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31 lines
1.5 KiB
Markdown
31 lines
1.5 KiB
Markdown
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# Semantic Description of `obialign` Backtracking Module
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The `_Backtracking` function implements a **traceback algorithm** for sequence alignment, reconstructing the optimal path through an alignment matrix.
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## Core Functionality
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- **Input**:
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- `pathMatrix`: Encodes alignment decisions (match/mismatch/gap) as integers.
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- `lseqA`, `lseqB`: Lengths of sequences A and B.
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- `path`: Pre-allocated slice to store the traceback path.
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- **Output**: A compact representation of alignment steps, alternating between:
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- Diagonal moves (`ldiag`): Matches/mismatches (one step in both sequences).
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- Horizontal/vertical moves (`lleft` or `lup`): Gaps in sequence B (horizontal) or A (vertical).
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## Algorithm Highlights
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- **Reverse traversal** from `(lseqA−1, lseqB−1)` to origin.
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- **Batching logic**: Consecutive gaps in same direction are aggregated (e.g., `lleft += step`) to compress run-length encoding.
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- **Path reconstruction**: Steps are pushed *backwards* into the `path` slice using a moving pointer `p`.
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- **Memory efficiency**: Uses `slices.Grow()` to preallocate space and logs resizing for debugging.
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## Encoded Path Semantics
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Each pair in the returned slice encodes:
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- `[diag_count, move_type]`, where `move_type` is either a gap length (`lleft > 0`: horizontal, or `lup < 0`: vertical) or zero (end of diagonal run).
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## Use Case
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Enables efficient reconstruction and serialization of alignment paths—ideal for tools requiring low-level control over dynamic programming backtracking (e.g., pairwise aligners, edit-distance decompositions).
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