ksg *KmerSetGroup) GetFloatAttribute(key string) (float64, bool) {
value, ok := ksg.GetAttribute(key)
if !ok {
return 0, false
}
switch v := value.(type) {
case float64:
return v, true
case float32:
return float64(v), true
case int:
return float64(v), true
case int64:
return float64(v), true
case string:
if f, err := strconv.ParseFloat(v, 64); err == nil {
return f, true
}
}
return 0, false
}
// GetNumericAttribute récupère un attribut numérique du groupe
func (ksg *KmerSetGroup) GetNumericAttribute(key string) (float64, bool) {
return ksg.GetFloatAttribute(key)
}
// GetStringAttribute récupère un attribut chaîne du groupe
func (ksg *KmerSetGroup) GetStringAttribute(key string) (string, bool) {
value, ok := ksg.GetAttribute(key)
if !ok {
return "", false
}
switch v := value.(type) {
case string:
return v, true
default:
return fmt.Sprintf("%v", v), true
}
}
// GetBoolAttribute récupère un attribut booléen du groupe
func (ksg *KmerSetGroup) GetBoolAttribute(key string) (bool, bool) {
value, ok := ksg.GetAttribute(key)
if !ok {
return false, false
}
switch v := value.(type) {
case bool:
return v, true
case int:
return v != 0, true
case string:
if b, err := strconv.ParseBool(v); err == nil {
return b, true
}
}
return false, false
}
// AttributeKeys returns the set of attribute keys du groupe
func (ksg *KmerSetGroup) AttributeKeys() obiutils.Set[string] {
keys := obiutils.MakeSet[string]()
for key := range ksg.Metadata {
keys.Add(key)
}
return keys
}
// Keys returns the set of group attribute keys (alias)
func (ksg *KmerSetGroup) Keys() obiutils.Set[string] {
return ksg.AttributeKeys()
}
// ==================================
// MÉTHODES POUR ACCÉDER AUX ATTRIBUTS DES SETS INDIVIDUELS VIA Get()
// Architecture zero-copy: ksg.Get(i).SetAttribute(...)
// ==================================
// Exemple d'utilisation:
// Pour accéder aux métadonnées d'un KmerSet individuel dans un groupe:
// ks := ksg.Get(0)
// ks.SetAttribute("level", 1)
// hasLevel := ks.HasAttribute("level")
//
// Pour les métadonnées du groupe:
// ksg.SetAttribute("name", "FrequencyFilter")
// name, ok := ksg.GetStringAttribute("name")
// AllAttributeKeys returns all unique attribute keys of the group AND all its sets
func (ksg *KmerSetGroup) AllAttributeKeys() obiutils.Set[string] {
keys := obiutils.MakeSet[string]()
// Ajouter les clés du groupe
for key := range ksg.Metadata {
keys.Add(key)
}
// Ajouter les clés de chaque set
for _, ks := range ksg.sets {
for key := range ks.Metadata {
keys.Add(key)
}
}
return keys
}

361
pkg/obikmer/kmer_set_builder.go Normal file
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package obikmer
import (
"fmt"
"math"
"os"
"path/filepath"
"runtime"
"sort"
"sync"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// BuilderOption is a functional option for KmerSetGroupBuilder.
type BuilderOption func(*builderConfig)
type builderConfig struct {
minFreq int // 0 means no frequency filtering (simple dedup)
}
// WithMinFrequency activates frequency filtering mode.
// Only k-mers seen >= minFreq times are kept in the final index.
func WithMinFrequency(minFreq int) BuilderOption {
return func(c *builderConfig) {
c.minFreq = minFreq
}
}
// KmerSetGroupBuilder constructs a KmerSetGroup on disk.
// During construction, super-kmers are written to temporary .skm files
// partitioned by minimizer. On Close(), each partition is finalized
// (sort, dedup, optional frequency filter) into .kdi files.
type KmerSetGroupBuilder struct {
dir string
k int
m int
n int // number of sets
P int // number of partitions
config builderConfig
writers [][]*SkmWriter // [setIndex][partIndex]
mu [][]sync.Mutex // per-writer mutex for concurrent access
closed bool
}
// NewKmerSetGroupBuilder creates a builder for a new KmerSetGroup.
//
// Parameters:
// - directory: destination directory (created if necessary)
// - k: k-mer size (1-31)
// - m: minimizer size (-1 for auto = ceil(k/2.5))
// - n: number of sets in the group
// - P: number of partitions (-1 for auto)
// - options: optional builder options (e.g. WithMinFrequency)
func NewKmerSetGroupBuilder(directory string, k, m, n, P int,
options ...BuilderOption) (*KmerSetGroupBuilder, error) {
if k < 2 || k > 31 {
return nil, fmt.Errorf("obikmer: k must be between 2 and 31, got %d", k)
}
if n < 1 {
return nil, fmt.Errorf("obikmer: n must be >= 1, got %d", n)
}
// Auto minimizer size
if m < 0 {
m = int(math.Ceil(float64(k) / 2.5))
}
if m < 1 {
m = 1
}
if m >= k {
m = k - 1
}
// Auto partition count
if P < 0 {
// Use 4^m as the maximum, capped at a reasonable value
maxP := 1 << (2 * m) // 4^m
P = maxP
if P > 4096 {
P = 4096
}
if P < 64 {
P = 64
}
}
// Apply options
var config builderConfig
for _, opt := range options {
opt(&config)
}
// Create build directory structure
buildDir := filepath.Join(directory, ".build")
for s := 0; s < n; s++ {
setDir := filepath.Join(buildDir, fmt.Sprintf("set_%d", s))
if err := os.MkdirAll(setDir, 0755); err != nil {
return nil, fmt.Errorf("obikmer: create build dir: %w", err)
}
}
// Create SKM writers
writers := make([][]*SkmWriter, n)
mutexes := make([][]sync.Mutex, n)
for s := 0; s < n; s++ {
writers[s] = make([]*SkmWriter, P)
mutexes[s] = make([]sync.Mutex, P)
for p := 0; p < P; p++ {
path := filepath.Join(buildDir, fmt.Sprintf("set_%d", s),
fmt.Sprintf("part_%04d.skm", p))
w, err := NewSkmWriter(path)
if err != nil {
// Close already-created writers
for ss := 0; ss <= s; ss++ {
for pp := 0; pp < P; pp++ {
if writers[ss][pp] != nil {
writers[ss][pp].Close()
}
}
}
return nil, fmt.Errorf("obikmer: create skm writer: %w", err)
}
writers[s][p] = w
}
}
return &KmerSetGroupBuilder{
dir: directory,
k: k,
m: m,
n: n,
P: P,
config: config,
writers: writers,
mu: mutexes,
}, nil
}
// AddSequence extracts super-kmers from a sequence and writes them
// to the appropriate partition files for the given set.
func (b *KmerSetGroupBuilder) AddSequence(setIndex int, seq *obiseq.BioSequence) {
if setIndex < 0 || setIndex >= b.n {
return
}
rawSeq := seq.Sequence()
if len(rawSeq) < b.k {
return
}
for sk := range IterSuperKmers(rawSeq, b.k, b.m) {
part := int(sk.Minimizer % uint64(b.P))
b.mu[setIndex][part].Lock()
b.writers[setIndex][part].Write(sk)
b.mu[setIndex][part].Unlock()
}
}
// AddSuperKmer writes a single super-kmer to the appropriate partition.
func (b *KmerSetGroupBuilder) AddSuperKmer(setIndex int, sk SuperKmer) {
if setIndex < 0 || setIndex >= b.n {
return
}
part := int(sk.Minimizer % uint64(b.P))
b.mu[setIndex][part].Lock()
b.writers[setIndex][part].Write(sk)
b.mu[setIndex][part].Unlock()
}
// Close finalizes the construction:
// 1. Flush and close all SKM writers
// 2. For each partition of each set (in parallel):
// - Load super-kmers from .skm
// - Extract canonical k-mers
// - Sort and deduplicate (count if frequency filter)
// - Write .kdi file
// 3. Write metadata.toml
// 4. Remove .build/ directory
//
// Returns the finalized KmerSetGroup in read-only mode.
func (b *KmerSetGroupBuilder) Close() (*KmerSetGroup, error) {
if b.closed {
return nil, fmt.Errorf("obikmer: builder already closed")
}
b.closed = true
// 1. Close all SKM writers
for s := 0; s < b.n; s++ {
for p := 0; p < b.P; p++ {
if err := b.writers[s][p].Close(); err != nil {
return nil, fmt.Errorf("obikmer: close skm writer set=%d part=%d: %w", s, p, err)
}
}
}
// 2. Create output directory structure
for s := 0; s < b.n; s++ {
setDir := filepath.Join(b.dir, fmt.Sprintf("set_%d", s))
if err := os.MkdirAll(setDir, 0755); err != nil {
return nil, fmt.Errorf("obikmer: create set dir: %w", err)
}
}
// Process partitions in parallel
counts := make([][]uint64, b.n)
for s := 0; s < b.n; s++ {
counts[s] = make([]uint64, b.P)
}
nWorkers := runtime.NumCPU()
if nWorkers > b.P {
nWorkers = b.P
}
type job struct {
setIdx int
partIdx int
}
jobs := make(chan job, b.n*b.P)
var wg sync.WaitGroup
var errMu sync.Mutex
var firstErr error
for w := 0; w < nWorkers; w++ {
wg.Add(1)
go func() {
defer wg.Done()
for j := range jobs {
if err := b.finalizePartition(j.setIdx, j.partIdx, &counts[j.setIdx][j.partIdx]); err != nil {
errMu.Lock()
if firstErr == nil {
firstErr = err
}
errMu.Unlock()
}
}
}()
}
for s := 0; s < b.n; s++ {
for p := 0; p < b.P; p++ {
jobs <- job{s, p}
}
}
close(jobs)
wg.Wait()
if firstErr != nil {
return nil, firstErr
}
// 3. Build KmerSetGroup and write metadata
totalCounts := make([]uint64, b.n)
for s := 0; s < b.n; s++ {
for p := 0; p < b.P; p++ {
totalCounts[s] += counts[s][p]
}
}
setsIDs := make([]string, b.n)
ksg := &KmerSetGroup{
path: b.dir,
k: b.k,
m: b.m,
partitions: b.P,
n: b.n,
setsIDs: setsIDs,
counts: totalCounts,
Metadata: make(map[string]interface{}),
}
if err := ksg.saveMetadata(); err != nil {
return nil, fmt.Errorf("obikmer: write metadata: %w", err)
}
// 4. Remove .build/ directory
buildDir := filepath.Join(b.dir, ".build")
os.RemoveAll(buildDir)
return ksg, nil
}
// finalizePartition processes a single partition: load SKM, extract k-mers,
// sort, dedup/count, write KDI.
func (b *KmerSetGroupBuilder) finalizePartition(setIdx, partIdx int, count *uint64) error {
skmPath := filepath.Join(b.dir, ".build",
fmt.Sprintf("set_%d", setIdx),
fmt.Sprintf("part_%04d.skm", partIdx))
kdiPath := filepath.Join(b.dir,
fmt.Sprintf("set_%d", setIdx),
fmt.Sprintf("part_%04d.kdi", partIdx))
// Load super-kmers and extract canonical k-mers
reader, err := NewSkmReader(skmPath)
if err != nil {
// If file doesn't exist or is empty, write empty KDI
return b.writeEmptyKdi(kdiPath, count)
}
var kmers []uint64
for {
sk, ok := reader.Next()
if !ok {
break
}
for kmer := range IterCanonicalKmers(sk.Sequence, b.k) {
kmers = append(kmers, kmer)
}
}
reader.Close()
if len(kmers) == 0 {
return b.writeEmptyKdi(kdiPath, count)
}
// Sort
sort.Slice(kmers, func(i, j int) bool { return kmers[i] < kmers[j] })
// Write KDI based on mode
w, err := NewKdiWriter(kdiPath)
if err != nil {
return err
}
minFreq := b.config.minFreq
if minFreq <= 0 {
minFreq = 1 // simple dedup
}
// Linear scan: count consecutive identical values
i := 0
for i < len(kmers) {
val := kmers[i]
c := 1
for i+c < len(kmers) && kmers[i+c] == val {
c++
}
if c >= minFreq {
if err := w.Write(val); err != nil {
w.Close()
return err
}
}
i += c
}
*count = w.Count()
return w.Close()
}
func (b *KmerSetGroupBuilder) writeEmptyKdi(path string, count *uint64) error {
w, err := NewKdiWriter(path)
if err != nil {
return err
}
*count = 0
return w.Close()
}

278
pkg/obikmer/kmer_set_builder_test.go Normal file
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package obikmer
import (
"sort"
"testing"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
func TestBuilderBasic(t *testing.T) {
dir := t.TempDir()
builder, err := NewKmerSetGroupBuilder(dir, 15, 7, 1, 64)
if err != nil {
t.Fatal(err)
}
seq := obiseq.NewBioSequence("test", []byte("ACGTACGTACGTACGTACGTACGTACGT"), "")
builder.AddSequence(0, seq)
ksg, err := builder.Close()
if err != nil {
t.Fatal(err)
}
if ksg.K() != 15 {
t.Fatalf("K() = %d, want 15", ksg.K())
}
if ksg.M() != 7 {
t.Fatalf("M() = %d, want 7", ksg.M())
}
if ksg.Partitions() != 64 {
t.Fatalf("Partitions() = %d, want 64", ksg.Partitions())
}
if ksg.Size() != 1 {
t.Fatalf("Size() = %d, want 1", ksg.Size())
}
if ksg.Len(0) == 0 {
t.Fatal("Len(0) = 0, expected some k-mers")
}
// Verify k-mers match what we'd compute directly
var expected []uint64
for kmer := range IterCanonicalKmers(seq.Sequence(), 15) {
expected = append(expected, kmer)
}
sort.Slice(expected, func(i, j int) bool { return expected[i] < expected[j] })
// Dedup
deduped := expected[:0]
for i, v := range expected {
if i == 0 || v != expected[i-1] {
deduped = append(deduped, v)
}
}
if ksg.Len(0) != uint64(len(deduped)) {
t.Fatalf("Len(0) = %d, expected %d unique k-mers", ksg.Len(0), len(deduped))
}
// Check iterator
var fromIter []uint64
for kmer := range ksg.Iterator(0) {
fromIter = append(fromIter, kmer)
}
// The iterator does a k-way merge so should be sorted
for i := 1; i < len(fromIter); i++ {
if fromIter[i] <= fromIter[i-1] {
t.Fatalf("iterator not sorted at %d: %d <= %d", i, fromIter[i], fromIter[i-1])
}
}
if len(fromIter) != len(deduped) {
t.Fatalf("iterator yielded %d k-mers, expected %d", len(fromIter), len(deduped))
}
for i, v := range fromIter {
if v != deduped[i] {
t.Fatalf("iterator kmer %d: got %d, want %d", i, v, deduped[i])
}
}
}
func TestBuilderMultipleSequences(t *testing.T) {
dir := t.TempDir()
builder, err := NewKmerSetGroupBuilder(dir, 15, 7, 1, 64)
if err != nil {
t.Fatal(err)
}
seqs := []string{
"ACGTACGTACGTACGTACGTACGTACGT",
"TTTTTTTTTTTTTTTTTTTTTTTTT",
"GGGGGGGGGGGGGGGGGGGGGGGG",
}
for _, s := range seqs {
seq := obiseq.NewBioSequence("", []byte(s), "")
builder.AddSequence(0, seq)
}
ksg, err := builder.Close()
if err != nil {
t.Fatal(err)
}
if ksg.Len(0) == 0 {
t.Fatal("expected k-mers after multiple sequences")
}
}
func TestBuilderFrequencyFilter(t *testing.T) {
dir := t.TempDir()
builder, err := NewKmerSetGroupBuilder(dir, 15, 7, 1, 64,
WithMinFrequency(3))
if err != nil {
t.Fatal(err)
}
// Add same sequence 3 times — all k-mers should survive freq=3
seq := obiseq.NewBioSequence("test", []byte("ACGTACGTACGTACGTACGTACGTACGT"), "")
for i := 0; i < 3; i++ {
builder.AddSequence(0, seq)
}
ksg, err := builder.Close()
if err != nil {
t.Fatal(err)
}
// All k-mers appear exactly 3 times → all should survive
var expected []uint64
for kmer := range IterCanonicalKmers(seq.Sequence(), 15) {
expected = append(expected, kmer)
}
sort.Slice(expected, func(i, j int) bool { return expected[i] < expected[j] })
deduped := expected[:0]
for i, v := range expected {
if i == 0 || v != expected[i-1] {
deduped = append(deduped, v)
}
}
if ksg.Len(0) != uint64(len(deduped)) {
t.Fatalf("Len(0) = %d, expected %d (all k-mers at freq=3)", ksg.Len(0), len(deduped))
}
}
func TestBuilderFrequencyFilterRejects(t *testing.T) {
dir := t.TempDir()
builder, err := NewKmerSetGroupBuilder(dir, 15, 7, 1, 64,
WithMinFrequency(5))
if err != nil {
t.Fatal(err)
}
// Use a non-repetitive sequence so each canonical k-mer appears once per pass.
// Adding it twice gives freq=2 per kmer, which is < minFreq=5 → all rejected.
seq := obiseq.NewBioSequence("test",
[]byte("ACGATCGATCTAGCTAGCTGATCGATCGATCG"), "")
builder.AddSequence(0, seq)
builder.AddSequence(0, seq)
ksg, err := builder.Close()
if err != nil {
t.Fatal(err)
}
if ksg.Len(0) != 0 {
t.Fatalf("Len(0) = %d, expected 0 (all k-mers at freq=2 < minFreq=5)", ksg.Len(0))
}
}
func TestBuilderMultipleSets(t *testing.T) {
dir := t.TempDir()
builder, err := NewKmerSetGroupBuilder(dir, 15, 7, 3, 64)
if err != nil {
t.Fatal(err)
}
seqs := []string{
"ACGTACGTACGTACGTACGTACGTACGT",
"TTTTTTTTTTTTTTTTTTTTTTTTT",
"GGGGGGGGGGGGGGGGGGGGGGGG",
}
for i, s := range seqs {
seq := obiseq.NewBioSequence("", []byte(s), "")
builder.AddSequence(i, seq)
}
ksg, err := builder.Close()
if err != nil {
t.Fatal(err)
}
if ksg.Size() != 3 {
t.Fatalf("Size() = %d, want 3", ksg.Size())
}
for s := 0; s < 3; s++ {
if ksg.Len(s) == 0 {
t.Fatalf("Len(%d) = 0, expected some k-mers", s)
}
}
}
func TestBuilderOpenRoundTrip(t *testing.T) {
dir := t.TempDir()
builder, err := NewKmerSetGroupBuilder(dir, 15, 7, 1, 64)
if err != nil {
t.Fatal(err)
}
seq := obiseq.NewBioSequence("test", []byte("ACGTACGTACGTACGTACGTACGTACGT"), "")
builder.AddSequence(0, seq)
ksg1, err := builder.Close()
if err != nil {
t.Fatal(err)
}
// Reopen
ksg2, err := OpenKmerSetGroup(dir)
if err != nil {
t.Fatal(err)
}
if ksg2.K() != ksg1.K() {
t.Fatalf("K mismatch: %d vs %d", ksg2.K(), ksg1.K())
}
if ksg2.M() != ksg1.M() {
t.Fatalf("M mismatch: %d vs %d", ksg2.M(), ksg1.M())
}
if ksg2.Partitions() != ksg1.Partitions() {
t.Fatalf("Partitions mismatch: %d vs %d", ksg2.Partitions(), ksg1.Partitions())
}
if ksg2.Len(0) != ksg1.Len(0) {
t.Fatalf("Len mismatch: %d vs %d", ksg2.Len(0), ksg1.Len(0))
}
}
func TestBuilderAttributes(t *testing.T) {
dir := t.TempDir()
builder, err := NewKmerSetGroupBuilder(dir, 15, 7, 1, 64)
if err != nil {
t.Fatal(err)
}
seq := obiseq.NewBioSequence("test", []byte("ACGTACGTACGTACGTACGTACGTACGT"), "")
builder.AddSequence(0, seq)
ksg, err := builder.Close()
if err != nil {
t.Fatal(err)
}
ksg.SetId("my_index")
ksg.SetAttribute("organism", "test")
ksg.SaveMetadata()
// Reopen and check
ksg2, err := OpenKmerSetGroup(dir)
if err != nil {
t.Fatal(err)
}
if ksg2.Id() != "my_index" {
t.Fatalf("Id() = %q, want %q", ksg2.Id(), "my_index")
}
if !ksg2.HasAttribute("organism") {
t.Fatal("expected 'organism' attribute")
}
v, _ := ksg2.GetAttribute("organism")
if v != "test" {
t.Fatalf("organism = %v, want 'test'", v)
}
}

580
pkg/obikmer/kmer_set_disk.go Normal file
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@@ -0,0 +1,580 @@
package obikmer
import (
"fmt"
"iter"
"os"
"path/filepath"
"sync"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidist"
"github.com/pelletier/go-toml/v2"
)
// MetadataFormat represents the metadata serialization format.
// Currently only TOML is used for disk-based indices, but the type
// is kept for backward compatibility with CLI options.
type MetadataFormat int
const (
FormatTOML MetadataFormat = iota
FormatYAML
FormatJSON
)
// String returns the file extension for the format.
func (f MetadataFormat) String() string {
switch f {
case FormatTOML:
return "toml"
case FormatYAML:
return "yaml"
case FormatJSON:
return "json"
default:
return "toml"
}
}
// KmerSetGroup is a disk-based collection of N k-mer sets sharing the same
// k, m, and partition count P. After construction (via KmerSetGroupBuilder),
// it is immutable and all operations are streaming (partition by partition).
//
// A KmerSetGroup with Size()==1 is effectively a KmerSet (singleton).
type KmerSetGroup struct {
path string // root directory
id string // user-assigned identifier
k int // k-mer size
m int // minimizer size
partitions int // number of partitions P
n int // number of sets N
setsIDs []string // IDs of individual sets
counts []uint64 // total k-mer count per set (sum over partitions)
Metadata map[string]interface{} // group-level user metadata
}
// diskMetadata is the TOML-serializable structure for metadata.toml.
type diskMetadata struct {
ID string `toml:"id,omitempty"`
K int `toml:"k"`
M int `toml:"m"`
Partitions int `toml:"partitions"`
Type string `toml:"type"`
Size int `toml:"size"`
SetsIDs []string `toml:"sets_ids,omitempty"`
Counts []uint64 `toml:"counts,omitempty"`
UserMetadata map[string]interface{} `toml:"user_metadata,omitempty"`
}
// OpenKmerSetGroup opens a finalized index directory in read-only mode.
func OpenKmerSetGroup(directory string) (*KmerSetGroup, error) {
metaPath := filepath.Join(directory, "metadata.toml")
f, err := os.Open(metaPath)
if err != nil {
return nil, fmt.Errorf("obikmer: open metadata: %w", err)
}
defer f.Close()
var meta diskMetadata
if err := toml.NewDecoder(f).Decode(&meta); err != nil {
return nil, fmt.Errorf("obikmer: decode metadata: %w", err)
}
ksg := &KmerSetGroup{
path: directory,
id: meta.ID,
k: meta.K,
m: meta.M,
partitions: meta.Partitions,
n: meta.Size,
setsIDs: meta.SetsIDs,
counts: meta.Counts,
Metadata: meta.UserMetadata,
}
if ksg.Metadata == nil {
ksg.Metadata = make(map[string]interface{})
}
if ksg.setsIDs == nil {
ksg.setsIDs = make([]string, ksg.n)
}
if ksg.counts == nil {
// Compute counts by scanning partitions
ksg.counts = make([]uint64, ksg.n)
for s := 0; s < ksg.n; s++ {
for p := 0; p < ksg.partitions; p++ {
path := ksg.partitionPath(s, p)
r, err := NewKdiReader(path)
if err != nil {
continue
}
ksg.counts[s] += r.Count()
r.Close()
}
}
}
return ksg, nil
}
// SaveMetadata writes the metadata.toml file. This is useful after
// modifying attributes or IDs on an already-finalized index.
func (ksg *KmerSetGroup) SaveMetadata() error {
return ksg.saveMetadata()
}
// saveMetadata writes the metadata.toml file (internal).
func (ksg *KmerSetGroup) saveMetadata() error {
meta := diskMetadata{
ID: ksg.id,
K: ksg.k,
M: ksg.m,
Partitions: ksg.partitions,
Type: "KmerSetGroup",
Size: ksg.n,
SetsIDs: ksg.setsIDs,
Counts: ksg.counts,
UserMetadata: ksg.Metadata,
}
metaPath := filepath.Join(ksg.path, "metadata.toml")
f, err := os.Create(metaPath)
if err != nil {
return err
}
defer f.Close()
return toml.NewEncoder(f).Encode(meta)
}
// partitionPath returns the file path for partition p of set s.
func (ksg *KmerSetGroup) partitionPath(setIndex, partIndex int) string {
return filepath.Join(ksg.path, fmt.Sprintf("set_%d", setIndex),
fmt.Sprintf("part_%04d.kdi", partIndex))
}
// Path returns the root directory of the index.
func (ksg *KmerSetGroup) Path() string {
return ksg.path
}
// K returns the k-mer size.
func (ksg *KmerSetGroup) K() int {
return ksg.k
}
// M returns the minimizer size.
func (ksg *KmerSetGroup) M() int {
return ksg.m
}
// Partitions returns the number of partitions P.
func (ksg *KmerSetGroup) Partitions() int {
return ksg.partitions
}
// Size returns the number of sets N.
func (ksg *KmerSetGroup) Size() int {
return ksg.n
}
// Id returns the group identifier.
func (ksg *KmerSetGroup) Id() string {
return ksg.id
}
// SetId sets the group identifier and persists the change.
func (ksg *KmerSetGroup) SetId(id string) {
ksg.id = id
}
// Len returns the total number of k-mers.
// Without argument: total across all sets.
// With argument setIndex: count for that specific set.
func (ksg *KmerSetGroup) Len(setIndex ...int) uint64 {
if len(setIndex) == 0 {
var total uint64
for _, c := range ksg.counts {
total += c
}
return total
}
idx := setIndex[0]
if idx < 0 || idx >= ksg.n {
return 0
}
return ksg.counts[idx]
}
// Contains checks if a k-mer is present in the specified set.
// Uses binary search on the appropriate partition's KDI file.
func (ksg *KmerSetGroup) Contains(setIndex int, kmer uint64) bool {
if setIndex < 0 || setIndex >= ksg.n {
return false
}
// Determine partition from minimizer
// For a canonical k-mer, we need to find which partition it would fall into.
// The partition is determined by the minimizer during construction.
// For Contains, we must scan all partitions of this set (linear search within each).
// A full binary-search approach would require an index file.
// For now, scan the partition determined by the k-mer's minimizer.
// Since we don't know the minimizer, we do a linear scan of all partitions.
// This is O(total_kmers / P) per partition on average.
// Optimization: scan all partitions in parallel
type result struct {
found bool
}
ch := make(chan result, ksg.partitions)
for p := 0; p < ksg.partitions; p++ {
go func(part int) {
r, err := NewKdiReader(ksg.partitionPath(setIndex, part))
if err != nil {
ch <- result{false}
return
}
defer r.Close()
for {
v, ok := r.Next()
if !ok {
ch <- result{false}
return
}
if v == kmer {
ch <- result{true}
return
}
if v > kmer {
ch <- result{false}
return
}
}
}(p)
}
for i := 0; i < ksg.partitions; i++ {
res := <-ch
if res.found {
// Drain remaining goroutines
go func() {
for j := i + 1; j < ksg.partitions; j++ {
<-ch
}
}()
return true
}
}
return false
}
// Iterator returns an iterator over all k-mers in the specified set,
// in sorted order within each partition. Since partitions are independent,
// to get a globally sorted stream, use iteratorSorted.
func (ksg *KmerSetGroup) Iterator(setIndex int) iter.Seq[uint64] {
return func(yield func(uint64) bool) {
if setIndex < 0 || setIndex >= ksg.n {
return
}
// Open all partition readers and merge them
readers := make([]*KdiReader, 0, ksg.partitions)
for p := 0; p < ksg.partitions; p++ {
r, err := NewKdiReader(ksg.partitionPath(setIndex, p))
if err != nil {
continue
}
if r.Count() > 0 {
readers = append(readers, r)
} else {
r.Close()
}
}
if len(readers) == 0 {
return
}
m := NewKWayMerge(readers)
defer m.Close()
for {
kmer, _, ok := m.Next()
if !ok {
return
}
if !yield(kmer) {
return
}
}
}
}
// ==============================
// Attribute API (compatible with old API)
// ==============================
// HasAttribute checks if a metadata key exists.
func (ksg *KmerSetGroup) HasAttribute(key string) bool {
_, ok := ksg.Metadata[key]
return ok
}
// GetAttribute returns the value of an attribute.
func (ksg *KmerSetGroup) GetAttribute(key string) (interface{}, bool) {
switch key {
case "id":
return ksg.Id(), true
case "k":
return ksg.K(), true
default:
value, ok := ksg.Metadata[key]
return value, ok
}
}
// SetAttribute sets a metadata attribute.
func (ksg *KmerSetGroup) SetAttribute(key string, value interface{}) {
switch key {
case "id":
if id, ok := value.(string); ok {
ksg.SetId(id)
} else {
panic(fmt.Sprintf("id must be a string, got %T", value))
}
case "k":
panic("k is immutable")
default:
ksg.Metadata[key] = value
}
}
// DeleteAttribute removes a metadata attribute.
func (ksg *KmerSetGroup) DeleteAttribute(key string) {
delete(ksg.Metadata, key)
}
// GetIntAttribute returns an attribute as int.
func (ksg *KmerSetGroup) GetIntAttribute(key string) (int, bool) {
v, ok := ksg.GetAttribute(key)
if !ok {
return 0, false
}
switch val := v.(type) {
case int:
return val, true
case int64:
return int(val), true
case float64:
return int(val), true
}
return 0, false
}
// GetStringAttribute returns an attribute as string.
func (ksg *KmerSetGroup) GetStringAttribute(key string) (string, bool) {
v, ok := ksg.GetAttribute(key)
if !ok {
return "", false
}
if s, ok := v.(string); ok {
return s, true
}
return fmt.Sprintf("%v", v), true
}
// ==============================
// Jaccard metrics (streaming, disk-based)
// ==============================
// JaccardDistanceMatrix computes a pairwise Jaccard distance matrix
// for all sets in the group. Operates partition by partition in streaming.
func (ksg *KmerSetGroup) JaccardDistanceMatrix() *obidist.DistMatrix {
n := ksg.n
labels := make([]string, n)
for i := 0; i < n; i++ {
if i < len(ksg.setsIDs) && ksg.setsIDs[i] != "" {
labels[i] = ksg.setsIDs[i]
} else {
labels[i] = fmt.Sprintf("set_%d", i)
}
}
dm := obidist.NewDistMatrixWithLabels(labels)
// Accumulate intersection and union counts
intersections := make([][]uint64, n)
unions := make([][]uint64, n)
for i := 0; i < n; i++ {
intersections[i] = make([]uint64, n)
unions[i] = make([]uint64, n)
}
// Process partition by partition
var mu sync.Mutex
var wg sync.WaitGroup
for p := 0; p < ksg.partitions; p++ {
wg.Add(1)
go func(part int) {
defer wg.Done()
// Open all set readers for this partition
readers := make([]*KdiReader, n)
for s := 0; s < n; s++ {
r, err := NewKdiReader(ksg.partitionPath(s, part))
if err != nil {
continue
}
readers[s] = r
}
defer func() {
for _, r := range readers {
if r != nil {
r.Close()
}
}
}()
// Merge all N readers to count intersections and unions
activeReaders := make([]*KdiReader, 0, n)
activeIndices := make([]int, 0, n)
for i, r := range readers {
if r != nil && r.Count() > 0 {
activeReaders = append(activeReaders, r)
activeIndices = append(activeIndices, i)
}
}
if len(activeReaders) == 0 {
return
}
merge := NewKWayMerge(activeReaders)
// Don't close merge here since readers are managed above
// We only want to iterate
// We need per-set presence tracking, so we use a custom merge
// Rebuild with a direct approach
merge.Close() // close the merge (which closes readers)
// Reopen readers for custom merge
for s := 0; s < n; s++ {
readers[s] = nil
r, err := NewKdiReader(ksg.partitionPath(s, part))
if err != nil {
continue
}
if r.Count() > 0 {
readers[s] = r
} else {
r.Close()
}
}
// Custom k-way merge that tracks which sets contain each kmer
type entry struct {
val uint64
setIdx int
}
// Use a simpler approach: read all values for this partition into memory
// for each set, then do a merge
setKmers := make([][]uint64, n)
for s := 0; s < n; s++ {
if readers[s] == nil {
continue
}
kmers := make([]uint64, 0, readers[s].Count())
for {
v, ok := readers[s].Next()
if !ok {
break
}
kmers = append(kmers, v)
}
setKmers[s] = kmers
readers[s].Close()
readers[s] = nil
}
// Count pairwise intersections using sorted merge
// For each pair (i,j), count kmers present in both
localInter := make([][]uint64, n)
localUnion := make([][]uint64, n)
for i := 0; i < n; i++ {
localInter[i] = make([]uint64, n)
localUnion[i] = make([]uint64, n)
}
for i := 0; i < n; i++ {
localUnion[i][i] = uint64(len(setKmers[i]))
for j := i + 1; j < n; j++ {
a, b := setKmers[i], setKmers[j]
var inter uint64
ai, bi := 0, 0
for ai < len(a) && bi < len(b) {
if a[ai] == b[bi] {
inter++
ai++
bi++
} else if a[ai] < b[bi] {
ai++
} else {
bi++
}
}
localInter[i][j] = inter
localUnion[i][j] = uint64(len(a)) + uint64(len(b)) - inter
}
}
mu.Lock()
for i := 0; i < n; i++ {
for j := i; j < n; j++ {
intersections[i][j] += localInter[i][j]
unions[i][j] += localUnion[i][j]
}
}
mu.Unlock()
}(p)
}
wg.Wait()
// Compute distances from accumulated counts
for i := 0; i < n-1; i++ {
for j := i + 1; j < n; j++ {
u := unions[i][j]
if u == 0 {
dm.Set(i, j, 1.0)
} else {
dm.Set(i, j, 1.0-float64(intersections[i][j])/float64(u))
}
}
}
return dm
}
// JaccardSimilarityMatrix computes a pairwise Jaccard similarity matrix.
func (ksg *KmerSetGroup) JaccardSimilarityMatrix() *obidist.DistMatrix {
n := ksg.n
labels := make([]string, n)
for i := 0; i < n; i++ {
if i < len(ksg.setsIDs) && ksg.setsIDs[i] != "" {
labels[i] = ksg.setsIDs[i]
} else {
labels[i] = fmt.Sprintf("set_%d", i)
}
}
// Reuse distance computation
dm := ksg.JaccardDistanceMatrix()
sm := obidist.NewSimilarityMatrixWithLabels(labels)
for i := 0; i < n-1; i++ {
for j := i + 1; j < n; j++ {
sm.Set(i, j, 1.0-dm.Get(i, j))
}
}
return sm
}

568
pkg/obikmer/kmer_set_disk_ops.go Normal file
View File

@@ -0,0 +1,568 @@
package obikmer
import (
"fmt"
"os"
"path/filepath"
"runtime"
"sync"
)
// Union computes the union of all sets in the group, producing a new
// singleton KmerSetGroup on disk. A k-mer is in the result if it
// appears in any set.
func (ksg *KmerSetGroup) Union(outputDir string) (*KmerSetGroup, error) {
return ksg.quorumOp(outputDir, 1, ksg.n)
}
// Intersect computes the intersection of all sets, producing a new
// singleton KmerSetGroup on disk. A k-mer is in the result if it
// appears in every set.
func (ksg *KmerSetGroup) Intersect(outputDir string) (*KmerSetGroup, error) {
return ksg.quorumOp(outputDir, ksg.n, ksg.n)
}
// Difference computes set_0 minus the union of all other sets.
func (ksg *KmerSetGroup) Difference(outputDir string) (*KmerSetGroup, error) {
return ksg.differenceOp(outputDir)
}
// QuorumAtLeast returns k-mers present in at least q sets.
func (ksg *KmerSetGroup) QuorumAtLeast(q int, outputDir string) (*KmerSetGroup, error) {
return ksg.quorumOp(outputDir, q, ksg.n)
}
// QuorumExactly returns k-mers present in exactly q sets.
func (ksg *KmerSetGroup) QuorumExactly(q int, outputDir string) (*KmerSetGroup, error) {
return ksg.quorumOp(outputDir, q, q)
}
// QuorumAtMost returns k-mers present in at most q sets.
func (ksg *KmerSetGroup) QuorumAtMost(q int, outputDir string) (*KmerSetGroup, error) {
return ksg.quorumOp(outputDir, 1, q)
}
// UnionWith merges this group with another, producing a new KmerSetGroup
// whose set_i is the union of this.set_i and other.set_i.
// Both groups must have the same k, m, P, and N.
func (ksg *KmerSetGroup) UnionWith(other *KmerSetGroup, outputDir string) (*KmerSetGroup, error) {
if err := ksg.checkCompatible(other); err != nil {
return nil, err
}
return ksg.pairwiseOp(other, outputDir, mergeUnion)
}
// IntersectWith merges this group with another, producing a new KmerSetGroup
// whose set_i is the intersection of this.set_i and other.set_i.
func (ksg *KmerSetGroup) IntersectWith(other *KmerSetGroup, outputDir string) (*KmerSetGroup, error) {
if err := ksg.checkCompatible(other); err != nil {
return nil, err
}
return ksg.pairwiseOp(other, outputDir, mergeIntersect)
}
// ==============================
// Internal implementation
// ==============================
func (ksg *KmerSetGroup) checkCompatible(other *KmerSetGroup) error {
if ksg.k != other.k {
return fmt.Errorf("obikmer: incompatible k: %d vs %d", ksg.k, other.k)
}
if ksg.m != other.m {
return fmt.Errorf("obikmer: incompatible m: %d vs %d", ksg.m, other.m)
}
if ksg.partitions != other.partitions {
return fmt.Errorf("obikmer: incompatible partitions: %d vs %d", ksg.partitions, other.partitions)
}
if ksg.n != other.n {
return fmt.Errorf("obikmer: incompatible size: %d vs %d", ksg.n, other.n)
}
return nil
}
// quorumOp processes all N sets partition by partition.
// For each partition, it opens N KdiReaders and does a k-way merge.
// A kmer is written to the result if minQ <= count <= maxQ.
func (ksg *KmerSetGroup) quorumOp(outputDir string, minQ, maxQ int) (*KmerSetGroup, error) {
if minQ < 1 {
minQ = 1
}
if maxQ > ksg.n {
maxQ = ksg.n
}
// Create output structure
setDir := filepath.Join(outputDir, "set_0")
if err := os.MkdirAll(setDir, 0755); err != nil {
return nil, err
}
counts := make([]uint64, ksg.partitions)
nWorkers := runtime.NumCPU()
if nWorkers > ksg.partitions {
nWorkers = ksg.partitions
}
jobs := make(chan int, ksg.partitions)
var wg sync.WaitGroup
var errMu sync.Mutex
var firstErr error
for w := 0; w < nWorkers; w++ {
wg.Add(1)
go func() {
defer wg.Done()
for p := range jobs {
c, err := ksg.quorumPartition(p, setDir, minQ, maxQ)
if err != nil {
errMu.Lock()
if firstErr == nil {
firstErr = err
}
errMu.Unlock()
return
}
counts[p] = c
}
}()
}
for p := 0; p < ksg.partitions; p++ {
jobs <- p
}
close(jobs)
wg.Wait()
if firstErr != nil {
return nil, firstErr
}
var totalCount uint64
for _, c := range counts {
totalCount += c
}
result := &KmerSetGroup{
path: outputDir,
k: ksg.k,
m: ksg.m,
partitions: ksg.partitions,
n: 1,
setsIDs: []string{""},
counts: []uint64{totalCount},
Metadata: make(map[string]interface{}),
}
if err := result.saveMetadata(); err != nil {
return nil, err
}
return result, nil
}
// quorumPartition processes a single partition for quorum filtering.
func (ksg *KmerSetGroup) quorumPartition(partIdx int, outSetDir string, minQ, maxQ int) (uint64, error) {
// Open readers for all sets
readers := make([]*KdiReader, 0, ksg.n)
for s := 0; s < ksg.n; s++ {
r, err := NewKdiReader(ksg.partitionPath(s, partIdx))
if err != nil {
// Close already-opened readers
for _, rr := range readers {
rr.Close()
}
return 0, err
}
if r.Count() > 0 {
readers = append(readers, r)
} else {
r.Close()
}
}
outPath := filepath.Join(outSetDir, fmt.Sprintf("part_%04d.kdi", partIdx))
if len(readers) == 0 {
// Write empty KDI
w, err := NewKdiWriter(outPath)
if err != nil {
return 0, err
}
return 0, w.Close()
}
merge := NewKWayMerge(readers)
// merge.Close() will close readers
w, err := NewKdiWriter(outPath)
if err != nil {
merge.Close()
return 0, err
}
for {
kmer, count, ok := merge.Next()
if !ok {
break
}
if count >= minQ && count <= maxQ {
if err := w.Write(kmer); err != nil {
merge.Close()
w.Close()
return 0, err
}
}
}
merge.Close()
cnt := w.Count()
return cnt, w.Close()
}
// differenceOp computes set_0 minus the union of all other sets.
func (ksg *KmerSetGroup) differenceOp(outputDir string) (*KmerSetGroup, error) {
if ksg.n < 1 {
return nil, fmt.Errorf("obikmer: difference requires at least 1 set")
}
setDir := filepath.Join(outputDir, "set_0")
if err := os.MkdirAll(setDir, 0755); err != nil {
return nil, err
}
counts := make([]uint64, ksg.partitions)
nWorkers := runtime.NumCPU()
if nWorkers > ksg.partitions {
nWorkers = ksg.partitions
}
jobs := make(chan int, ksg.partitions)
var wg sync.WaitGroup
var errMu sync.Mutex
var firstErr error
for w := 0; w < nWorkers; w++ {
wg.Add(1)
go func() {
defer wg.Done()
for p := range jobs {
c, err := ksg.differencePartition(p, setDir)
if err != nil {
errMu.Lock()
if firstErr == nil {
firstErr = err
}
errMu.Unlock()
return
}
counts[p] = c
}
}()
}
for p := 0; p < ksg.partitions; p++ {
jobs <- p
}
close(jobs)
wg.Wait()
if firstErr != nil {
return nil, firstErr
}
var totalCount uint64
for _, c := range counts {
totalCount += c
}
result := &KmerSetGroup{
path: outputDir,
k: ksg.k,
m: ksg.m,
partitions: ksg.partitions,
n: 1,
setsIDs: []string{""},
counts: []uint64{totalCount},
Metadata: make(map[string]interface{}),
}
if err := result.saveMetadata(); err != nil {
return nil, err
}
return result, nil
}
// differencePartition computes set_0 - union(set_1..set_{n-1}) for one partition.
func (ksg *KmerSetGroup) differencePartition(partIdx int, outSetDir string) (uint64, error) {
outPath := filepath.Join(outSetDir, fmt.Sprintf("part_%04d.kdi", partIdx))
// Open set_0 reader
r0, err := NewKdiReader(ksg.partitionPath(0, partIdx))
if err != nil {
return 0, err
}
if r0.Count() == 0 {
r0.Close()
w, err := NewKdiWriter(outPath)
if err != nil {
return 0, err
}
return 0, w.Close()
}
// Open readers for the other sets and merge them
var otherReaders []*KdiReader
for s := 1; s < ksg.n; s++ {
r, err := NewKdiReader(ksg.partitionPath(s, partIdx))
if err != nil {
r0.Close()
for _, rr := range otherReaders {
rr.Close()
}
return 0, err
}
if r.Count() > 0 {
otherReaders = append(otherReaders, r)
} else {
r.Close()
}
}
w, err := NewKdiWriter(outPath)
if err != nil {
r0.Close()
for _, rr := range otherReaders {
rr.Close()
}
return 0, err
}
if len(otherReaders) == 0 {
// No other sets — copy set_0
for {
v, ok := r0.Next()
if !ok {
break
}
if err := w.Write(v); err != nil {
r0.Close()
w.Close()
return 0, err
}
}
r0.Close()
cnt := w.Count()
return cnt, w.Close()
}
// Merge other sets to get the "subtraction" stream
otherMerge := NewKWayMerge(otherReaders)
// Streaming difference: advance both streams
v0, ok0 := r0.Next()
vo, _, oko := otherMerge.Next()
for ok0 {
if !oko || v0 < vo {
// v0 not in others → emit
if err := w.Write(v0); err != nil {
r0.Close()
otherMerge.Close()
w.Close()
return 0, err
}
v0, ok0 = r0.Next()
} else if v0 == vo {
// v0 in others → skip
v0, ok0 = r0.Next()
vo, _, oko = otherMerge.Next()
} else {
// vo < v0 → advance others
vo, _, oko = otherMerge.Next()
}
}
r0.Close()
otherMerge.Close()
cnt := w.Count()
return cnt, w.Close()
}
// mergeMode defines how to combine two values during pairwise operations.
type mergeMode int
const (
mergeUnion mergeMode = iota // emit if in either
mergeIntersect // emit if in both
)
// pairwiseOp applies a merge operation between corresponding sets of two groups.
func (ksg *KmerSetGroup) pairwiseOp(other *KmerSetGroup, outputDir string, mode mergeMode) (*KmerSetGroup, error) {
for s := 0; s < ksg.n; s++ {
setDir := filepath.Join(outputDir, fmt.Sprintf("set_%d", s))
if err := os.MkdirAll(setDir, 0755); err != nil {
return nil, err
}
}
counts := make([][]uint64, ksg.n)
for s := 0; s < ksg.n; s++ {
counts[s] = make([]uint64, ksg.partitions)
}
nWorkers := runtime.NumCPU()
if nWorkers > ksg.partitions {
nWorkers = ksg.partitions
}
type job struct {
setIdx int
partIdx int
}
jobs := make(chan job, ksg.n*ksg.partitions)
var wg sync.WaitGroup
var errMu sync.Mutex
var firstErr error
for w := 0; w < nWorkers; w++ {
wg.Add(1)
go func() {
defer wg.Done()
for j := range jobs {
c, err := pairwiseMergePartition(
ksg.partitionPath(j.setIdx, j.partIdx),
other.partitionPath(j.setIdx, j.partIdx),
filepath.Join(outputDir, fmt.Sprintf("set_%d", j.setIdx),
fmt.Sprintf("part_%04d.kdi", j.partIdx)),
mode,
)
if err != nil {
errMu.Lock()
if firstErr == nil {
firstErr = err
}
errMu.Unlock()
return
}
counts[j.setIdx][j.partIdx] = c
}
}()
}
for s := 0; s < ksg.n; s++ {
for p := 0; p < ksg.partitions; p++ {
jobs <- job{s, p}
}
}
close(jobs)
wg.Wait()
if firstErr != nil {
return nil, firstErr
}
totalCounts := make([]uint64, ksg.n)
setsIDs := make([]string, ksg.n)
for s := 0; s < ksg.n; s++ {
for p := 0; p < ksg.partitions; p++ {
totalCounts[s] += counts[s][p]
}
}
result := &KmerSetGroup{
path: outputDir,
k: ksg.k,
m: ksg.m,
partitions: ksg.partitions,
n: ksg.n,
setsIDs: setsIDs,
counts: totalCounts,
Metadata: make(map[string]interface{}),
}
if err := result.saveMetadata(); err != nil {
return nil, err
}
return result, nil
}
// pairwiseMergePartition merges two KDI files (sorted streams) with the given mode.
func pairwiseMergePartition(pathA, pathB, outPath string, mode mergeMode) (uint64, error) {
rA, err := NewKdiReader(pathA)
if err != nil {
return 0, err
}
rB, err := NewKdiReader(pathB)
if err != nil {
rA.Close()
return 0, err
}
w, err := NewKdiWriter(outPath)
if err != nil {
rA.Close()
rB.Close()
return 0, err
}
cnt, mergeErr := doPairwiseMerge(rA, rB, w, mode)
rA.Close()
rB.Close()
closeErr := w.Close()
if mergeErr != nil {
return 0, mergeErr
}
return cnt, closeErr
}
func doPairwiseMerge(rA, rB *KdiReader, w *KdiWriter, mode mergeMode) (uint64, error) {
vA, okA := rA.Next()
vB, okB := rB.Next()
for okA && okB {
if vA == vB {
if err := w.Write(vA); err != nil {
return 0, err
}
vA, okA = rA.Next()
vB, okB = rB.Next()
} else if vA < vB {
if mode == mergeUnion {
if err := w.Write(vA); err != nil {
return 0, err
}
}
vA, okA = rA.Next()
} else {
if mode == mergeUnion {
if err := w.Write(vB); err != nil {
return 0, err
}
}
vB, okB = rB.Next()
}
}
if mode == mergeUnion {
for okA {
if err := w.Write(vA); err != nil {
return 0, err
}
vA, okA = rA.Next()
}
for okB {
if err := w.Write(vB); err != nil {
return 0, err
}
vB, okB = rB.Next()
}
}
return w.Count(), nil
}

251
pkg/obikmer/kmer_set_disk_ops_test.go Normal file
View File

@@ -0,0 +1,251 @@
package obikmer
import (
"path/filepath"
"testing"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// buildGroupFromSeqs creates a KmerSetGroup with one set per sequence.
func buildGroupFromSeqs(t *testing.T, dir string, k, m int, seqs []string) *KmerSetGroup {
t.Helper()
n := len(seqs)
builder, err := NewKmerSetGroupBuilder(dir, k, m, n, 64)
if err != nil {
t.Fatal(err)
}
for i, s := range seqs {
seq := obiseq.NewBioSequence("", []byte(s), "")
builder.AddSequence(i, seq)
}
ksg, err := builder.Close()
if err != nil {
t.Fatal(err)
}
return ksg
}
func collectKmers(t *testing.T, ksg *KmerSetGroup, setIdx int) []uint64 {
t.Helper()
var result []uint64
for kmer := range ksg.Iterator(setIdx) {
result = append(result, kmer)
}
return result
}
func TestDiskOpsUnion(t *testing.T) {
dir := t.TempDir()
indexDir := filepath.Join(dir, "index")
outDir := filepath.Join(dir, "union")
// Two sequences with some overlap
seqs := []string{
"ACGATCGATCTAGCTAGCTGATCGATCGATCG",
"CTAGCTAGCTGATCGATCGATCGTTTAAACCC",
}
ksg := buildGroupFromSeqs(t, indexDir, 15, 7, seqs)
result, err := ksg.Union(outDir)
if err != nil {
t.Fatal(err)
}
// Union should have at least as many k-mers as each individual set
unionLen := result.Len(0)
if unionLen == 0 {
t.Fatal("union is empty")
}
if unionLen < ksg.Len(0) || unionLen < ksg.Len(1) {
t.Fatalf("union (%d) smaller than an input set (%d, %d)", unionLen, ksg.Len(0), ksg.Len(1))
}
// Union should not exceed the sum of both sets
if unionLen > ksg.Len(0)+ksg.Len(1) {
t.Fatalf("union (%d) larger than sum of sets (%d)", unionLen, ksg.Len(0)+ksg.Len(1))
}
}
func TestDiskOpsIntersect(t *testing.T) {
dir := t.TempDir()
indexDir := filepath.Join(dir, "index")
outDir := filepath.Join(dir, "intersect")
// Two sequences with some shared k-mers
seqs := []string{
"ACGATCGATCTAGCTAGCTGATCGATCGATCG",
"CTAGCTAGCTGATCGATCGATCGTTTAAACCC",
}
ksg := buildGroupFromSeqs(t, indexDir, 15, 7, seqs)
result, err := ksg.Intersect(outDir)
if err != nil {
t.Fatal(err)
}
interLen := result.Len(0)
// Intersection should not be bigger than any individual set
if interLen > ksg.Len(0) || interLen > ksg.Len(1) {
t.Fatalf("intersection (%d) larger than input sets (%d, %d)", interLen, ksg.Len(0), ksg.Len(1))
}
}
func TestDiskOpsDifference(t *testing.T) {
dir := t.TempDir()
indexDir := filepath.Join(dir, "index")
outDir := filepath.Join(dir, "diff")
seqs := []string{
"ACGATCGATCTAGCTAGCTGATCGATCGATCG",
"CTAGCTAGCTGATCGATCGATCGTTTAAACCC",
}
ksg := buildGroupFromSeqs(t, indexDir, 15, 7, seqs)
result, err := ksg.Difference(outDir)
if err != nil {
t.Fatal(err)
}
diffLen := result.Len(0)
// Difference = set_0 - set_1, so should be <= set_0
if diffLen > ksg.Len(0) {
t.Fatalf("difference (%d) larger than set_0 (%d)", diffLen, ksg.Len(0))
}
}
func TestDiskOpsConsistency(t *testing.T) {
dir := t.TempDir()
indexDir := filepath.Join(dir, "index")
seqs := []string{
"ACGATCGATCTAGCTAGCTGATCGATCGATCG",
"CTAGCTAGCTGATCGATCGATCGTTTAAACCC",
}
ksg := buildGroupFromSeqs(t, indexDir, 15, 7, seqs)
unionResult, err := ksg.Union(filepath.Join(dir, "union"))
if err != nil {
t.Fatal(err)
}
interResult, err := ksg.Intersect(filepath.Join(dir, "intersect"))
if err != nil {
t.Fatal(err)
}
diffResult, err := ksg.Difference(filepath.Join(dir, "diff"))
if err != nil {
t.Fatal(err)
}
unionLen := unionResult.Len(0)
interLen := interResult.Len(0)
diffLen := diffResult.Len(0)
// |A ∪ B| = |A| + |B| - |A ∩ B|
expectedUnion := ksg.Len(0) + ksg.Len(1) - interLen
if unionLen != expectedUnion {
t.Fatalf("|A∪B|=%d, expected |A|+|B|-|A∩B|=%d+%d-%d=%d",
unionLen, ksg.Len(0), ksg.Len(1), interLen, expectedUnion)
}
// |A \ B| = |A| - |A ∩ B|
expectedDiff := ksg.Len(0) - interLen
if diffLen != expectedDiff {
t.Fatalf("|A\\B|=%d, expected |A|-|A∩B|=%d-%d=%d",
diffLen, ksg.Len(0), interLen, expectedDiff)
}
}
func TestDiskOpsQuorum(t *testing.T) {
dir := t.TempDir()
indexDir := filepath.Join(dir, "index")
// Three sets
seqs := []string{
"ACGATCGATCTAGCTAGCTGATCGATCGATCG",
"CTAGCTAGCTGATCGATCGATCGTTTAAACCC",
"GATCGATCGATCGAAATTTCCCGGG",
}
ksg := buildGroupFromSeqs(t, indexDir, 15, 7, seqs)
// QuorumAtLeast(1) = Union
q1, err := ksg.QuorumAtLeast(1, filepath.Join(dir, "q1"))
if err != nil {
t.Fatal(err)
}
union, err := ksg.Union(filepath.Join(dir, "union"))
if err != nil {
t.Fatal(err)
}
if q1.Len(0) != union.Len(0) {
t.Fatalf("QuorumAtLeast(1)=%d != Union=%d", q1.Len(0), union.Len(0))
}
// QuorumAtLeast(3) = Intersect
q3, err := ksg.QuorumAtLeast(3, filepath.Join(dir, "q3"))
if err != nil {
t.Fatal(err)
}
inter, err := ksg.Intersect(filepath.Join(dir, "inter"))
if err != nil {
t.Fatal(err)
}
if q3.Len(0) != inter.Len(0) {
t.Fatalf("QuorumAtLeast(3)=%d != Intersect=%d", q3.Len(0), inter.Len(0))
}
// QuorumAtLeast(2) should be between Intersect and Union
q2, err := ksg.QuorumAtLeast(2, filepath.Join(dir, "q2"))
if err != nil {
t.Fatal(err)
}
if q2.Len(0) < q3.Len(0) || q2.Len(0) > q1.Len(0) {
t.Fatalf("QuorumAtLeast(2)=%d not between intersect=%d and union=%d",
q2.Len(0), q3.Len(0), q1.Len(0))
}
}
func TestDiskOpsJaccard(t *testing.T) {
dir := t.TempDir()
indexDir := filepath.Join(dir, "index")
seqs := []string{
"ACGATCGATCTAGCTAGCTGATCGATCGATCG",
"ACGATCGATCTAGCTAGCTGATCGATCGATCG", // identical to first
"TTTTTTTTTTTTTTTTTTTTTTTTT", // completely different
}
ksg := buildGroupFromSeqs(t, indexDir, 15, 7, seqs)
dm := ksg.JaccardDistanceMatrix()
if dm == nil {
t.Fatal("JaccardDistanceMatrix returned nil")
}
// Identical sets should have distance 0
d01 := dm.Get(0, 1)
if d01 != 0.0 {
t.Fatalf("distance(0,1) = %f, expected 0.0 for identical sets", d01)
}
// Completely different sets should have distance 1.0
d02 := dm.Get(0, 2)
if d02 != 1.0 {
t.Fatalf("distance(0,2) = %f, expected 1.0 for disjoint sets", d02)
}
// Similarity matrix
sm := ksg.JaccardSimilarityMatrix()
if sm == nil {
t.Fatal("JaccardSimilarityMatrix returned nil")
}
s01 := sm.Get(0, 1)
if s01 != 1.0 {
t.Fatalf("similarity(0,1) = %f, expected 1.0 for identical sets", s01)
}
s02 := sm.Get(0, 2)
if s02 != 0.0 {
t.Fatalf("similarity(0,2) = %f, expected 0.0 for disjoint sets", s02)
}
}

347
pkg/obikmer/kmer_set_group.go
View File

@@ -1,347 +0,0 @@
package obikmer
import (
"fmt"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidist"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// KmerSetGroup represents a vector of KmerSet
// Used to manage multiple k-mer sets (for example, by frequency level)
type KmerSetGroup struct {
id string // Unique identifier of the KmerSetGroup
k int // Size of k-mers (immutable)
sets []*KmerSet // Vector of KmerSet
Metadata map[string]interface{} // Group metadata (not individual sets)
}
// NewKmerSetGroup creates a new group of n KmerSets
func NewKmerSetGroup(k int, n int) *KmerSetGroup {
if n < 1 {
panic("KmerSetGroup size must be >= 1")
}
sets := make([]*KmerSet, n)
for i := range sets {
sets[i] = NewKmerSet(k)
}
return &KmerSetGroup{
k: k,
sets: sets,
Metadata: make(map[string]interface{}),
}
}
// K returns the size of k-mers (immutable)
func (ksg *KmerSetGroup) K() int {
return ksg.k
}
// Size returns the number of KmerSet in the group
func (ksg *KmerSetGroup) Size() int {
return len(ksg.sets)
}
// Get returns the KmerSet at the given index
// Returns nil if the index is invalid
func (ksg *KmerSetGroup) Get(index int) *KmerSet {
if index < 0 || index >= len(ksg.sets) {
return nil
}
return ksg.sets[index]
}
// Set replaces the KmerSet at the given index
// Panics if the index is invalid or if k does not match
func (ksg *KmerSetGroup) Set(index int, ks *KmerSet) {
if index < 0 || index >= len(ksg.sets) {
panic(fmt.Sprintf("Index out of bounds: %d (size: %d)", index, len(ksg.sets)))
}
if ks.k != ksg.k {
panic(fmt.Sprintf("KmerSet k mismatch: expected %d, got %d", ksg.k, ks.k))
}
ksg.sets[index] = ks
}
// Len returns the number of k-mers in a specific KmerSet
// Without argument: returns the number of k-mers in the last KmerSet
// With argument index: returns the number of k-mers in the KmerSet at this index
func (ksg *KmerSetGroup) Len(index ...int) uint64 {
if len(index) == 0 {
// Without argument: last KmerSet
return ksg.sets[len(ksg.sets)-1].Len()
}
// With argument: specific KmerSet
idx := index[0]
if idx < 0 || idx >= len(ksg.sets) {
return 0
}
return ksg.sets[idx].Len()
}
// MemoryUsage returns the total memory usage in bytes
func (ksg *KmerSetGroup) MemoryUsage() uint64 {
total := uint64(0)
for _, ks := range ksg.sets {
total += ks.MemoryUsage()
}
return total
}
// Clear empties all KmerSet in the group
func (ksg *KmerSetGroup) Clear() {
for _, ks := range ksg.sets {
ks.Clear()
}
}
// Copy creates a complete copy of the group (consistent with BioSequence.Copy)
func (ksg *KmerSetGroup) Copy() *KmerSetGroup {
copiedSets := make([]*KmerSet, len(ksg.sets))
for i, ks := range ksg.sets {
copiedSets[i] = ks.Copy() // Copy each KmerSet with its metadata
}
// Copy group metadata
groupMetadata := make(map[string]interface{}, len(ksg.Metadata))
for k, v := range ksg.Metadata {
groupMetadata[k] = v
}
return &KmerSetGroup{
id: ksg.id,
k: ksg.k,
sets: copiedSets,
Metadata: groupMetadata,
}
}
// Id returns the identifier of the KmerSetGroup (consistent with BioSequence.Id)
func (ksg *KmerSetGroup) Id() string {
return ksg.id
}
// SetId sets the identifier of the KmerSetGroup (consistent with BioSequence.SetId)
func (ksg *KmerSetGroup) SetId(id string) {
ksg.id = id
}
// AddSequence adds all k-mers from a sequence to a specific KmerSet
func (ksg *KmerSetGroup) AddSequence(seq *obiseq.BioSequence, index int) {
if index < 0 || index >= len(ksg.sets) {
panic(fmt.Sprintf("Index out of bounds: %d (size: %d)", index, len(ksg.sets)))
}
ksg.sets[index].AddSequence(seq)
}
// AddSequences adds all k-mers from multiple sequences to a specific KmerSet
func (ksg *KmerSetGroup) AddSequences(sequences *obiseq.BioSequenceSlice, index int) {
if index < 0 || index >= len(ksg.sets) {
panic(fmt.Sprintf("Index out of bounds: %d (size: %d)", index, len(ksg.sets)))
}
ksg.sets[index].AddSequences(sequences)
}
// AddSequenceSlice adds all k-mers from a slice of sequences to a specific KmerSet
func (ksg *KmerSetGroup) AddSequenceSlice(sequences *obiseq.BioSequenceSlice, index int) {
if index < 0 || index >= len(ksg.sets) {
panic(fmt.Sprintf("Index out of bounds: %d (size: %d)", index, len(ksg.sets)))
}
ksg.sets[index].AddSequenceSlice(sequences)
}
// Union returns the union of all KmerSet in the group
// Optimization: starts from the largest set to minimize operations
func (ksg *KmerSetGroup) Union() *KmerSet {
if len(ksg.sets) == 0 {
return NewKmerSet(ksg.k)
}
if len(ksg.sets) == 1 {
return ksg.sets[0].Copy()
}
// Find the index of the largest set (the one with the most k-mers)
maxIdx := 0
maxCard := ksg.sets[0].Len()
for i := 1; i < len(ksg.sets); i++ {
card := ksg.sets[i].Len()
if card > maxCard {
maxCard = card
maxIdx = i
}
}
// Copy the largest set and perform unions in-place
result := ksg.sets[maxIdx].bitmap.Clone()
for i := 0; i < len(ksg.sets); i++ {
if i != maxIdx {
result.Or(ksg.sets[i].bitmap)
}
}
return NewKmerSetFromBitmap(ksg.k, result)
}
// Intersect returns the intersection of all KmerSet in the group
// Optimization: starts from the smallest set to minimize operations
func (ksg *KmerSetGroup) Intersect() *KmerSet {
if len(ksg.sets) == 0 {
return NewKmerSet(ksg.k)
}
if len(ksg.sets) == 1 {
return ksg.sets[0].Copy()
}
// Find the index of the smallest set (the one with the fewest k-mers)
minIdx := 0
minCard := ksg.sets[0].Len()
for i := 1; i < len(ksg.sets); i++ {
card := ksg.sets[i].Len()
if card < minCard {
minCard = card
minIdx = i
}
}
// Copy the smallest set and perform intersections in-place
result := ksg.sets[minIdx].bitmap.Clone()
for i := 0; i < len(ksg.sets); i++ {
if i != minIdx {
result.And(ksg.sets[i].bitmap)
}
}
return NewKmerSetFromBitmap(ksg.k, result)
}
// Stats returns statistics for each KmerSet in the group
type KmerSetGroupStats struct {
K int
Size int // Number of KmerSet
TotalBytes uint64 // Total memory used
Sets []KmerSetStats // Stats of each KmerSet
}
type KmerSetStats struct {
Index int // Index of the KmerSet in the group
Len uint64 // Number of k-mers
SizeBytes uint64 // Size in bytes
}
func (ksg *KmerSetGroup) Stats() KmerSetGroupStats {
stats := KmerSetGroupStats{
K: ksg.k,
Size: len(ksg.sets),
Sets: make([]KmerSetStats, len(ksg.sets)),
}
for i, ks := range ksg.sets {
sizeBytes := ks.MemoryUsage()
stats.Sets[i] = KmerSetStats{
Index: i,
Len: ks.Len(),
SizeBytes: sizeBytes,
}
stats.TotalBytes += sizeBytes
}
return stats
}
func (ksgs KmerSetGroupStats) String() string {
result := fmt.Sprintf(`KmerSetGroup Statistics (k=%d, size=%d):
Total memory: %.2f MB
Set breakdown:
`, ksgs.K, ksgs.Size, float64(ksgs.TotalBytes)/1024/1024)
for _, set := range ksgs.Sets {
result += fmt.Sprintf(" Set[%d]: %d k-mers (%.2f MB)\n",
set.Index,
set.Len,
float64(set.SizeBytes)/1024/1024)
}
return result
}
// JaccardDistanceMatrix computes a pairwise Jaccard distance matrix for all KmerSets in the group.
// Returns a triangular distance matrix where element (i, j) represents the Jaccard distance
// between set i and set j.
//
// The Jaccard distance is: 1 - (|A ∩ B| / |A ∪ B|)
//
// The matrix labels are set to the IDs of the individual KmerSets if available,
// otherwise they are set to "set_0", "set_1", etc.
//
// Time complexity: O(n² × (|A| + |B|)) where n is the number of sets
// Space complexity: O(n²) for the distance matrix
func (ksg *KmerSetGroup) JaccardDistanceMatrix() *obidist.DistMatrix {
n := len(ksg.sets)
// Create labels from set IDs
labels := make([]string, n)
for i, ks := range ksg.sets {
if ks.Id() != "" {
labels[i] = ks.Id()
} else {
labels[i] = fmt.Sprintf("set_%d", i)
}
}
dm := obidist.NewDistMatrixWithLabels(labels)
// Compute pairwise distances
for i := 0; i < n-1; i++ {
for j := i + 1; j < n; j++ {
distance := ksg.sets[i].JaccardDistance(ksg.sets[j])
dm.Set(i, j, distance)
}
}
return dm
}
// JaccardSimilarityMatrix computes a pairwise Jaccard similarity matrix for all KmerSets in the group.
// Returns a similarity matrix where element (i, j) represents the Jaccard similarity
// between set i and set j.
//
// The Jaccard similarity is: |A ∩ B| / |A ∪ B|
//
// The diagonal is 1.0 (similarity of a set to itself).
//
// The matrix labels are set to the IDs of the individual KmerSets if available,
// otherwise they are set to "set_0", "set_1", etc.
//
// Time complexity: O(n² × (|A| + |B|)) where n is the number of sets
// Space complexity: O(n²) for the similarity matrix
func (ksg *KmerSetGroup) JaccardSimilarityMatrix() *obidist.DistMatrix {
n := len(ksg.sets)
// Create labels from set IDs
labels := make([]string, n)
for i, ks := range ksg.sets {
if ks.Id() != "" {
labels[i] = ks.Id()
} else {
labels[i] = fmt.Sprintf("set_%d", i)
}
}
sm := obidist.NewSimilarityMatrixWithLabels(labels)
// Compute pairwise similarities
for i := 0; i < n-1; i++ {
for j := i + 1; j < n; j++ {
similarity := ksg.sets[i].JaccardSimilarity(ksg.sets[j])
sm.Set(i, j, similarity)
}
}
return sm
}

231
pkg/obikmer/kmer_set_group_jaccard_test.go
View File

@@ -1,231 +0,0 @@
package obikmer
import (
"math"
"testing"
)
func TestKmerSetGroupJaccardDistanceMatrix(t *testing.T) {
ksg := NewKmerSetGroup(5, 3)
// Set 0: {1, 2, 3}
ksg.Get(0).AddKmerCode(1)
ksg.Get(0).AddKmerCode(2)
ksg.Get(0).AddKmerCode(3)
ksg.Get(0).SetId("set_A")
// Set 1: {2, 3, 4}
ksg.Get(1).AddKmerCode(2)
ksg.Get(1).AddKmerCode(3)
ksg.Get(1).AddKmerCode(4)
ksg.Get(1).SetId("set_B")
// Set 2: {5, 6, 7}
ksg.Get(2).AddKmerCode(5)
ksg.Get(2).AddKmerCode(6)
ksg.Get(2).AddKmerCode(7)
ksg.Get(2).SetId("set_C")
dm := ksg.JaccardDistanceMatrix()
// Check labels
if dm.GetLabel(0) != "set_A" {
t.Errorf("Expected label 'set_A' at index 0, got '%s'", dm.GetLabel(0))
}
if dm.GetLabel(1) != "set_B" {
t.Errorf("Expected label 'set_B' at index 1, got '%s'", dm.GetLabel(1))
}
if dm.GetLabel(2) != "set_C" {
t.Errorf("Expected label 'set_C' at index 2, got '%s'", dm.GetLabel(2))
}
// Check distances
// Distance(0, 1):
// Intersection: {2, 3} -> 2 elements
// Union: {1, 2, 3, 4} -> 4 elements
// Similarity: 2/4 = 0.5
// Distance: 1 - 0.5 = 0.5
expectedDist01 := 0.5
actualDist01 := dm.Get(0, 1)
if math.Abs(actualDist01-expectedDist01) > 1e-10 {
t.Errorf("Distance(0, 1): expected %f, got %f", expectedDist01, actualDist01)
}
// Distance(0, 2):
// Intersection: {} -> 0 elements
// Union: {1, 2, 3, 5, 6, 7} -> 6 elements
// Similarity: 0/6 = 0
// Distance: 1 - 0 = 1.0
expectedDist02 := 1.0
actualDist02 := dm.Get(0, 2)
if math.Abs(actualDist02-expectedDist02) > 1e-10 {
t.Errorf("Distance(0, 2): expected %f, got %f", expectedDist02, actualDist02)
}
// Distance(1, 2):
// Intersection: {} -> 0 elements
// Union: {2, 3, 4, 5, 6, 7} -> 6 elements
// Similarity: 0/6 = 0
// Distance: 1 - 0 = 1.0
expectedDist12 := 1.0
actualDist12 := dm.Get(1, 2)
if math.Abs(actualDist12-expectedDist12) > 1e-10 {
t.Errorf("Distance(1, 2): expected %f, got %f", expectedDist12, actualDist12)
}
// Check symmetry
if dm.Get(0, 1) != dm.Get(1, 0) {
t.Errorf("Matrix not symmetric: Get(0, 1) = %f, Get(1, 0) = %f",
dm.Get(0, 1), dm.Get(1, 0))
}
// Check diagonal
if dm.Get(0, 0) != 0.0 {
t.Errorf("Diagonal should be 0, got %f", dm.Get(0, 0))
}
if dm.Get(1, 1) != 0.0 {
t.Errorf("Diagonal should be 0, got %f", dm.Get(1, 1))
}
if dm.Get(2, 2) != 0.0 {
t.Errorf("Diagonal should be 0, got %f", dm.Get(2, 2))
}
}
func TestKmerSetGroupJaccardSimilarityMatrix(t *testing.T) {
ksg := NewKmerSetGroup(5, 3)
// Set 0: {1, 2, 3}
ksg.Get(0).AddKmerCode(1)
ksg.Get(0).AddKmerCode(2)
ksg.Get(0).AddKmerCode(3)
// Set 1: {2, 3, 4}
ksg.Get(1).AddKmerCode(2)
ksg.Get(1).AddKmerCode(3)
ksg.Get(1).AddKmerCode(4)
// Set 2: {1, 2, 3} (same as set 0)
ksg.Get(2).AddKmerCode(1)
ksg.Get(2).AddKmerCode(2)
ksg.Get(2).AddKmerCode(3)
sm := ksg.JaccardSimilarityMatrix()
// Check similarities
// Similarity(0, 1): 0.5 (as calculated above)
expectedSim01 := 0.5
actualSim01 := sm.Get(0, 1)
if math.Abs(actualSim01-expectedSim01) > 1e-10 {
t.Errorf("Similarity(0, 1): expected %f, got %f", expectedSim01, actualSim01)
}
// Similarity(0, 2): 1.0 (identical sets)
expectedSim02 := 1.0
actualSim02 := sm.Get(0, 2)
if math.Abs(actualSim02-expectedSim02) > 1e-10 {
t.Errorf("Similarity(0, 2): expected %f, got %f", expectedSim02, actualSim02)
}
// Similarity(1, 2): 0.5
// Intersection: {2, 3} -> 2
// Union: {1, 2, 3, 4} -> 4
// Similarity: 2/4 = 0.5
expectedSim12 := 0.5
actualSim12 := sm.Get(1, 2)
if math.Abs(actualSim12-expectedSim12) > 1e-10 {
t.Errorf("Similarity(1, 2): expected %f, got %f", expectedSim12, actualSim12)
}
// Check diagonal (similarity to self = 1.0)
if sm.Get(0, 0) != 1.0 {
t.Errorf("Diagonal should be 1.0, got %f", sm.Get(0, 0))
}
if sm.Get(1, 1) != 1.0 {
t.Errorf("Diagonal should be 1.0, got %f", sm.Get(1, 1))
}
if sm.Get(2, 2) != 1.0 {
t.Errorf("Diagonal should be 1.0, got %f", sm.Get(2, 2))
}
}
func TestKmerSetGroupJaccardMatricesRelation(t *testing.T) {
ksg := NewKmerSetGroup(5, 4)
// Create different sets
ksg.Get(0).AddKmerCode(1)
ksg.Get(0).AddKmerCode(2)
ksg.Get(1).AddKmerCode(2)
ksg.Get(1).AddKmerCode(3)
ksg.Get(2).AddKmerCode(1)
ksg.Get(2).AddKmerCode(2)
ksg.Get(2).AddKmerCode(3)
ksg.Get(3).AddKmerCode(10)
ksg.Get(3).AddKmerCode(20)
dm := ksg.JaccardDistanceMatrix()
sm := ksg.JaccardSimilarityMatrix()
// For all pairs (including diagonal), distance + similarity should equal 1.0
for i := 0; i < 4; i++ {
for j := 0; j < 4; j++ {
distance := dm.Get(i, j)
similarity := sm.Get(i, j)
sum := distance + similarity
if math.Abs(sum-1.0) > 1e-10 {
t.Errorf("At (%d, %d): distance %f + similarity %f = %f, expected 1.0",
i, j, distance, similarity, sum)
}
}
}
}
func TestKmerSetGroupJaccardMatrixLabels(t *testing.T) {
ksg := NewKmerSetGroup(5, 3)
// Don't set IDs - should use default labels
ksg.Get(0).AddKmerCode(1)
ksg.Get(1).AddKmerCode(2)
ksg.Get(2).AddKmerCode(3)
dm := ksg.JaccardDistanceMatrix()
// Check default labels
if dm.GetLabel(0) != "set_0" {
t.Errorf("Expected default label 'set_0', got '%s'", dm.GetLabel(0))
}
if dm.GetLabel(1) != "set_1" {
t.Errorf("Expected default label 'set_1', got '%s'", dm.GetLabel(1))
}
if dm.GetLabel(2) != "set_2" {
t.Errorf("Expected default label 'set_2', got '%s'", dm.GetLabel(2))
}
}
func TestKmerSetGroupJaccardMatrixSize(t *testing.T) {
ksg := NewKmerSetGroup(5, 5)
for i := 0; i < 5; i++ {
ksg.Get(i).AddKmerCode(uint64(i))
}
dm := ksg.JaccardDistanceMatrix()
if dm.Size() != 5 {
t.Errorf("Expected matrix size 5, got %d", dm.Size())
}
// All sets are disjoint, so all distances should be 1.0
for i := 0; i < 5; i++ {
for j := i + 1; j < 5; j++ {
dist := dm.Get(i, j)
if math.Abs(dist-1.0) > 1e-10 {
t.Errorf("Expected distance 1.0 for disjoint sets (%d, %d), got %f",
i, j, dist)
}
}
}
}

235
pkg/obikmer/kmer_set_group_quorum.go
View File

@@ -1,235 +0,0 @@
package obikmer
import (
"container/heap"
"github.com/RoaringBitmap/roaring/roaring64"
)
// heapItem represents an element in the min-heap for k-way merge
type heapItem struct {
value uint64
idx int
}
// kmerMinHeap implements heap.Interface for k-way merge algorithm
type kmerMinHeap []heapItem
func (h kmerMinHeap) Len() int { return len(h) }
func (h kmerMinHeap) Less(i, j int) bool { return h[i].value < h[j].value }
func (h kmerMinHeap) Swap(i, j int) { h[i], h[j] = h[j], h[i] }
func (h *kmerMinHeap) Push(x interface{}) {
*h = append(*h, x.(heapItem))
}
func (h *kmerMinHeap) Pop() interface{} {
old := *h
n := len(old)
x := old[n-1]
*h = old[0 : n-1]
return x
}
// QuorumAtLeast returns k-mers present in at least q sets
//
// Algorithm: K-way merge with min-heap counting
//
// The algorithm processes all k-mers in sorted order using a min-heap:
//
// 1. Initialize one iterator per non-empty set
// 2. Build a min-heap of (value, set_index) pairs, one per iterator
// 3. While heap is not empty:
// a. Extract the minimum value v from heap
// b. Pop ALL heap items with value == v (counting occurrences)
// c. If count >= q, add v to result
// d. Advance each popped iterator and re-insert into heap if valid
//
// This ensures each unique k-mer is counted exactly once across all sets.
//
// Time complexity: O(M log N)
// - M = sum of all set cardinalities (total k-mer occurrences)
// - N = number of sets
// - Each k-mer occurrence is inserted/extracted from heap once: O(M) operations
// - Each heap operation costs O(log N)
//
// Space complexity: O(N)
// - Heap contains at most N elements (one per set iterator)
// - Output bitmap size depends on quorum result
//
// Special cases (optimized):
// - q <= 0: returns empty set
// - q == 1: delegates to Union() (native OR operations)
// - q == n: delegates to Intersect() (native AND operations)
// - q > n: returns empty set (impossible to satisfy)
func (ksg *KmerSetGroup) QuorumAtLeast(q int) *KmerSet {
n := len(ksg.sets)
// Edge cases
if q <= 0 || n == 0 {
return NewKmerSet(ksg.k)
}
if q > n {
return NewKmerSet(ksg.k)
}
if q == 1 {
return ksg.Union()
}
if q == n {
return ksg.Intersect()
}
// Initialize iterators for all non-empty sets
iterators := make([]roaring64.IntIterable64, 0, n)
iterIndices := make([]int, 0, n)
for i, set := range ksg.sets {
if set.Len() > 0 {
iter := set.bitmap.Iterator()
if iter.HasNext() {
iterators = append(iterators, iter)
iterIndices = append(iterIndices, i)
}
}
}
if len(iterators) == 0 {
return NewKmerSet(ksg.k)
}
// Initialize heap with first value from each iterator
h := make(kmerMinHeap, len(iterators))
for i, iter := range iterators {
h[i] = heapItem{value: iter.Next(), idx: i}
}
heap.Init(&h)
// Result bitmap
result := roaring64.New()
// K-way merge with counting
for len(h) > 0 {
minVal := h[0].value
count := 0
activeIndices := make([]int, 0, len(h))
// Pop all elements with same value (count occurrences)
for len(h) > 0 && h[0].value == minVal {
item := heap.Pop(&h).(heapItem)
count++
activeIndices = append(activeIndices, item.idx)
}
// Add to result if quorum reached
if count >= q {
result.Add(minVal)
}
// Advance iterators and re-insert into heap
for _, iterIdx := range activeIndices {
if iterators[iterIdx].HasNext() {
heap.Push(&h, heapItem{
value: iterators[iterIdx].Next(),
idx: iterIdx,
})
}
}
}
return NewKmerSetFromBitmap(ksg.k, result)
}
// QuorumAtMost returns k-mers present in at most q sets
//
// Algorithm: Uses the mathematical identity
// AtMost(q) = Union() - AtLeast(q+1)
//
// Proof:
// - Union() contains all k-mers present in at least 1 set
// - AtLeast(q+1) contains all k-mers present in q+1 or more sets
// - Their difference contains only k-mers present in at most q sets
//
// Implementation:
// 1. Compute U = Union()
// 2. Compute A = QuorumAtLeast(q+1)
// 3. Return U - A using bitmap AndNot operation
//
// Time complexity: O(M log N)
// - Union(): O(M) with native OR operations
// - QuorumAtLeast(q+1): O(M log N)
// - AndNot: O(|U|) where |U| <= M
// - Total: O(M log N)
//
// Space complexity: O(N)
// - Inherited from QuorumAtLeast heap
//
// Special cases:
// - q <= 0: returns empty set
// - q >= n: returns Union() (all k-mers are in at most n sets)
func (ksg *KmerSetGroup) QuorumAtMost(q int) *KmerSet {
n := len(ksg.sets)
// Edge cases
if q <= 0 {
return NewKmerSet(ksg.k)
}
if q >= n {
return ksg.Union()
}
// Compute Union() - AtLeast(q+1)
union := ksg.Union()
atLeastQ1 := ksg.QuorumAtLeast(q + 1)
// Difference: elements in union but not in atLeastQ1
result := union.bitmap.Clone()
result.AndNot(atLeastQ1.bitmap)
return NewKmerSetFromBitmap(ksg.k, result)
}
// QuorumExactly returns k-mers present in exactly q sets
//
// Algorithm: Uses the mathematical identity
// Exactly(q) = AtLeast(q) - AtLeast(q+1)
//
// Proof:
// - AtLeast(q) contains all k-mers present in q or more sets
// - AtLeast(q+1) contains all k-mers present in q+1 or more sets
// - Their difference contains only k-mers present in exactly q sets
//
// Implementation:
// 1. Compute A = QuorumAtLeast(q)
// 2. Compute B = QuorumAtLeast(q+1)
// 3. Return A - B using bitmap AndNot operation
//
// Time complexity: O(M log N)
// - Two calls to QuorumAtLeast: 2 * O(M log N)
// - One AndNot operation: O(|A|) where |A| <= M
// - Total: O(M log N) since AndNot is dominated by merge operations
//
// Space complexity: O(N)
// - Inherited from QuorumAtLeast heap
// - Two temporary bitmaps for intermediate results
//
// Special cases:
// - q <= 0: returns empty set
// - q > n: returns empty set (impossible to have k-mer in more than n sets)
func (ksg *KmerSetGroup) QuorumExactly(q int) *KmerSet {
n := len(ksg.sets)
// Edge cases
if q <= 0 || q > n {
return NewKmerSet(ksg.k)
}
// Compute AtLeast(q) - AtLeast(q+1)
aq := ksg.QuorumAtLeast(q)
aq1 := ksg.QuorumAtLeast(q + 1)
// Difference: elements in aq but not in aq1
result := aq.bitmap.Clone()
result.AndNot(aq1.bitmap)
return NewKmerSetFromBitmap(ksg.k, result)
}

395
pkg/obikmer/kmer_set_group_quorum_test.go
View File

@@ -1,395 +0,0 @@
package obikmer
import (
"testing"
)
// TestQuorumAtLeastEdgeCases tests edge cases for QuorumAtLeast
func TestQuorumAtLeastEdgeCases(t *testing.T) {
k := 5
// Test group with all empty sets
emptyGroup := NewKmerSetGroup(k, 3)
result := emptyGroup.QuorumAtLeast(1)
if result.Len() != 0 {
t.Errorf("Empty sets: expected 0 k-mers, got %d", result.Len())
}
// Test q <= 0
group := NewKmerSetGroup(k, 3)
result = group.QuorumAtLeast(0)
if result.Len() != 0 {
t.Errorf("q=0: expected 0 k-mers, got %d", result.Len())
}
result = group.QuorumAtLeast(-1)
if result.Len() != 0 {
t.Errorf("q=-1: expected 0 k-mers, got %d", result.Len())
}
// Test q > n
group.Get(0).AddKmerCode(1)
result = group.QuorumAtLeast(10)
if result.Len() != 0 {
t.Errorf("q>n: expected 0 k-mers, got %d", result.Len())
}
}
// TestQuorumAtLeastQ1 tests q=1 (should equal Union)
func TestQuorumAtLeastQ1(t *testing.T) {
k := 5
group := NewKmerSetGroup(k, 3)
// Add different k-mers to each set
group.Get(0).AddKmerCode(1)
group.Get(0).AddKmerCode(2)
group.Get(1).AddKmerCode(2)
group.Get(1).AddKmerCode(3)
group.Get(2).AddKmerCode(3)
group.Get(2).AddKmerCode(4)
quorum := group.QuorumAtLeast(1)
union := group.Union()
if quorum.Len() != union.Len() {
t.Errorf("QuorumAtLeast(1) length %d != Union length %d", quorum.Len(), union.Len())
}
// Check all elements match
for kmer := uint64(1); kmer <= 4; kmer++ {
if quorum.Contains(kmer) != union.Contains(kmer) {
t.Errorf("Mismatch for k-mer %d", kmer)
}
}
}
// TestQuorumAtLeastQN tests q=n (should equal Intersect)
func TestQuorumAtLeastQN(t *testing.T) {
k := 5
group := NewKmerSetGroup(k, 3)
// Add some common k-mers and some unique
for i := 0; i < 3; i++ {
group.Get(i).AddKmerCode(10) // common to all
group.Get(i).AddKmerCode(20) // common to all
}
group.Get(0).AddKmerCode(1) // unique to set 0
group.Get(1).AddKmerCode(2) // unique to set 1
quorum := group.QuorumAtLeast(3)
intersect := group.Intersect()
if quorum.Len() != intersect.Len() {
t.Errorf("QuorumAtLeast(n) length %d != Intersect length %d", quorum.Len(), intersect.Len())
}
if quorum.Len() != 2 {
t.Errorf("Expected 2 common k-mers, got %d", quorum.Len())
}
if !quorum.Contains(10) || !quorum.Contains(20) {
t.Error("Missing common k-mers")
}
if quorum.Contains(1) || quorum.Contains(2) {
t.Error("Unique k-mers should not be in result")
}
}
// TestQuorumAtLeastGeneral tests general quorum values
func TestQuorumAtLeastGeneral(t *testing.T) {
k := 5
group := NewKmerSetGroup(k, 5)
// Setup: k-mer i appears in i sets (for i=1..5)
// k-mer 1: in set 0
// k-mer 2: in sets 0,1
// k-mer 3: in sets 0,1,2
// k-mer 4: in sets 0,1,2,3
// k-mer 5: in sets 0,1,2,3,4 (all)
for kmer := uint64(1); kmer <= 5; kmer++ {
for setIdx := 0; setIdx < int(kmer); setIdx++ {
group.Get(setIdx).AddKmerCode(kmer)
}
}
tests := []struct {
q int
expected map[uint64]bool
}{
{1, map[uint64]bool{1: true, 2: true, 3: true, 4: true, 5: true}},
{2, map[uint64]bool{2: true, 3: true, 4: true, 5: true}},
{3, map[uint64]bool{3: true, 4: true, 5: true}},
{4, map[uint64]bool{4: true, 5: true}},
{5, map[uint64]bool{5: true}},
}
for _, tt := range tests {
result := group.QuorumAtLeast(tt.q)
if result.Len() != uint64(len(tt.expected)) {
t.Errorf("q=%d: expected %d k-mers, got %d", tt.q, len(tt.expected), result.Len())
}
for kmer := uint64(1); kmer <= 5; kmer++ {
shouldContain := tt.expected[kmer]
doesContain := result.Contains(kmer)
if shouldContain != doesContain {
t.Errorf("q=%d, k-mer=%d: expected contains=%v, got %v", tt.q, kmer, shouldContain, doesContain)
}
}
}
}
// TestQuorumExactlyBasic tests QuorumExactly basic functionality
func TestQuorumExactlyBasic(t *testing.T) {
k := 5
group := NewKmerSetGroup(k, 5)
// Setup: k-mer i appears in exactly i sets
for kmer := uint64(1); kmer <= 5; kmer++ {
for setIdx := 0; setIdx < int(kmer); setIdx++ {
group.Get(setIdx).AddKmerCode(kmer)
}
}
tests := []struct {
q int
expected []uint64
}{
{1, []uint64{1}},
{2, []uint64{2}},
{3, []uint64{3}},
{4, []uint64{4}},
{5, []uint64{5}},
}
for _, tt := range tests {
result := group.QuorumExactly(tt.q)
if result.Len() != uint64(len(tt.expected)) {
t.Errorf("q=%d: expected %d k-mers, got %d", tt.q, len(tt.expected), result.Len())
}
for _, kmer := range tt.expected {
if !result.Contains(kmer) {
t.Errorf("q=%d: missing k-mer %d", tt.q, kmer)
}
}
}
}
// TestQuorumIdentity tests the mathematical identity: Exactly(q) = AtLeast(q) - AtLeast(q+1)
func TestQuorumIdentity(t *testing.T) {
k := 5
group := NewKmerSetGroup(k, 4)
// Add random distribution
group.Get(0).AddKmerCode(1)
group.Get(0).AddKmerCode(2)
group.Get(0).AddKmerCode(3)
group.Get(1).AddKmerCode(2)
group.Get(1).AddKmerCode(3)
group.Get(1).AddKmerCode(4)
group.Get(2).AddKmerCode(3)
group.Get(2).AddKmerCode(4)
group.Get(3).AddKmerCode(4)
for q := 1; q <= 4; q++ {
exactly := group.QuorumExactly(q)
atLeast := group.QuorumAtLeast(q)
atLeastPlus1 := group.QuorumAtLeast(q + 1)
// Verify: every element in exactly(q) is in atLeast(q)
iter := exactly.Iterator()
for iter.HasNext() {
kmer := iter.Next()
if !atLeast.Contains(kmer) {
t.Errorf("q=%d: k-mer %d in Exactly but not in AtLeast", q, kmer)
}
if atLeastPlus1.Contains(kmer) {
t.Errorf("q=%d: k-mer %d in Exactly but also in AtLeast(q+1)", q, kmer)
}
}
}
}
// TestQuorumDisjointSets tests quorum on completely disjoint sets
func TestQuorumDisjointSets(t *testing.T) {
k := 5
group := NewKmerSetGroup(k, 3)
// Each set has unique k-mers
group.Get(0).AddKmerCode(1)
group.Get(1).AddKmerCode(2)
group.Get(2).AddKmerCode(3)
// q=1 should give all
result := group.QuorumAtLeast(1)
if result.Len() != 3 {
t.Errorf("Disjoint sets q=1: expected 3, got %d", result.Len())
}
// q=2 should give none
result = group.QuorumAtLeast(2)
if result.Len() != 0 {
t.Errorf("Disjoint sets q=2: expected 0, got %d", result.Len())
}
}
// TestQuorumIdenticalSets tests quorum on identical sets
func TestQuorumIdenticalSets(t *testing.T) {
k := 5
group := NewKmerSetGroup(k, 3)
// All sets have same k-mers
for i := 0; i < 3; i++ {
group.Get(i).AddKmerCode(10)
group.Get(i).AddKmerCode(20)
group.Get(i).AddKmerCode(30)
}
// Any q <= n should give all k-mers
for q := 1; q <= 3; q++ {
result := group.QuorumAtLeast(q)
if result.Len() != 3 {
t.Errorf("Identical sets q=%d: expected 3, got %d", q, result.Len())
}
}
}
// TestQuorumLargeNumbers tests with large k-mer values
func TestQuorumLargeNumbers(t *testing.T) {
k := 21
group := NewKmerSetGroup(k, 3)
// Use large uint64 values (actual k-mer encodings)
largeKmers := []uint64{
0x1234567890ABCDEF,
0xFEDCBA0987654321,
0xAAAAAAAAAAAAAAAA,
}
// Add to multiple sets
for i := 0; i < 3; i++ {
for j := 0; j <= i; j++ {
group.Get(j).AddKmerCode(largeKmers[i])
}
}
result := group.QuorumAtLeast(2)
if result.Len() != 2 {
t.Errorf("Large numbers q=2: expected 2, got %d", result.Len())
}
if !result.Contains(largeKmers[1]) || !result.Contains(largeKmers[2]) {
t.Error("Large numbers: wrong k-mers in result")
}
}
// TestQuorumAtMostBasic tests QuorumAtMost basic functionality
func TestQuorumAtMostBasic(t *testing.T) {
k := 5
group := NewKmerSetGroup(k, 5)
// Setup: k-mer i appears in exactly i sets
for kmer := uint64(1); kmer <= 5; kmer++ {
for setIdx := 0; setIdx < int(kmer); setIdx++ {
group.Get(setIdx).AddKmerCode(kmer)
}
}
tests := []struct {
q int
expected []uint64
}{
{0, []uint64{}}, // at most 0: none
{1, []uint64{1}}, // at most 1: only k-mer 1
{2, []uint64{1, 2}}, // at most 2: k-mers 1,2
{3, []uint64{1, 2, 3}}, // at most 3: k-mers 1,2,3
{4, []uint64{1, 2, 3, 4}}, // at most 4: k-mers 1,2,3,4
{5, []uint64{1, 2, 3, 4, 5}}, // at most 5: all k-mers
{10, []uint64{1, 2, 3, 4, 5}}, // at most 10: all k-mers
}
for _, tt := range tests {
result := group.QuorumAtMost(tt.q)
if result.Len() != uint64(len(tt.expected)) {
t.Errorf("q=%d: expected %d k-mers, got %d", tt.q, len(tt.expected), result.Len())
}
for _, kmer := range tt.expected {
if !result.Contains(kmer) {
t.Errorf("q=%d: missing k-mer %d", tt.q, kmer)
}
}
}
}
// TestQuorumComplementIdentity tests that AtLeast and AtMost are complementary
func TestQuorumComplementIdentity(t *testing.T) {
k := 5
group := NewKmerSetGroup(k, 4)
// Add random distribution
group.Get(0).AddKmerCode(1)
group.Get(0).AddKmerCode(2)
group.Get(0).AddKmerCode(3)
group.Get(1).AddKmerCode(2)
group.Get(1).AddKmerCode(3)
group.Get(1).AddKmerCode(4)
group.Get(2).AddKmerCode(3)
group.Get(2).AddKmerCode(4)
group.Get(3).AddKmerCode(4)
union := group.Union()
for q := 1; q < 4; q++ {
atMost := group.QuorumAtMost(q)
atLeast := group.QuorumAtLeast(q + 1)
// Verify: AtMost(q) ∪ AtLeast(q+1) = Union()
combined := atMost.Union(atLeast)
if combined.Len() != union.Len() {
t.Errorf("q=%d: AtMost(q) ∪ AtLeast(q+1) has %d k-mers, Union has %d",
q, combined.Len(), union.Len())
}
// Verify: AtMost(q) ∩ AtLeast(q+1) = ∅
overlap := atMost.Intersect(atLeast)
if overlap.Len() != 0 {
t.Errorf("q=%d: AtMost(q) and AtLeast(q+1) overlap with %d k-mers",
q, overlap.Len())
}
}
}
// BenchmarkQuorumAtLeast benchmarks quorum operations
func BenchmarkQuorumAtLeast(b *testing.B) {
k := 21
n := 10
group := NewKmerSetGroup(k, n)
// Populate with realistic data
for i := 0; i < n; i++ {
for j := uint64(0); j < 10000; j++ {
if (j % uint64(n)) <= uint64(i) {
group.Get(i).AddKmerCode(j)
}
}
}
b.ResetTimer()
for i := 0; i < b.N; i++ {
_ = group.QuorumAtLeast(5)
}
}

376
pkg/obikmer/kmer_set_persistence.go
View File

@@ -1,376 +0,0 @@
package obikmer
import (
"encoding/json"
"fmt"
"os"
"path/filepath"
"strings"
"github.com/pelletier/go-toml/v2"
"gopkg.in/yaml.v3"
)
// MetadataFormat represents the metadata serialization format
type MetadataFormat int
const (
FormatTOML MetadataFormat = iota
FormatYAML
FormatJSON
)
// String returns the file extension for the format
func (f MetadataFormat) String() string {
switch f {
case FormatTOML:
return "toml"
case FormatYAML:
return "yaml"
case FormatJSON:
return "json"
default:
return "toml"
}
}
// KmerSetMetadata contient les métadonnées d'un KmerSet ou KmerSetGroup
type KmerSetMetadata struct {
ID string `toml:"id,omitempty" yaml:"id,omitempty" json:"id,omitempty"` // Identifiant unique
K int `toml:"k" yaml:"k" json:"k"` // Taille des k-mers
Type string `toml:"type" yaml:"type" json:"type"` // "KmerSet" ou "KmerSetGroup"
Size int `toml:"size" yaml:"size" json:"size"` // 1 pour KmerSet, n pour KmerSetGroup
Files []string `toml:"files" yaml:"files" json:"files"` // Liste des fichiers .roaring
SetsIDs []string `toml:"sets_ids,omitempty" yaml:"sets_ids,omitempty" json:"sets_ids,omitempty"` // IDs des KmerSet individuels
UserMetadata map[string]interface{} `toml:"user_metadata,omitempty" yaml:"user_metadata,omitempty" json:"user_metadata,omitempty"` // Métadonnées KmerSet ou KmerSetGroup
SetsMetadata []map[string]interface{} `toml:"sets_metadata,omitempty" yaml:"sets_metadata,omitempty" json:"sets_metadata,omitempty"` // Métadonnées des KmerSet individuels dans un KmerSetGroup
}
// SaveKmerSet sauvegarde un KmerSet dans un répertoire
// Format: directory/metadata.{toml,yaml,json} + directory/set_0.roaring
func (ks *KmerSet) Save(directory string, format MetadataFormat) error {
// Créer le répertoire si nécessaire
if err := os.MkdirAll(directory, 0755); err != nil {
return fmt.Errorf("failed to create directory %s: %w", directory, err)
}
// Métadonnées
metadata := KmerSetMetadata{
ID: ks.id,
K: ks.k,
Type: "KmerSet",
Size: 1,
Files: []string{"set_0.roaring"},
UserMetadata: ks.Metadata, // Sauvegarder les métadonnées utilisateur
}
// Sauvegarder les métadonnées
if err := saveMetadata(filepath.Join(directory, "metadata."+format.String()), metadata, format); err != nil {
return err
}
// Sauvegarder le bitmap
bitmapPath := filepath.Join(directory, "set_0.roaring")
file, err := os.Create(bitmapPath)
if err != nil {
return fmt.Errorf("failed to create bitmap file %s: %w", bitmapPath, err)
}
defer file.Close()
if _, err := ks.bitmap.WriteTo(file); err != nil {
return fmt.Errorf("failed to write bitmap: %w", err)
}
return nil
}
// LoadKmerSet charge un KmerSet depuis un répertoire
func LoadKmerSet(directory string) (*KmerSet, error) {
// Lire les métadonnées (essayer tous les formats)
metadata, err := loadMetadata(directory)
if err != nil {
return nil, err
}
// Vérifier le type
if metadata.Type != "KmerSet" {
return nil, fmt.Errorf("invalid type: expected KmerSet, got %s", metadata.Type)
}
// Vérifier qu'il n'y a qu'un seul fichier
if metadata.Size != 1 || len(metadata.Files) != 1 {
return nil, fmt.Errorf("KmerSet must have exactly 1 bitmap file, got %d", len(metadata.Files))
}
// Charger le bitmap
bitmapPath := filepath.Join(directory, metadata.Files[0])
file, err := os.Open(bitmapPath)
if err != nil {
return nil, fmt.Errorf("failed to open bitmap file %s: %w", bitmapPath, err)
}
defer file.Close()
ks := NewKmerSet(metadata.K)
// Charger l'ID
ks.id = metadata.ID
// Charger les métadonnées utilisateur
if metadata.UserMetadata != nil {
ks.Metadata = metadata.UserMetadata
}
if _, err := ks.bitmap.ReadFrom(file); err != nil {
return nil, fmt.Errorf("failed to read bitmap: %w", err)
}
return ks, nil
}
// SaveKmerSetGroup sauvegarde un KmerSetGroup dans un répertoire
// Format: directory/metadata.{toml,yaml,json} + directory/set_0.roaring, set_1.roaring, ...
func (ksg *KmerSetGroup) Save(directory string, format MetadataFormat) error {
// Créer le répertoire si nécessaire
if err := os.MkdirAll(directory, 0755); err != nil {
return fmt.Errorf("failed to create directory %s: %w", directory, err)
}
// Métadonnées
files := make([]string, len(ksg.sets))
for i := range ksg.sets {
files[i] = fmt.Sprintf("set_%d.roaring", i)
}
// Collecter les IDs et métadonnées de chaque KmerSet individuel
setsIDs := make([]string, len(ksg.sets))
setsMetadata := make([]map[string]interface{}, len(ksg.sets))
for i, ks := range ksg.sets {
setsIDs[i] = ks.id
setsMetadata[i] = ks.Metadata
}
metadata := KmerSetMetadata{
ID: ksg.id,
K: ksg.k,
Type: "KmerSetGroup",
Size: len(ksg.sets),
Files: files,
SetsIDs: setsIDs, // IDs de chaque set
UserMetadata: ksg.Metadata, // Métadonnées du groupe
SetsMetadata: setsMetadata, // Métadonnées de chaque set
}
// Sauvegarder les métadonnées
if err := saveMetadata(filepath.Join(directory, "metadata."+format.String()), metadata, format); err != nil {
return err
}
// Sauvegarder chaque bitmap
for i, ks := range ksg.sets {
bitmapPath := filepath.Join(directory, files[i])
file, err := os.Create(bitmapPath)
if err != nil {
return fmt.Errorf("failed to create bitmap file %s: %w", bitmapPath, err)
}
if _, err := ks.bitmap.WriteTo(file); err != nil {
file.Close()
return fmt.Errorf("failed to write bitmap %d: %w", i, err)
}
file.Close()
}
return nil
}
// LoadKmerSetGroup charge un KmerSetGroup depuis un répertoire
func LoadKmerSetGroup(directory string) (*KmerSetGroup, error) {
// Lire les métadonnées (essayer tous les formats)
metadata, err := loadMetadata(directory)
if err != nil {
return nil, err
}
// Vérifier le type
if metadata.Type != "KmerSetGroup" {
return nil, fmt.Errorf("invalid type: expected KmerSetGroup, got %s", metadata.Type)
}
// Vérifier la cohérence
if metadata.Size != len(metadata.Files) {
return nil, fmt.Errorf("size mismatch: size=%d but %d files listed", metadata.Size, len(metadata.Files))
}
// Créer le groupe
ksg := NewKmerSetGroup(metadata.K, metadata.Size)
// Charger l'ID du groupe
ksg.id = metadata.ID
// Charger les métadonnées du groupe
if metadata.UserMetadata != nil {
ksg.Metadata = metadata.UserMetadata
}
// Charger les IDs de chaque KmerSet
if metadata.SetsIDs != nil && len(metadata.SetsIDs) == metadata.Size {
for i := range ksg.sets {
ksg.sets[i].id = metadata.SetsIDs[i]
}
}
// Charger les métadonnées de chaque KmerSet individuel
if metadata.SetsMetadata != nil {
if len(metadata.SetsMetadata) != metadata.Size {
return nil, fmt.Errorf("sets metadata size mismatch: expected %d, got %d", metadata.Size, len(metadata.SetsMetadata))
}
for i := range ksg.sets {
ksg.sets[i].Metadata = metadata.SetsMetadata[i]
}
}
// Charger chaque bitmap
for i, filename := range metadata.Files {
bitmapPath := filepath.Join(directory, filename)
file, err := os.Open(bitmapPath)
if err != nil {
return nil, fmt.Errorf("failed to open bitmap file %s: %w", bitmapPath, err)
}
if _, err := ksg.sets[i].bitmap.ReadFrom(file); err != nil {
file.Close()
return nil, fmt.Errorf("failed to read bitmap %d: %w", i, err)
}
file.Close()
}
return ksg, nil
}
// saveMetadata sauvegarde les métadonnées dans le format spécifié
func saveMetadata(path string, metadata KmerSetMetadata, format MetadataFormat) error {
file, err := os.Create(path)
if err != nil {
return fmt.Errorf("failed to create metadata file %s: %w", path, err)
}
defer file.Close()
var encoder interface{ Encode(interface{}) error }
switch format {
case FormatTOML:
encoder = toml.NewEncoder(file)
case FormatYAML:
encoder = yaml.NewEncoder(file)
case FormatJSON:
jsonEncoder := json.NewEncoder(file)
jsonEncoder.SetIndent("", " ")
encoder = jsonEncoder
default:
return fmt.Errorf("unsupported format: %v", format)
}
if err := encoder.Encode(metadata); err != nil {
return fmt.Errorf("failed to encode metadata: %w", err)
}
return nil
}
// loadMetadata charge les métadonnées depuis un répertoire
// Essaie tous les formats (TOML, YAML, JSON) dans l'ordre
func loadMetadata(directory string) (*KmerSetMetadata, error) {
formats := []MetadataFormat{FormatTOML, FormatYAML, FormatJSON}
var lastErr error
for _, format := range formats {
path := filepath.Join(directory, "metadata."+format.String())
// Vérifier si le fichier existe
if _, err := os.Stat(path); os.IsNotExist(err) {
continue
}
metadata, err := loadMetadataFromFile(path, format)
if err != nil {
lastErr = err
continue
}
return metadata, nil
}
if lastErr != nil {
return nil, fmt.Errorf("failed to load metadata: %w", lastErr)
}
return nil, fmt.Errorf("no metadata file found in %s (tried .toml, .yaml, .json)", directory)
}
// loadMetadataFromFile charge les métadonnées depuis un fichier spécifique
func loadMetadataFromFile(path string, format MetadataFormat) (*KmerSetMetadata, error) {
file, err := os.Open(path)
if err != nil {
return nil, fmt.Errorf("failed to open metadata file %s: %w", path, err)
}
defer file.Close()
var metadata KmerSetMetadata
var decoder interface{ Decode(interface{}) error }
switch format {
case FormatTOML:
decoder = toml.NewDecoder(file)
case FormatYAML:
decoder = yaml.NewDecoder(file)
case FormatJSON:
decoder = json.NewDecoder(file)
default:
return nil, fmt.Errorf("unsupported format: %v", format)
}
if err := decoder.Decode(&metadata); err != nil {
return nil, fmt.Errorf("failed to decode metadata: %w", err)
}
return &metadata, nil
}
// DetectFormat détecte le format des métadonnées dans un répertoire
func DetectFormat(directory string) (MetadataFormat, error) {
formats := []MetadataFormat{FormatTOML, FormatYAML, FormatJSON}
for _, format := range formats {
path := filepath.Join(directory, "metadata."+format.String())
if _, err := os.Stat(path); err == nil {
return format, nil
}
}
return FormatTOML, fmt.Errorf("no metadata file found in %s", directory)
}
// IsKmerSetDirectory vérifie si un répertoire contient un KmerSet ou KmerSetGroup
func IsKmerSetDirectory(directory string) (bool, string, error) {
metadata, err := loadMetadata(directory)
if err != nil {
return false, "", err
}
return true, metadata.Type, nil
}
// ListBitmapFiles liste tous les fichiers .roaring dans un répertoire
func ListBitmapFiles(directory string) ([]string, error) {
entries, err := os.ReadDir(directory)
if err != nil {
return nil, fmt.Errorf("failed to read directory %s: %w", directory, err)
}
var files []string
for _, entry := range entries {
if !entry.IsDir() && strings.HasSuffix(entry.Name(), ".roaring") {
files = append(files, entry.Name())
}
}
return files, nil
}

272
pkg/obikmer/kmer_set_test.go
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@@ -1,272 +0,0 @@
package obikmer
import (
"math"
"testing"
)
func TestJaccardDistanceIdentical(t *testing.T) {
ks1 := NewKmerSet(5)
ks1.AddKmerCode(100)
ks1.AddKmerCode(200)
ks1.AddKmerCode(300)
ks2 := NewKmerSet(5)
ks2.AddKmerCode(100)
ks2.AddKmerCode(200)
ks2.AddKmerCode(300)
distance := ks1.JaccardDistance(ks2)
similarity := ks1.JaccardSimilarity(ks2)
if distance != 0.0 {
t.Errorf("Expected distance 0.0 for identical sets, got %f", distance)
}
if similarity != 1.0 {
t.Errorf("Expected similarity 1.0 for identical sets, got %f", similarity)
}
}
func TestJaccardDistanceDisjoint(t *testing.T) {
ks1 := NewKmerSet(5)
ks1.AddKmerCode(100)
ks1.AddKmerCode(200)
ks1.AddKmerCode(300)
ks2 := NewKmerSet(5)
ks2.AddKmerCode(400)
ks2.AddKmerCode(500)
ks2.AddKmerCode(600)
distance := ks1.JaccardDistance(ks2)
similarity := ks1.JaccardSimilarity(ks2)
if distance != 1.0 {
t.Errorf("Expected distance 1.0 for disjoint sets, got %f", distance)
}
if similarity != 0.0 {
t.Errorf("Expected similarity 0.0 for disjoint sets, got %f", similarity)
}
}
func TestJaccardDistancePartialOverlap(t *testing.T) {
// Set 1: {1, 2, 3}
ks1 := NewKmerSet(5)
ks1.AddKmerCode(1)
ks1.AddKmerCode(2)
ks1.AddKmerCode(3)
// Set 2: {2, 3, 4}
ks2 := NewKmerSet(5)
ks2.AddKmerCode(2)
ks2.AddKmerCode(3)
ks2.AddKmerCode(4)
// Intersection: {2, 3} -> cardinality = 2
// Union: {1, 2, 3, 4} -> cardinality = 4
// Similarity = 2/4 = 0.5
// Distance = 1 - 0.5 = 0.5
distance := ks1.JaccardDistance(ks2)
similarity := ks1.JaccardSimilarity(ks2)
expectedDistance := 0.5
expectedSimilarity := 0.5
if math.Abs(distance-expectedDistance) > 1e-10 {
t.Errorf("Expected distance %f, got %f", expectedDistance, distance)
}
if math.Abs(similarity-expectedSimilarity) > 1e-10 {
t.Errorf("Expected similarity %f, got %f", expectedSimilarity, similarity)
}
}
func TestJaccardDistanceOneSubsetOfOther(t *testing.T) {
// Set 1: {1, 2}
ks1 := NewKmerSet(5)
ks1.AddKmerCode(1)
ks1.AddKmerCode(2)
// Set 2: {1, 2, 3, 4}
ks2 := NewKmerSet(5)
ks2.AddKmerCode(1)
ks2.AddKmerCode(2)
ks2.AddKmerCode(3)
ks2.AddKmerCode(4)
// Intersection: {1, 2} -> cardinality = 2
// Union: {1, 2, 3, 4} -> cardinality = 4
// Similarity = 2/4 = 0.5
// Distance = 1 - 0.5 = 0.5
distance := ks1.JaccardDistance(ks2)
similarity := ks1.JaccardSimilarity(ks2)
expectedDistance := 0.5
expectedSimilarity := 0.5
if math.Abs(distance-expectedDistance) > 1e-10 {
t.Errorf("Expected distance %f, got %f", expectedDistance, distance)
}
if math.Abs(similarity-expectedSimilarity) > 1e-10 {
t.Errorf("Expected similarity %f, got %f", expectedSimilarity, similarity)
}
}
func TestJaccardDistanceEmptySets(t *testing.T) {
ks1 := NewKmerSet(5)
ks2 := NewKmerSet(5)
distance := ks1.JaccardDistance(ks2)
similarity := ks1.JaccardSimilarity(ks2)
// By convention, distance = 1.0 for empty sets
if distance != 1.0 {
t.Errorf("Expected distance 1.0 for empty sets, got %f", distance)
}
if similarity != 0.0 {
t.Errorf("Expected similarity 0.0 for empty sets, got %f", similarity)
}
}
func TestJaccardDistanceOneEmpty(t *testing.T) {
ks1 := NewKmerSet(5)
ks1.AddKmerCode(1)
ks1.AddKmerCode(2)
ks1.AddKmerCode(3)
ks2 := NewKmerSet(5)
distance := ks1.JaccardDistance(ks2)
similarity := ks1.JaccardSimilarity(ks2)
// Intersection: {} -> cardinality = 0
// Union: {1, 2, 3} -> cardinality = 3
// Similarity = 0/3 = 0.0
// Distance = 1.0
if distance != 1.0 {
t.Errorf("Expected distance 1.0 when one set is empty, got %f", distance)
}
if similarity != 0.0 {
t.Errorf("Expected similarity 0.0 when one set is empty, got %f", similarity)
}
}
func TestJaccardDistanceDifferentK(t *testing.T) {
ks1 := NewKmerSet(5)
ks1.AddKmerCode(1)
ks2 := NewKmerSet(7)
ks2.AddKmerCode(1)
defer func() {
if r := recover(); r == nil {
t.Errorf("Expected panic when computing Jaccard distance with different k values")
}
}()
_ = ks1.JaccardDistance(ks2)
}
func TestJaccardDistanceSimilarityRelation(t *testing.T) {
// Test that distance + similarity = 1.0 for all cases
testCases := []struct {
name string
ks1 *KmerSet
ks2 *KmerSet
}{
{
name: "partial overlap",
ks1: func() *KmerSet {
ks := NewKmerSet(5)
ks.AddKmerCode(1)
ks.AddKmerCode(2)
ks.AddKmerCode(3)
return ks
}(),
ks2: func() *KmerSet {
ks := NewKmerSet(5)
ks.AddKmerCode(2)
ks.AddKmerCode(3)
ks.AddKmerCode(4)
ks.AddKmerCode(5)
return ks
}(),
},
{
name: "identical",
ks1: func() *KmerSet {
ks := NewKmerSet(5)
ks.AddKmerCode(10)
ks.AddKmerCode(20)
return ks
}(),
ks2: func() *KmerSet {
ks := NewKmerSet(5)
ks.AddKmerCode(10)
ks.AddKmerCode(20)
return ks
}(),
},
{
name: "disjoint",
ks1: func() *KmerSet {
ks := NewKmerSet(5)
ks.AddKmerCode(1)
return ks
}(),
ks2: func() *KmerSet {
ks := NewKmerSet(5)
ks.AddKmerCode(100)
return ks
}(),
},
}
for _, tc := range testCases {
t.Run(tc.name, func(t *testing.T) {
distance := tc.ks1.JaccardDistance(tc.ks2)
similarity := tc.ks1.JaccardSimilarity(tc.ks2)
sum := distance + similarity
if math.Abs(sum-1.0) > 1e-10 {
t.Errorf("Expected distance + similarity = 1.0, got %f + %f = %f",
distance, similarity, sum)
}
})
}
}
func TestJaccardDistanceSymmetry(t *testing.T) {
ks1 := NewKmerSet(5)
ks1.AddKmerCode(1)
ks1.AddKmerCode(2)
ks1.AddKmerCode(3)
ks2 := NewKmerSet(5)
ks2.AddKmerCode(2)
ks2.AddKmerCode(3)
ks2.AddKmerCode(4)
distance1 := ks1.JaccardDistance(ks2)
distance2 := ks2.JaccardDistance(ks1)
similarity1 := ks1.JaccardSimilarity(ks2)
similarity2 := ks2.JaccardSimilarity(ks1)
if math.Abs(distance1-distance2) > 1e-10 {
t.Errorf("Jaccard distance not symmetric: %f vs %f", distance1, distance2)
}
if math.Abs(similarity1-similarity2) > 1e-10 {
t.Errorf("Jaccard similarity not symmetric: %f vs %f", similarity1, similarity2)
}
}

47
pkg/obikmer/minimizer_utils.go Normal file
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@@ -0,0 +1,47 @@
package obikmer
import (
"math"
log "github.com/sirupsen/logrus"
)
// DefaultMinimizerSize returns ceil(k / 2.5) as a reasonable default minimizer size.
func DefaultMinimizerSize(k int) int {
m := int(math.Ceil(float64(k) / 2.5))
if m < 1 {
m = 1
}
if m >= k {
m = k - 1
}
return m
}
// MinMinimizerSize returns the minimum m such that 4^m >= nworkers,
// i.e. ceil(log(nworkers) / log(4)).
func MinMinimizerSize(nworkers int) int {
if nworkers <= 1 {
return 1
}
return int(math.Ceil(math.Log(float64(nworkers)) / math.Log(4)))
}
// ValidateMinimizerSize checks and adjusts the minimizer size to satisfy constraints:
// - m >= ceil(log(nworkers)/log(4))
// - 1 <= m < k
func ValidateMinimizerSize(m, k, nworkers int) int {
minM := MinMinimizerSize(nworkers)
if m < minM {
log.Warnf("Minimizer size %d too small for %d workers (4^%d = %d < %d), adjusting to %d",
m, nworkers, m, 1<<(2*m), nworkers, minM)
m = minM
}
if m < 1 {
m = 1
}
if m >= k {
m = k - 1
}
return m
}

67
pkg/obikmer/skm_reader.go Normal file
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@@ -0,0 +1,67 @@
package obikmer
import (
"bufio"
"encoding/binary"
"io"
"os"
)
// decode2bit maps 2-bit codes back to nucleotide bytes.
var decode2bit = [4]byte{'a', 'c', 'g', 't'}
// SkmReader reads super-kmers from a binary .skm file.
type SkmReader struct {
r *bufio.Reader
file *os.File
}
// NewSkmReader opens a .skm file for reading.
func NewSkmReader(path string) (*SkmReader, error) {
f, err := os.Open(path)
if err != nil {
return nil, err
}
return &SkmReader{
r: bufio.NewReaderSize(f, 65536),
file: f,
}, nil
}
// Next reads the next super-kmer from the file.
// Returns the SuperKmer and true, or a zero SuperKmer and false at EOF.
func (sr *SkmReader) Next() (SuperKmer, bool) {
// Read length
var lenbuf [2]byte
if _, err := io.ReadFull(sr.r, lenbuf[:]); err != nil {
return SuperKmer{}, false
}
seqLen := int(binary.LittleEndian.Uint16(lenbuf[:]))
// Read packed bytes
nBytes := (seqLen + 3) / 4
packed := make([]byte, nBytes)
if _, err := io.ReadFull(sr.r, packed); err != nil {
return SuperKmer{}, false
}
// Decode to nucleotide bytes
seq := make([]byte, seqLen)
for i := 0; i < seqLen; i++ {
byteIdx := i / 4
bitPos := uint(6 - (i%4)*2)
code := (packed[byteIdx] >> bitPos) & 0x03
seq[i] = decode2bit[code]
}
return SuperKmer{
Sequence: seq,
Start: 0,
End: seqLen,
}, true
}
// Close closes the underlying file.
func (sr *SkmReader) Close() error {
return sr.file.Close()
}

176
pkg/obikmer/skm_test.go Normal file
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@@ -0,0 +1,176 @@
package obikmer
import (
"os"
"path/filepath"
"testing"
)
func TestSkmRoundTrip(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "test.skm")
// Create super-kmers from a known sequence
seq := []byte("ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT")
k := 21
m := 9
superKmers := ExtractSuperKmers(seq, k, m, nil)
if len(superKmers) == 0 {
t.Fatal("no super-kmers extracted")
}
// Write
w, err := NewSkmWriter(path)
if err != nil {
t.Fatal(err)
}
for _, sk := range superKmers {
if err := w.Write(sk); err != nil {
t.Fatal(err)
}
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
// Read back
r, err := NewSkmReader(path)
if err != nil {
t.Fatal(err)
}
defer r.Close()
idx := 0
for {
sk, ok := r.Next()
if !ok {
break
}
if idx >= len(superKmers) {
t.Fatal("read more super-kmers than written")
}
expected := superKmers[idx]
if len(sk.Sequence) != len(expected.Sequence) {
t.Fatalf("super-kmer %d: length mismatch: got %d, want %d",
idx, len(sk.Sequence), len(expected.Sequence))
}
// Compare nucleotide-by-nucleotide (case insensitive since decode produces lowercase)
for j := range sk.Sequence {
got := sk.Sequence[j] | 0x20
want := expected.Sequence[j] | 0x20
if got != want {
t.Fatalf("super-kmer %d pos %d: got %c, want %c", idx, j, got, want)
}
}
idx++
}
if idx != len(superKmers) {
t.Fatalf("read %d super-kmers, want %d", idx, len(superKmers))
}
}
func TestSkmEmptyFile(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "empty.skm")
// Write nothing
w, err := NewSkmWriter(path)
if err != nil {
t.Fatal(err)
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
// Read back
r, err := NewSkmReader(path)
if err != nil {
t.Fatal(err)
}
defer r.Close()
_, ok := r.Next()
if ok {
t.Fatal("expected no super-kmers in empty file")
}
}
func TestSkmSingleBase(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "single.skm")
// Test with sequences of various lengths to check padding
sequences := [][]byte{
[]byte("A"),
[]byte("AC"),
[]byte("ACG"),
[]byte("ACGT"),
[]byte("ACGTA"),
}
w, err := NewSkmWriter(path)
if err != nil {
t.Fatal(err)
}
for _, seq := range sequences {
sk := SuperKmer{Sequence: seq}
if err := w.Write(sk); err != nil {
t.Fatal(err)
}
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
r, err := NewSkmReader(path)
if err != nil {
t.Fatal(err)
}
defer r.Close()
for i, expected := range sequences {
sk, ok := r.Next()
if !ok {
t.Fatalf("expected super-kmer %d, got EOF", i)
}
if len(sk.Sequence) != len(expected) {
t.Fatalf("sk %d: length %d, want %d", i, len(sk.Sequence), len(expected))
}
for j := range sk.Sequence {
got := sk.Sequence[j] | 0x20
want := expected[j] | 0x20
if got != want {
t.Fatalf("sk %d pos %d: got %c, want %c", i, j, got, want)
}
}
}
}
func TestSkmFileSize(t *testing.T) {
dir := t.TempDir()
path := filepath.Join(dir, "size.skm")
// Write a sequence of known length
seq := []byte("ACGTACGTAC") // 10 bases
sk := SuperKmer{Sequence: seq}
w, err := NewSkmWriter(path)
if err != nil {
t.Fatal(err)
}
if err := w.Write(sk); err != nil {
t.Fatal(err)
}
if err := w.Close(); err != nil {
t.Fatal(err)
}
// Expected: 2 bytes (length) + ceil(10/4)=3 bytes (data) = 5 bytes
info, err := os.Stat(path)
if err != nil {
t.Fatal(err)
}
if info.Size() != 5 {
t.Fatalf("file size: got %d, want 5", info.Size())
}
}

74
pkg/obikmer/skm_writer.go Normal file
View File

@@ -0,0 +1,74 @@
package obikmer
import (
"bufio"
"encoding/binary"
"os"
)
// SkmWriter writes super-kmers to a binary .skm file.
//
// Format per super-kmer:
//
// [len: uint16 LE] length of the super-kmer in bases
// [data: ceil(len/4) bytes] sequence encoded 2 bits/base, packed
//
// Nucleotide encoding: A=00, C=01, G=10, T=11.
// The last byte is zero-padded on the low bits if len%4 != 0.
type SkmWriter struct {
w *bufio.Writer
file *os.File
}
// NewSkmWriter creates a new SkmWriter writing to the given file path.
func NewSkmWriter(path string) (*SkmWriter, error) {
f, err := os.Create(path)
if err != nil {
return nil, err
}
return &SkmWriter{
w: bufio.NewWriterSize(f, 65536),
file: f,
}, nil
}
// Write encodes a SuperKmer to the .skm file.
// The sequence bytes are packed 2 bits per base.
func (sw *SkmWriter) Write(sk SuperKmer) error {
seq := sk.Sequence
seqLen := uint16(len(seq))
// Write length
var lenbuf [2]byte
binary.LittleEndian.PutUint16(lenbuf[:], seqLen)
if _, err := sw.w.Write(lenbuf[:]); err != nil {
return err
}
// Encode and write packed sequence (2 bits/base)
nBytes := (int(seqLen) + 3) / 4
for i := 0; i < nBytes; i++ {
var packed byte
for j := 0; j < 4; j++ {
pos := i*4 + j
packed <<= 2
if pos < int(seqLen) {
packed |= __single_base_code__[seq[pos]&31]
}
}
if err := sw.w.WriteByte(packed); err != nil {
return err
}
}
return nil
}
// Close flushes buffered data and closes the underlying file.
func (sw *SkmWriter) Close() error {
if err := sw.w.Flush(); err != nil {
sw.file.Close()
return err
}
return sw.file.Close()
}

53
pkg/obikmer/varint.go Normal file
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@@ -0,0 +1,53 @@
package obikmer
import "io"
// EncodeVarint writes a uint64 value as a variable-length integer to w.
// Uses 7 bits per byte with the high bit as a continuation flag
// (identical to protobuf unsigned varint encoding).
// Returns the number of bytes written.
func EncodeVarint(w io.Writer, v uint64) (int, error) {
var buf [10]byte // max 10 bytes for uint64 varint
n := 0
for v >= 0x80 {
buf[n] = byte(v) | 0x80
v >>= 7
n++
}
buf[n] = byte(v)
n++
return w.Write(buf[:n])
}
// DecodeVarint reads a variable-length encoded uint64 from r.
// Returns the decoded value and any error encountered.
func DecodeVarint(r io.Reader) (uint64, error) {
var val uint64
var shift uint
var buf [1]byte
for {
if _, err := io.ReadFull(r, buf[:]); err != nil {
return 0, err
}
b := buf[0]
val |= uint64(b&0x7F) << shift
if b < 0x80 {
return val, nil
}
shift += 7
if shift >= 70 {
return 0, io.ErrUnexpectedEOF
}
}
}
// VarintLen returns the number of bytes needed to encode v as a varint.
func VarintLen(v uint64) int {
n := 1
for v >= 0x80 {
v >>= 7
n++
}
return n
}

82
pkg/obikmer/varint_test.go Normal file
View File

@@ -0,0 +1,82 @@
package obikmer
import (
"bytes"
"testing"
)
func TestVarintRoundTrip(t *testing.T) {
values := []uint64{
0, 1, 127, 128, 255, 256,
16383, 16384,
1<<21 - 1, 1 << 21,
1<<28 - 1, 1 << 28,
1<<35 - 1, 1 << 35,
1<<42 - 1, 1 << 42,
1<<49 - 1, 1 << 49,
1<<56 - 1, 1 << 56,
1<<63 - 1, 1 << 63,
^uint64(0), // max uint64
}
for _, v := range values {
var buf bytes.Buffer
n, err := EncodeVarint(&buf, v)
if err != nil {
t.Fatalf("EncodeVarint(%d): %v", v, err)
}
if n != VarintLen(v) {
t.Fatalf("EncodeVarint(%d): wrote %d bytes, VarintLen says %d", v, n, VarintLen(v))
}
decoded, err := DecodeVarint(&buf)
if err != nil {
t.Fatalf("DecodeVarint for %d: %v", v, err)
}
if decoded != v {
t.Fatalf("roundtrip failed: encoded %d, decoded %d", v, decoded)
}
}
}
func TestVarintLen(t *testing.T) {
tests := []struct {
value uint64
expected int
}{
{0, 1},
{127, 1},
{128, 2},
{16383, 2},
{16384, 3},
{^uint64(0), 10},
}
for _, tc := range tests {
got := VarintLen(tc.value)
if got != tc.expected {
t.Errorf("VarintLen(%d) = %d, want %d", tc.value, got, tc.expected)
}
}
}
func TestVarintSequence(t *testing.T) {
var buf bytes.Buffer
values := []uint64{0, 42, 1000000, ^uint64(0), 1}
for _, v := range values {
if _, err := EncodeVarint(&buf, v); err != nil {
t.Fatalf("EncodeVarint(%d): %v", v, err)
}
}
for _, expected := range values {
got, err := DecodeVarint(&buf)
if err != nil {
t.Fatalf("DecodeVarint: %v", err)
}
if got != expected {
t.Errorf("got %d, want %d", got, expected)
}
}
}

92
pkg/obitools/obikindex/obikindex.go
View File

@@ -7,8 +7,8 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
)
// CLIBuildKmerIndex reads sequences from the iterator and builds a kmer index
// saved as a roaring bitmap directory.
// CLIBuildKmerIndex reads sequences from the iterator and builds a
// disk-based kmer index using the KmerSetGroupBuilder.
func CLIBuildKmerIndex(iterator obiiter.IBioSequence) {
// Validate output directory
outDir := CLIOutputDirectory()
@@ -31,64 +31,56 @@ func CLIBuildKmerIndex(iterator obiiter.IBioSequence) {
log.Fatalf("Invalid min-occurrence: %d (must be >= 1)", minOcc)
}
// Resolve metadata format
format := CLIMetadataFormat()
log.Infof("Building kmer index: k=%d, m=%d, min-occurrence=%d", k, m, minOcc)
if minOcc <= 1 {
// Simple KmerSet mode
ks := obikmer.BuildKmerIndex(iterator, k, m)
// Build options
var opts []obikmer.BuilderOption
if minOcc > 1 {
opts = append(opts, obikmer.WithMinFrequency(minOcc))
}
// Apply metadata
applyKmerSetMetadata(ks)
// Create builder (1 set, auto partitions)
builder, err := obikmer.NewKmerSetGroupBuilder(outDir, k, m, 1, -1, opts...)
if err != nil {
log.Fatalf("Failed to create kmer index builder: %v", err)
}
// Save
log.Infof("Saving KmerSet to %s", outDir)
if err := ks.Save(outDir, format); err != nil {
log.Fatalf("Failed to save kmer index: %v", err)
}
} else {
// FrequencyFilter mode
ff := obikmer.BuildFrequencyFilterIndex(iterator, k, m, minOcc)
if CLISaveFullFilter() {
// Save the full filter (all levels)
applyMetadataGroup(ff.KmerSetGroup)
log.Infof("Saving full FrequencyFilter to %s", outDir)
if err := ff.Save(outDir, format); err != nil {
log.Fatalf("Failed to save frequency filter: %v", err)
}
} else {
// Save only the filtered KmerSet (k-mers with freq >= minOcc)
ks := ff.GetFilteredSet()
applyKmerSetMetadata(ks)
ks.SetAttribute("min_occurrence", minOcc)
log.Infof("Saving filtered KmerSet (freq >= %d) to %s", minOcc, outDir)
if err := ks.Save(outDir, format); err != nil {
log.Fatalf("Failed to save filtered kmer index: %v", err)
}
// Feed sequences
seqCount := 0
for iterator.Next() {
batch := iterator.Get()
for _, seq := range batch.Slice() {
builder.AddSequence(0, seq)
seqCount++
}
}
log.Infof("Processed %d sequences", seqCount)
// Finalize
ksg, err := builder.Close()
if err != nil {
log.Fatalf("Failed to finalize kmer index: %v", err)
}
// Apply metadata
applyMetadata(ksg)
if minOcc > 1 {
ksg.SetAttribute("min_occurrence", minOcc)
}
// Persist metadata updates
if err := ksg.SaveMetadata(); err != nil {
log.Fatalf("Failed to save metadata: %v", err)
}
log.Infof("Index contains %d k-mers in %s", ksg.Len(0), outDir)
log.Info("Done.")
}
// applyKmerSetMetadata sets index-id and --set-tag metadata on a KmerSet.
func applyKmerSetMetadata(ks *obikmer.KmerSet) {
if id := CLIIndexId(); id != "" {
ks.SetId(id)
}
for key, value := range CLISetTag() {
ks.SetAttribute(key, value)
}
}
// applyMetadataGroup sets index-id and --set-tag metadata on a KmerSetGroup.
func applyMetadataGroup(ksg *obikmer.KmerSetGroup) {
// applyMetadata sets index-id and --set-tag metadata on a KmerSetGroup.
func applyMetadata(ksg *obikmer.KmerSetGroup) {
if id := CLIIndexId(); id != "" {
ksg.SetId(id)
}