Merge commit 'd803bfe2b1fe7f5e219e50ac20d6801a0a58ac75' as 'vendor/ruvector'

vendor/ruvector/examples/dna/src/lib.rs

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+//! # rvDNA — AI-Native Genomic Analysis
+//!
+//! Fast, accurate genomic analysis in pure Rust with WASM support.
+//! Includes the `.rvdna` binary file format for storing pre-computed
+//! AI features alongside raw DNA sequences.
+//!
+//! - **K-mer HNSW Indexing**: Sequence similarity search via vector embeddings
+//! - **Smith-Waterman Alignment**: Local alignment with CIGAR and mapping quality
+//! - **Bayesian Variant Calling**: SNP/indel detection with Phred quality scores
+//! - **Protein Translation**: DNA-to-protein with GNN contact graph prediction
+//! - **Epigenomics**: Methylation profiling and Horvath biological age clock
+//! - **Pharmacogenomics**: CYP enzyme star allele calling and drug recommendations
+//! - **Pipeline Orchestration**: DAG-based multi-stage execution
+//! - **RVDNA Format**: AI-native binary file format with pre-computed tensors
+
+#![warn(missing_docs)]
+#![allow(clippy::all)]
+
+pub mod alignment;
+pub mod biomarker;
+pub mod biomarker_stream;
+pub mod epigenomics;
+pub mod error;
+pub mod genotyping;
+pub mod health;
+pub mod kmer;
+pub mod kmer_pagerank;
+pub mod pharma;
+pub mod pipeline;
+pub mod protein;
+pub mod real_data;
+pub mod rvdna;
+pub mod types;
+pub mod variant;
+
+pub use alignment::{AlignmentConfig, SmithWaterman};
+pub use epigenomics::{
+    CancerSignalDetector, CancerSignalResult, CpGSite, HorvathClock, MethylationProfile,
+};
+pub use error::{DnaError, Result};
+pub use pharma::{
+    call_cyp2c19_allele, call_star_allele, get_recommendations, predict_cyp2c19_phenotype,
+    predict_phenotype, Cyp2c19Allele, DrugRecommendation, MetabolizerPhenotype, PharmaVariant,
+    StarAllele,
+};
+pub use protein::{isoelectric_point, molecular_weight, translate_dna, AminoAcid};
+pub use rvdna::{
+    decode_2bit, encode_2bit, fasta_to_rvdna, Codec, KmerVectorBlock, RvdnaHeader, RvdnaReader,
+    RvdnaStats, RvdnaWriter, SparseAttention, VariantTensor,
+};
+pub use types::{
+    AlignmentResult, AnalysisConfig, CigarOp, ContactGraph, DnaSequence, GenomicPosition,
+    KmerIndex, Nucleotide, ProteinResidue, ProteinSequence, QualityScore, Variant,
+};
+pub use variant::{
+    FilterStatus, Genotype, PileupColumn, VariantCall, VariantCaller, VariantCallerConfig,
+};
+
+pub use ruvector_core::{
+    types::{DbOptions, DistanceMetric, HnswConfig, SearchQuery, SearchResult, VectorEntry},
+    VectorDB,
+};
+
+pub use biomarker::{BiomarkerClassification, BiomarkerProfile, BiomarkerReference, CategoryScore};
+pub use biomarker_stream::{
+    BiomarkerReading, RingBuffer, StreamConfig, StreamProcessor, StreamStats,
+};
+pub use genotyping::{
+    CallConfidence, CypDiplotype, GenomeBuild, GenotypeAnalysis, GenotypeData, Snp,
+};
+pub use health::{ApoeResult, HealthVariantResult, MthfrResult, PainProfile};
+pub use kmer_pagerank::{KmerGraphRanker, SequenceRank};
+
+/// Prelude module for common imports
+pub mod prelude {
+    pub use crate::alignment::*;
+    pub use crate::epigenomics::*;
+    pub use crate::error::{DnaError, Result};
+    pub use crate::kmer::*;
+    pub use crate::pharma::*;
+    pub use crate::protein::*;
+    pub use crate::types::*;
+    pub use crate::variant::*;
+}