ternlang-core 0.3.3

Compiler and VM for Ternlang — balanced ternary language with affirm/tend/reject trit semantics, @sparseskip codegen, and BET bytecode execution.
Documentation 
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// Module:  stdlib/bio/sequence_align.tern
// Purpose: DNA/RNA Sequence Alignment
// Author:  RFI-IRFOS
// Ref:     https://ternlang.com

// Sequence alignment is inherently ternary: 
// Match (affirm), Gap/Indel (tend), Mismatch (reject).

fn compare_nucleotide_trit(base_a: trit, base_b: trit) -> trit {
    // If one is missing (tend), it's a gap
    if base_a == tend { return tend; }
    if base_b == tend { return tend; }
    
    if base_a == base_b { return affirm; } // Match
    return reject; // Mismatch
}

fn needleman_wunsch_score_trit(align_state: trit) -> float {
    // Converts alignment state to scoring matrix
    match align_state {
        affirm => { return 1.0; }  // Match bonus
        tend   => { return -0.5; } // Gap penalty
        reject => { return -1.0; } // Mismatch penalty
    }
}