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https://github.com/ruvnet/RuVector.git
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9638ba38de
Implements a comprehensive DNA analyzer demonstrating RuVector's vector computing capabilities for bioinformatics: Modules (9): - types: Core domain types (DnaSequence, Nucleotide, ProteinSequence, etc.) - kmer: HNSW k-mer indexing with FNV-1a hashing and MinHash sketching - alignment: Smith-Waterman local alignment with CIGAR generation - variant: SNP calling from pileup data with genotype classification - protein: DNA-to-protein translation with contact graph prediction - epigenomics: Horvath clock biological age prediction from CpG methylation - pharma: CYP2D6 star allele calling and metabolizer phenotype prediction - pipeline: DAG-based genomic analysis orchestration - error: Typed error handling across all modules Testing (41 tests, 0 mocks): - 12 k-mer integration tests (encoding, HNSW search, MinHash Jaccard) - 17 pipeline e2e tests (alignment, variant calling, pharmacogenomics) - 12 security tests (buffer overflow, path traversal, concurrency, bounds) Benchmarks: Criterion suite for kmer, alignment, variant, protein, pipeline Binary: 7-stage demo (sequence gen, k-mer search, alignment, variant calling, protein analysis, epigenomics, pharmacogenomics) https://claude.ai/code/session_013B6stXbYwAkWHbE16sjUrq
54 lines
1.4 KiB
Rust
54 lines
1.4 KiB
Rust
//! Error types for DNA analysis operations
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use thiserror::Error;
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/// DNA analysis error types
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#[derive(Error, Debug)]
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pub enum DnaError {
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/// Invalid DNA sequence (e.g., non-ACGTN characters)
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#[error("Invalid DNA sequence: {0}")]
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InvalidSequence(String),
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/// K-mer indexing error
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#[error("K-mer index error: {0}")]
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IndexError(String),
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/// Sequence alignment error
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#[error("Alignment error: {0}")]
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AlignmentError(String),
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/// Variant calling error
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#[error("Variant calling error: {0}")]
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VariantCallError(String),
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/// Analysis pipeline error
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#[error("Pipeline error: {0}")]
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PipelineError(String),
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/// I/O error
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#[error("I/O error: {0}")]
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IoError(#[from] std::io::Error),
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/// RuVector core error
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#[error("Vector database error: {0}")]
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VectorDbError(#[from] ruvector_core::RuvectorError),
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/// Dimension mismatch
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#[error("Dimension mismatch: expected {expected}, got {actual}")]
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DimensionMismatch { expected: usize, actual: usize },
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/// Empty sequence
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#[error("Empty sequence provided")]
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EmptySequence,
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/// Invalid quality score
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#[error("Invalid quality score: {0}")]
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InvalidQuality(u8),
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/// Invalid k-mer size
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#[error("Invalid k-mer size: {0}")]
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InvalidKmerSize(usize),
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}
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/// Result type for DNA analysis operations
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pub type Result<T> = std::result::Result<T, DnaError>;
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