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BitVecBestAlignment

BitVecBestAlignment

Description

Find best overlapping alignment between two bitvectors. Returns the offset that gives the best alignment score.

Parameters

Name Direction Description
bv1 in First bitvector (reference)
bv2 in Second bitvector (query)

Usage example (from documentation) 

  u64 offset = BitVecBestAlignment(&reference, &query);

Success

Returns the offset in bv1 at which bv2 produces the highest alignment score. Neither operand is modified.

Failure

Returns SIZE_MAX when either operand is empty or no candidate alignment yields a positive score. The bitvectors are not modified.

Usage example (Cross-references)

Usage examples (Cross-references) 
    }
    
    u64 BitVecBestAlignment(BitVec *bv1, BitVec *bv2) {
        ValidateBitVec(bv1);
        ValidateBitVec(bv2);
        DefaultAllocator alloc = DefaultAllocatorInit();
    
        WriteFmt("Testing BitVecBestAlignment basic functionality\n");
    
        BitVec bv1    = BitVecInit(ALLOCATOR_OF(&alloc));
        BitVecPush(&bv2, false);
    
        u64 best_pos = BitVecBestAlignment(&bv1, &bv2);
        result       = result && (best_pos == 0 || best_pos == 4);
        DefaultAllocator alloc = DefaultAllocatorInit();
    
        WriteFmt("Testing BitVecBestAlignment edge cases\n");
    
        BitVec bv1    = BitVecInit(ALLOCATOR_OF(&alloc));
    
        // Test empty bitvectors
        u64 best_pos = BitVecBestAlignment(&bv1, &bv2);
        result       = result && (best_pos == 0);
        BitVecPush(&bv2, false);
    
        best_pos = BitVecBestAlignment(&bv1, &bv2);
        result   = result && (best_pos == 0);
        double entropy1    = BitVecEntropy(&bv1);
        int    align_score = BitVecAlignmentScore(&bv1, &bv2, 1, -1);
        u64    best_align  = BitVecBestAlignment(&bv1, &bv2);
    
        // Test edit distance with smaller vectors (expensive operation)

        DefaultAllocator alloc = DefaultAllocatorInit();
    
        WriteFmt("Testing BitVecBestAlignment(NULL, bv2) - should fatal\n");
        BitVec bv2 = BitVecInit(ALLOCATOR_OF(&alloc));
        BitVecPush(&bv2, true);
        BitVec bv2 = BitVecInit(ALLOCATOR_OF(&alloc));
        BitVecPush(&bv2, true);
        BitVecBestAlignment(NULL, &bv2);
        BitVecDeinit(&bv2);
        DefaultAllocatorDeinit(&alloc);
        DefaultAllocator alloc = DefaultAllocatorInit();
    
        WriteFmt("Testing BitVecBestAlignment(bv1, NULL) - should fatal\n");
        BitVec bv1 = BitVecInit(ALLOCATOR_OF(&alloc));
        BitVecPush(&bv1, true);
        BitVec bv1 = BitVecInit(ALLOCATOR_OF(&alloc));
        BitVecPush(&bv1, true);
        BitVecBestAlignment(&bv1, NULL);
        BitVecDeinit(&bv1);
        DefaultAllocatorDeinit(&alloc);
Last updated on
BitVecAlignmentScoreBitVecClone