Merge commit 'd803bfe2b1fe7f5e219e50ac20d6801a0a58ac75' as 'vendor/ruvector'

vendor/ruvector/examples/dna/tests/pipeline_tests.rs

@@ -0,0 +1,353 @@
+//! End-to-End Integration Tests for DNA Analysis Pipeline
+//!
+//! Real data, real computation, real assertions. No mocks, no stubs.
+//! Tests the complete DNA analysis workflow from nucleotide encoding
+//! through variant calling, protein translation, epigenetics, and pharmacogenomics.
+
+use ::rvdna::*;
+
+// ============================================================================
+// NUCLEOTIDE & SEQUENCE TESTS
+// ============================================================================
+
+#[test]
+fn test_nucleotide_encoding() {
+    assert_eq!(Nucleotide::A.to_u8(), 0);
+    assert_eq!(Nucleotide::C.to_u8(), 1);
+    assert_eq!(Nucleotide::G.to_u8(), 2);
+    assert_eq!(Nucleotide::T.to_u8(), 3);
+    assert_eq!(Nucleotide::N.to_u8(), 4);
+
+    assert_eq!(Nucleotide::from_u8(0).unwrap(), Nucleotide::A);
+    assert_eq!(Nucleotide::from_u8(1).unwrap(), Nucleotide::C);
+    assert_eq!(Nucleotide::from_u8(2).unwrap(), Nucleotide::G);
+    assert_eq!(Nucleotide::from_u8(3).unwrap(), Nucleotide::T);
+    assert_eq!(Nucleotide::from_u8(4).unwrap(), Nucleotide::N);
+}
+
+#[test]
+fn test_dna_sequence_reverse_complement() {
+    let seq1 = DnaSequence::from_str("ACGT").unwrap();
+    let rc1 = seq1.reverse_complement();
+    assert_eq!(rc1.to_string(), "ACGT");
+
+    let seq2 = DnaSequence::from_str("AACG").unwrap();
+    let rc2 = seq2.reverse_complement();
+    assert_eq!(rc2.to_string(), "CGTT");
+
+    let seq3 = DnaSequence::from_str("ATGCATGC").unwrap();
+    let rc3 = seq3.reverse_complement();
+    assert_eq!(rc3.to_string(), "GCATGCAT");
+}
+
+// ============================================================================
+// VARIANT CALLING TESTS
+// ============================================================================
+
+#[test]
+fn test_variant_calling_homozygous_snp() {
+    let caller = VariantCaller::new(VariantCallerConfig::default());
+
+    let pileup = PileupColumn {
+        bases: vec![b'G'; 15],
+        qualities: vec![40; 15],
+        position: 1000,
+        chromosome: 1,
+    };
+
+    let call = caller.call_snp(&pileup, b'A').expect("Should call variant");
+    assert_eq!(call.genotype, Genotype::HomAlt);
+    assert_eq!(call.alt_allele, b'G');
+    assert_eq!(call.ref_allele, b'A');
+    assert!(call.quality > 20.0);
+}
+
+#[test]
+fn test_variant_calling_heterozygous_snp() {
+    let caller = VariantCaller::new(VariantCallerConfig::default());
+
+    let mut bases = vec![b'A'; 10];
+    bases.extend(vec![b'G'; 10]);
+
+    let pileup = PileupColumn {
+        bases,
+        qualities: vec![40; 20],
+        position: 2000,
+        chromosome: 1,
+    };
+
+    let call = caller.call_snp(&pileup, b'A').expect("Should call variant");
+    assert_eq!(call.genotype, Genotype::Het);
+    assert_eq!(call.alt_allele, b'G');
+    assert!(call.quality > 20.0);
+}
+
+#[test]
+fn test_variant_calling_no_variant() {
+    let caller = VariantCaller::new(VariantCallerConfig::default());
+
+    let pileup = PileupColumn {
+        bases: vec![b'A'; 20],
+        qualities: vec![40; 20],
+        position: 3000,
+        chromosome: 1,
+    };
+
+    let call = caller.call_snp(&pileup, b'A');
+    if let Some(c) = call {
+        assert_eq!(c.ref_allele, b'A');
+        assert!((c.allele_depth as f32 / c.depth as f32) < 0.2);
+    }
+}
+
+#[test]
+fn test_variant_quality_filtering() {
+    let mut config = VariantCallerConfig::default();
+    config.min_quality = 30;
+    config.min_depth = 10;
+    let caller = VariantCaller::new(config);
+
+    let mut calls = vec![
+        VariantCall {
+            chromosome: 1,
+            position: 1000,
+            ref_allele: b'A',
+            alt_allele: b'G',
+            quality: 35.0,
+            genotype: Genotype::Het,
+            depth: 20,
+            allele_depth: 10,
+            filter_status: FilterStatus::Pass,
+        },
+        VariantCall {
+            chromosome: 1,
+            position: 2000,
+            ref_allele: b'C',
+            alt_allele: b'T',
+            quality: 25.0,
+            genotype: Genotype::Het,
+            depth: 20,
+            allele_depth: 10,
+            filter_status: FilterStatus::Pass,
+        },
+        VariantCall {
+            chromosome: 1,
+            position: 3000,
+            ref_allele: b'G',
+            alt_allele: b'A',
+            quality: 40.0,
+            genotype: Genotype::Het,
+            depth: 5,
+            allele_depth: 2,
+            filter_status: FilterStatus::Pass,
+        },
+    ];
+
+    caller.filter_variants(&mut calls);
+    assert_eq!(calls[0].filter_status, FilterStatus::Pass);
+    assert_eq!(calls[1].filter_status, FilterStatus::LowQuality);
+    assert_eq!(calls[2].filter_status, FilterStatus::LowDepth);
+}
+
+// ============================================================================
+// PROTEIN TRANSLATION TESTS
+// ============================================================================
+
+#[test]
+fn test_protein_translation() {
+    use ::rvdna::protein::{translate_dna, AminoAcid};
+    let proteins = translate_dna(b"ATGGCAGGT");
+    assert_eq!(proteins.len(), 3);
+    assert_eq!(proteins[0], AminoAcid::Met);
+    assert_eq!(proteins[1], AminoAcid::Ala);
+    assert_eq!(proteins[2], AminoAcid::Gly);
+}
+
+#[test]
+fn test_protein_translation_stop_codon() {
+    use ::rvdna::protein::{translate_dna, AminoAcid};
+    let p1 = translate_dna(b"ATGGCATAA");
+    assert_eq!(p1.len(), 2);
+    assert_eq!(p1[0], AminoAcid::Met);
+
+    let p2 = translate_dna(b"ATGGCATAG");
+    assert_eq!(p2.len(), 2);
+
+    let p3 = translate_dna(b"ATGGCATGA");
+    assert_eq!(p3.len(), 2);
+}
+
+#[test]
+fn test_amino_acid_hydrophobicity() {
+    use ::rvdna::protein::AminoAcid;
+    assert_eq!(AminoAcid::Ile.hydrophobicity(), 4.5);
+    assert_eq!(AminoAcid::Arg.hydrophobicity(), -4.5);
+    assert_eq!(AminoAcid::Val.hydrophobicity(), 4.2);
+    assert_eq!(AminoAcid::Lys.hydrophobicity(), -3.9);
+    assert_eq!(AminoAcid::Gly.hydrophobicity(), -0.4);
+}
+
+// ============================================================================
+// EPIGENETICS TESTS
+// ============================================================================
+
+#[test]
+fn test_methylation_profile_creation() {
+    let positions = vec![(1, 1000), (1, 2000), (2, 3000), (2, 4000)];
+    let betas = vec![0.1, 0.5, 0.8, 0.3];
+    let profile = MethylationProfile::from_beta_values(positions, betas);
+    assert_eq!(profile.sites.len(), 4);
+    let mean = profile.mean_methylation();
+    assert!((mean - 0.425).abs() < 0.001);
+}
+
+#[test]
+fn test_horvath_clock_prediction() {
+    let clock = HorvathClock::default_clock();
+    let positions: Vec<(u8, u64)> = (0..700).map(|i| (1, i * 1000)).collect();
+    let betas: Vec<f32> = (0..700)
+        .map(|i| {
+            if i < 100 {
+                0.3
+            } else if i < 200 {
+                0.7
+            } else {
+                0.5
+            }
+        })
+        .collect();
+    let profile = MethylationProfile::from_beta_values(positions, betas);
+    let predicted_age = clock.predict_age(&profile);
+    assert!(predicted_age > 0.0);
+    assert!(predicted_age < 150.0);
+}
+
+// ============================================================================
+// PHARMACOGENOMICS TESTS
+// ============================================================================
+
+#[test]
+fn test_pharma_star_allele_calling() {
+    assert_eq!(call_star_allele(&[]), StarAllele::Star1);
+    assert_eq!(
+        call_star_allele(&[(42130692, b'G', b'A')]),
+        StarAllele::Star4
+    );
+    assert_eq!(
+        call_star_allele(&[(42126611, b'T', b'-')]),
+        StarAllele::Star5
+    );
+}
+
+#[test]
+fn test_pharma_metabolizer_phenotype() {
+    assert_eq!(
+        predict_phenotype(&StarAllele::Star1, &StarAllele::Star1),
+        MetabolizerPhenotype::Normal
+    );
+    assert_eq!(
+        predict_phenotype(&StarAllele::Star1, &StarAllele::Star4),
+        MetabolizerPhenotype::Normal
+    );
+    assert_eq!(
+        predict_phenotype(&StarAllele::Star4, &StarAllele::Star4),
+        MetabolizerPhenotype::Poor
+    );
+}
+
+// ============================================================================
+// ALIGNMENT TESTS
+// ============================================================================
+
+#[test]
+fn test_smith_waterman_alignment() {
+    let aligner = SmithWaterman::new(AlignmentConfig::default());
+    let query = DnaSequence::from_str("ACGT").unwrap();
+    let reference = DnaSequence::from_str("ACGT").unwrap();
+    let result = aligner.align(&query, &reference).unwrap();
+    assert_eq!(result.score, 8); // 4 matches * 2 points each
+}
+
+#[test]
+fn test_attention_alignment() {
+    let query = DnaSequence::from_str("ATCGATCG").unwrap();
+    let reference = DnaSequence::from_str("TTTTATCGATCGTTTT").unwrap();
+    let alignment = query.align_with_attention(&reference).unwrap();
+    assert!(alignment.score > 0);
+}
+
+// ============================================================================
+// FULL PIPELINE INTEGRATION
+// ============================================================================
+
+#[test]
+fn test_pipeline_config_defaults() {
+    let config = AnalysisConfig::default();
+    assert_eq!(config.kmer_size, 11);
+    assert_eq!(config.vector_dims, 512);
+    assert_eq!(config.min_quality, 20);
+    assert!(config.parameters.is_empty());
+}
+
+#[test]
+fn test_full_pipeline_runs() {
+    // 1. Create and manipulate DNA
+    let dna_seq = DnaSequence::from_str("ATGCGATCGATCGATCGATCGTAGCTAGCTAGC").unwrap();
+    let rev_comp = dna_seq.reverse_complement();
+    assert_eq!(rev_comp.len(), dna_seq.len());
+
+    // 2. K-mer vector
+    let kmer_vec = dna_seq.to_kmer_vector(11, 512).unwrap();
+    assert_eq!(kmer_vec.len(), 512);
+
+    // 3. Variant calling
+    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![40; 10],
+        position: 1000,
+        chromosome: 1,
+    };
+    assert!(caller.call_snp(&pileup, b'A').is_some());
+
+    // 4. Protein translation
+    let proteins = translate_dna(b"ATGGCAGGTAAACCC");
+    assert!(!proteins.is_empty());
+
+    // 5. Methylation + Horvath
+    let profile = MethylationProfile::from_beta_values(
+        vec![(1, 1000), (1, 2000), (1, 3000)],
+        vec![0.3, 0.5, 0.7],
+    );
+    let age = HorvathClock::default_clock().predict_age(&profile);
+    assert!(age > 0.0);
+
+    // 6. Pharmacogenomics
+    let allele = call_star_allele(&[(42130692, b'G', b'A')]);
+    assert_eq!(allele, StarAllele::Star4);
+    let phenotype = predict_phenotype(&allele, &StarAllele::Star1);
+    assert_eq!(phenotype, MetabolizerPhenotype::Normal);
+
+    // 7. Alignment
+    let alignment = dna_seq.align_with_attention(&rev_comp).unwrap();
+    assert!(alignment.score > 0);
+
+    // 8. Protein contact graph
+    let protein = ProteinSequence::new(vec![
+        ProteinResidue::A,
+        ProteinResidue::V,
+        ProteinResidue::L,
+        ProteinResidue::I,
+        ProteinResidue::F,
+        ProteinResidue::G,
+        ProteinResidue::K,
+        ProteinResidue::D,
+        ProteinResidue::E,
+        ProteinResidue::R,
+        ProteinResidue::M,
+        ProteinResidue::N,
+    ]);
+    let graph = protein.build_contact_graph(8.0).unwrap();
+    let contacts = protein.predict_contacts(&graph).unwrap();
+    assert!(!contacts.is_empty());
+}