⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)
This commit is contained in:
Eric Coissac
2026-04-07 08:36:50 +02:00
parent 670edc1958
commit 8c7017a99d
392 changed files with 18875 additions and 141 deletions
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# Semantic Description of `obialign` Backtracking Module
The `_Backtracking` function implements a **traceback algorithm** for sequence alignment, reconstructing the optimal path through an alignment matrix.
## Core Functionality
- **Input**:
- `pathMatrix`: Encodes alignment decisions (match/mismatch/gap) as integers.
- `lseqA`, `lseqB`: Lengths of sequences A and B.
- `path`: Pre-allocated slice to store the traceback path.
- **Output**: A compact representation of alignment steps, alternating between:
- Diagonal moves (`ldiag`): Matches/mismatches (one step in both sequences).
- Horizontal/vertical moves (`lleft` or `lup`): Gaps in sequence B (horizontal) or A (vertical).
## Algorithm Highlights
- **Reverse traversal** from `(lseqA1, lseqB1)` to origin.
- **Batching logic**: Consecutive gaps in same direction are aggregated (e.g., `lleft += step`) to compress run-length encoding.
- **Path reconstruction**: Steps are pushed *backwards* into the `path` slice using a moving pointer `p`.
- **Memory efficiency**: Uses `slices.Grow()` to preallocate space and logs resizing for debugging.
## Encoded Path Semantics
Each pair in the returned slice encodes:
- `[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).
## Use Case
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).