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//! Criterion benchmarks for DNA Analyzer
//!
//! Comprehensive performance benchmarks covering:
//! - K-mer encoding and HNSW indexing
//! - Sequence alignment
//! - Variant calling
//! - Protein translation
//! - Full pipeline integration
use ::rvdna::prelude::*;
use ::rvdna::types::KmerIndex as TypesKmerIndex;
use criterion::{black_box, criterion_group, criterion_main, Criterion};
use rand::rngs::StdRng;
use rand::{Rng, SeedableRng};
/// Generate random DNA sequence of specified length
fn random_dna(len: usize, seed: u64) -> DnaSequence {
let mut rng = StdRng::seed_from_u64(seed);
let bases = [Nucleotide::A, Nucleotide::C, Nucleotide::G, Nucleotide::T];
let sequence: Vec<Nucleotide> = (0..len).map(|_| bases[rng.gen_range(0..4)]).collect();
DnaSequence::new(sequence)
}
/// Generate multiple random sequences
fn random_sequences(count: usize, len: usize, seed: u64) -> Vec<DnaSequence> {
(0..count)
.map(|i| random_dna(len, seed + i as u64))
.collect()
}
// ============================================================================
// K-mer Benchmarks
// ============================================================================
fn kmer_benchmarks(c: &mut Criterion) {
let mut group = c.benchmark_group("kmer");
group.bench_function("encode_1kb", |b| {
let seq = random_dna(1_000, 42);
b.iter(|| black_box(seq.to_kmer_vector(11, 512).unwrap()));
});
group.bench_function("encode_10kb", |b| {
let seq = random_dna(10_000, 42);
b.iter(|| black_box(seq.to_kmer_vector(11, 512).unwrap()));
});
group.bench_function("encode_100kb", |b| {
let seq = random_dna(100_000, 42);
b.iter(|| black_box(seq.to_kmer_vector(11, 512).unwrap()));
});
// HNSW index insertion
group.bench_function("index_insert_100", |b| {
let sequences = random_sequences(100, 100, 42);
b.iter(|| {
let temp = tempfile::TempDir::new().unwrap();
let index =
TypesKmerIndex::new(11, 512, temp.path().join("idx").to_str().unwrap()).unwrap();
for (i, seq) in sequences.iter().enumerate() {
let vec = seq.to_kmer_vector(11, 512).unwrap();
index
.db()
.insert(ruvector_core::VectorEntry {
id: Some(format!("seq{}", i)),
vector: vec,
metadata: None,
})
.unwrap();
}
black_box(index)
});
});
// HNSW search
group.bench_function("search_top10", |b| {
let sequences = random_sequences(100, 100, 42);
let temp = tempfile::TempDir::new().unwrap();
let index =
TypesKmerIndex::new(11, 512, temp.path().join("idx").to_str().unwrap()).unwrap();
for (i, seq) in sequences.iter().enumerate() {
let vec = seq.to_kmer_vector(11, 512).unwrap();
index
.db()
.insert(ruvector_core::VectorEntry {
id: Some(format!("seq{}", i)),
vector: vec,
metadata: None,
})
.unwrap();
}
let query = random_dna(100, 999);
let query_vec = query.to_kmer_vector(11, 512).unwrap();
b.iter(|| {
black_box(
index
.db()
.search(ruvector_core::SearchQuery {
vector: query_vec.clone(),
k: 10,
filter: None,
ef_search: None,
})
.unwrap(),
)
});
});
group.finish();
}
// ============================================================================
// Alignment Benchmarks
// ============================================================================
fn alignment_benchmarks(c: &mut Criterion) {
let mut group = c.benchmark_group("alignment");
group.bench_function("one_hot_encoding_1kb", |b| {
let seq = random_dna(1_000, 42);
b.iter(|| black_box(seq.encode_one_hot()));
});
group.bench_function("attention_align_100bp", |b| {
let query = random_dna(100, 42);
let reference = random_dna(1_000, 43);
b.iter(|| black_box(query.align_with_attention(&reference).unwrap()));
});
group.bench_function("smith_waterman_100bp", |b| {
let query = random_dna(100, 42);
let reference = random_dna(500, 43);
let aligner = SmithWaterman::new(AlignmentConfig::default());
b.iter(|| black_box(aligner.align(&query, &reference).unwrap()));
});
group.finish();
}
// ============================================================================
// Variant Calling Benchmarks
// ============================================================================
fn variant_benchmarks(c: &mut Criterion) {
let mut group = c.benchmark_group("variant");
group.bench_function("snp_calling_single", |b| {
let caller = VariantCaller::new(VariantCallerConfig::default());
let pileup = PileupColumn {
bases: vec![b'A', b'A', b'G', b'G', b'G', b'G', b'G', b'G', b'G', b'G'],
qualities: vec![35; 10],
position: 12345,
chromosome: 1,
};
b.iter(|| black_box(caller.call_snp(&pileup, b'A')));
});
group.bench_function("snp_calling_1000_positions", |b| {
let caller = VariantCaller::new(VariantCallerConfig::default());
let mut rng = StdRng::seed_from_u64(42);
let pileups: Vec<(PileupColumn, u8)> = (0..1000)
.map(|i| {
let bases: Vec<u8> = (0..20)
.map(|_| [b'A', b'C', b'G', b'T'][rng.gen_range(0..4)])
.collect();
let quals: Vec<u8> = (0..20).map(|_| rng.gen_range(20..41)).collect();
let ref_base = [b'A', b'C', b'G', b'T'][i % 4];
(
PileupColumn {
bases,
qualities: quals,
position: i as u64,
chromosome: 1,
},
ref_base,
)
})
.collect();
b.iter(|| {
let mut count = 0;
for (pileup, ref_base) in &pileups {
if caller.call_snp(pileup, *ref_base).is_some() {
count += 1;
}
}
black_box(count)
});
});
group.finish();
}
// ============================================================================
// Protein Analysis Benchmarks
// ============================================================================
fn protein_benchmarks(c: &mut Criterion) {
let mut group = c.benchmark_group("protein");
group.bench_function("translate_1kb", |b| {
let seq = random_dna(1_002, 42);
b.iter(|| black_box(seq.translate().unwrap()));
});
group.bench_function("contact_graph_100residues", |b| {
let protein = create_random_protein(100, 42);
b.iter(|| black_box(protein.build_contact_graph(8.0).unwrap()));
});
group.bench_function("contact_prediction_100residues", |b| {
let protein = create_random_protein(100, 42);
let graph = protein.build_contact_graph(8.0).unwrap();
b.iter(|| black_box(protein.predict_contacts(&graph).unwrap()));
});
group.finish();
}
// ============================================================================
// RVDNA Format Benchmarks
// ============================================================================
fn rvdna_benchmarks(c: &mut Criterion) {
let mut group = c.benchmark_group("rvdna");
group.bench_function("encode_2bit_1kb", |b| {
let seq = random_dna(1_000, 42);
b.iter(|| black_box(rvdna::encode_2bit(seq.bases())));
});
group.bench_function("encode_2bit_100kb", |b| {
let seq = random_dna(100_000, 42);
b.iter(|| black_box(rvdna::encode_2bit(seq.bases())));
});
group.bench_function("fasta_to_rvdna_1kb", |b| {
let seq_str: String = random_dna(1_000, 42)
.bases()
.iter()
.map(|n| match n {
Nucleotide::A => 'A',
Nucleotide::C => 'C',
Nucleotide::G => 'G',
Nucleotide::T => 'T',
_ => 'N',
})
.collect();
b.iter(|| black_box(rvdna::fasta_to_rvdna(&seq_str, 11, 256, 1000).unwrap()));
});
group.finish();
}
// ============================================================================
// Epigenomics Benchmarks
// ============================================================================
fn epigenomics_benchmarks(c: &mut Criterion) {
let mut group = c.benchmark_group("epigenomics");
group.bench_function("cancer_signal_1000_sites", |b| {
let positions: Vec<(u8, u64)> = (0..1000).map(|i| (1u8, i as u64)).collect();
let betas: Vec<f32> = (0..1000).map(|i| (i as f32 / 1000.0)).collect();
let profile = rvdna::MethylationProfile::from_beta_values(positions, betas);
let detector = rvdna::CancerSignalDetector::new();
b.iter(|| black_box(detector.detect(&profile)));
});
group.bench_function("horvath_clock_1000_sites", |b| {
let positions: Vec<(u8, u64)> = (0..1000).map(|i| (1u8, i as u64)).collect();
let betas: Vec<f32> = (0..1000).map(|i| (i as f32 / 2000.0 + 0.25)).collect();
let profile = rvdna::MethylationProfile::from_beta_values(positions, betas);
let clock = rvdna::HorvathClock::default_clock();
b.iter(|| black_box(clock.predict_age(&profile)));
});
group.finish();
}
// ============================================================================
// Protein Analysis Benchmarks (extended)
// ============================================================================
fn protein_extended_benchmarks(c: &mut Criterion) {
let mut group = c.benchmark_group("protein_analysis");
group.bench_function("molecular_weight_300aa", |b| {
let protein = rvdna::translate_dna(
&random_dna(900, 42)
.bases()
.iter()
.map(|n| match n {
Nucleotide::A => b'A',
Nucleotide::C => b'C',
Nucleotide::G => b'G',
Nucleotide::T => b'T',
_ => b'N',
})
.collect::<Vec<u8>>(),
);
b.iter(|| black_box(rvdna::molecular_weight(&protein)));
});
group.bench_function("isoelectric_point_300aa", |b| {
let protein = rvdna::translate_dna(
&random_dna(900, 42)
.bases()
.iter()
.map(|n| match n {
Nucleotide::A => b'A',
Nucleotide::C => b'C',
Nucleotide::G => b'G',
Nucleotide::T => b'T',
_ => b'N',
})
.collect::<Vec<u8>>(),
);
b.iter(|| black_box(rvdna::isoelectric_point(&protein)));
});
group.finish();
}
// ============================================================================
// Full Pipeline Benchmarks
// ============================================================================
fn pipeline_benchmarks(c: &mut Criterion) {
let mut group = c.benchmark_group("pipeline");
group.bench_function("full_pipeline_1kb", |b| {
let reference = random_dna(1_000, 42);
let reads = random_sequences(20, 150, 43);
let caller = VariantCaller::new(VariantCallerConfig::default());
b.iter(|| {
// K-mer encoding
let ref_vec = reference.to_kmer_vector(11, 512).unwrap();
// Align reads
let mut alignments = Vec::new();
for read in &reads {
if let Ok(alignment) = read.align_with_attention(&reference) {
alignments.push(alignment);
}
}
// Call variants at a few positions
let mut variants = Vec::new();
let pileup = PileupColumn {
bases: vec![b'A', b'G', b'G', b'G', b'A', b'G', b'G', b'A', b'G', b'G'],
qualities: vec![35; 10],
position: 0,
chromosome: 1,
};
if let Some(v) = caller.call_snp(&pileup, b'A') {
variants.push(v);
}
// Translate to protein
let protein = reference.translate().unwrap();
black_box((ref_vec, alignments, variants, protein))
});
});
group.finish();
}
// ============================================================================
// Helpers
// ============================================================================
fn create_random_protein(len: usize, seed: u64) -> ProteinSequence {
let mut rng = StdRng::seed_from_u64(seed);
let residues = [
ProteinResidue::A,
ProteinResidue::C,
ProteinResidue::D,
ProteinResidue::E,
ProteinResidue::F,
ProteinResidue::G,
ProteinResidue::H,
ProteinResidue::I,
ProteinResidue::K,
ProteinResidue::L,
ProteinResidue::M,
ProteinResidue::N,
];
let sequence: Vec<ProteinResidue> = (0..len)
.map(|_| residues[rng.gen_range(0..residues.len())])
.collect();
ProteinSequence::new(sequence)
}
// ============================================================================
// Criterion Configuration
// ============================================================================
criterion_group!(
benches,
kmer_benchmarks,
alignment_benchmarks,
variant_benchmarks,
protein_benchmarks,
rvdna_benchmarks,
epigenomics_benchmarks,
protein_extended_benchmarks,
pipeline_benchmarks
);
criterion_main!(benches);