Crate rvdna 

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

Re-exports

pub use alignment::AlignmentConfig;

pub use alignment::SmithWaterman;

pub use epigenomics::CancerSignalDetector;

pub use epigenomics::CancerSignalResult;

pub use epigenomics::CpGSite;

pub use epigenomics::HorvathClock;

pub use epigenomics::MethylationProfile;

pub use error::DnaError;

pub use error::Result;

pub use pharma::call_cyp2c19_allele;

pub use pharma::call_star_allele;

pub use pharma::get_recommendations;

pub use pharma::predict_cyp2c19_phenotype;

pub use pharma::predict_phenotype;

pub use pharma::Cyp2c19Allele;

pub use pharma::DrugRecommendation;

pub use pharma::MetabolizerPhenotype;

pub use pharma::PharmaVariant;

pub use pharma::StarAllele;

pub use protein::isoelectric_point;

pub use protein::molecular_weight;

pub use protein::translate_dna;

pub use protein::AminoAcid;

pub use rvdna::decode_2bit;

pub use rvdna::encode_2bit;

pub use rvdna::fasta_to_rvdna;

pub use rvdna::Codec;

pub use rvdna::KmerVectorBlock;

pub use rvdna::RvdnaHeader;

pub use rvdna::RvdnaReader;

pub use rvdna::RvdnaStats;

pub use rvdna::RvdnaWriter;

pub use rvdna::SparseAttention;

pub use rvdna::VariantTensor;

pub use types::AlignmentResult;

pub use types::AnalysisConfig;

pub use types::CigarOp;

pub use types::ContactGraph;

pub use types::DnaSequence;

pub use types::GenomicPosition;

pub use types::KmerIndex;

pub use types::Nucleotide;

pub use types::ProteinResidue;

pub use types::ProteinSequence;

pub use types::QualityScore;

pub use types::Variant;

pub use variant::FilterStatus;

pub use variant::Genotype;

pub use variant::PileupColumn;

pub use variant::VariantCall;

pub use variant::VariantCaller;

pub use variant::VariantCallerConfig;

pub use genotyping::CallConfidence;

pub use genotyping::CypDiplotype;

pub use genotyping::GenomeBuild;

pub use genotyping::GenotypeAnalysis;

pub use genotyping::GenotypeData;

pub use genotyping::Snp;

pub use health::ApoeResult;

pub use health::HealthVariantResult;

pub use health::MthfrResult;

pub use health::PainProfile;

pub use biomarker::BiomarkerClassification;

pub use biomarker::BiomarkerProfile;

pub use biomarker::BiomarkerReference;

pub use biomarker::CategoryScore;

pub use biomarker_stream::BiomarkerReading;

pub use biomarker_stream::RingBuffer;

pub use biomarker_stream::StreamConfig;

pub use biomarker_stream::StreamProcessor;

pub use biomarker_stream::StreamStats;

pub use kmer_pagerank::KmerGraphRanker;

pub use kmer_pagerank::SequenceRank;

Modules

alignment

Sequence alignment module using attention-based scoring

biomarker

Composite health biomarker analysis engine – combines SNP genotype data with clinical biomarker reference ranges to produce composite risk scores, 64-dim profile vectors (for HNSW indexing), and synthetic populations.

biomarker_stream

Streaming biomarker data simulator with ring buffer and anomaly detection.

epigenomics

Epigenomics analysis module

error

Error types for DNA analysis operations

genotyping

Native 23andMe genotyping analysis

health

Health variant analysis for genotyping data

kmer

K-mer encoding and HNSW vector indexing for DNA sequences

kmer_pagerank

K-mer Graph PageRank for DNA Sequence Ranking

pharma

Pharmacogenomics module

pipeline

DAG-based genomic analysis pipeline orchestrator

prelude

Prelude module for common imports

protein

Protein translation and amino acid analysis module

real_data

Real DNA Reference Sequences from Public Databases

rvdna

RVDNA - AI-Native Genomic File Format

types

Core types for DNA analysis

variant

Variant calling module for DNA analysis

Structs

DbOptions

Database configuration options

HnswConfig

HNSW index configuration

SearchQuery

Search query parameters

SearchResult

Search result with similarity score

VectorDB

Main vector database

VectorEntry

Vector entry with metadata

Enums

DistanceMetric

Distance metric for similarity calculation