BitVecAlignmentScore

Documentation

API Reference

Description

Calculate alignment score between two bitvectors. Used in bioinformatics-style sequence alignment with match/mismatch scoring.

Parameters

Name	Direction	Description
`bv1`	in	First bitvector
`bv2`	in	Second bitvector
`match`	in	Score for matching bits
`mismatch`	in	Score for mismatching bits

Usage example (from documentation)

  int score = BitVecAlignmentScore(&seq1, &seq2, 2, -1);

Returns

Total alignment score

Usage example (Cross-references)

Usage examples (Cross-references)

In BitVec.c:1343:

    }
    
    int BitVecAlignmentScore(BitVec *bv1, BitVec *bv2, int match, int mismatch) {
        ValidateBitVec(bv1);
        ValidateBitVec(bv2);

In BitVec.Math.c:513:

    // Test BitVecAlignmentScore basic functionality
    bool test_bitvec_alignment_score_basic(void) {
        WriteFmt("Testing BitVecAlignmentScore basic functionality\n");
    
        BitVec bv1    = BitVecInit();

In BitVec.Math.c:527:

        BitVecPush(&bv2, true);
    
        int score = BitVecAlignmentScore(&bv1, &bv2, 2, -1);
        result    = result && (score == 6); // 3 matches * 2

In BitVec.Math.c:536:

        BitVecPush(&bv2, false);
    
        score  = BitVecAlignmentScore(&bv1, &bv2, 2, -1);
        result = result && (score == -3); // 3 mismatches * -1

In BitVec.Math.c:546:

    // Test BitVecAlignmentScore edge cases
    bool test_bitvec_alignment_score_edge_cases(void) {
        WriteFmt("Testing BitVecAlignmentScore edge cases\n");
    
        BitVec bv1    = BitVecInit();

In BitVec.Math.c:553:

    
        // Test empty bitvectors
        int score = BitVecAlignmentScore(&bv1, &bv2, 1, -1);
        result    = result && (score == 0);

In BitVec.Math.c:563:

        BitVecPush(&bv2, false);
    
        score  = BitVecAlignmentScore(&bv1, &bv2, 1, -1);
        result = result && (score == 2); // 2 matches

In BitVec.Math.c:647:

        double correlation = BitVecCorrelation(&bv1, &bv2);
        double entropy1    = BitVecEntropy(&bv1);
        int    align_score = BitVecAlignmentScore(&bv1, &bv2, 1, -1);
        u64    best_align  = BitVecBestAlignment(&bv1, &bv2);

In BitVec.Math.c:794:

    
    bool test_bitvec_alignment_score_null_bv1(void) {
        WriteFmt("Testing BitVecAlignmentScore(NULL, bv2, 1, -1) - should fatal\n");
        BitVec bv2 = BitVecInit();
        BitVecPush(&bv2, true);

In BitVec.Math.c:797:

        BitVec bv2 = BitVecInit();
        BitVecPush(&bv2, true);
        BitVecAlignmentScore(NULL, &bv2, 1, -1);
        BitVecDeinit(&bv2);
        return true;

In BitVec.Math.c:803:

    
    bool test_bitvec_alignment_score_null_bv2(void) {
        WriteFmt("Testing BitVecAlignmentScore(bv1, NULL, 1, -1) - should fatal\n");
        BitVec bv1 = BitVecInit();
        BitVecPush(&bv1, true);

In BitVec.Math.c:806:

        BitVec bv1 = BitVecInit();
        BitVecPush(&bv1, true);
        BitVecAlignmentScore(&bv1, NULL, 1, -1);
        BitVecDeinit(&bv1);
        return true;

Last updated on April 20, 2026

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