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20 lines
1.5 KiB
Markdown
20 lines
1.5 KiB
Markdown
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## `obialign` Package: Semantic Overview (≤50 lines)
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The `obialign` package provides a lightweight, high-performance utility for **detecting single-edit-distance relationships** between biological sequences (`obiseq.BioSequence`). Its core function, `D1Or0`, determines whether two sequences are either **identical** or differ by exactly **one substitution, insertion, or deletion (indel)**.
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- `abs[k]`: A generic helper computing absolute values for integers or floats (via Go generics).
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- `D1Or0(...)`: Returns a 4-tuple:
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- **`int` (first)**: `0` if identical, `1` if differing by one edit, `-1` otherwise.
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- **`int` (second)**: Position of the differing site (`-1` if identical).
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- **`byte`, `byte`**: Mismatched characters (or `'-'` for gaps indicating indels).
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**Algorithmic strategy:**
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1. Early rejection if length difference exceeds 1.
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2. Forward scan until first mismatch → identifies left boundary of divergence.
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3. Backward scan from ends to find rightmost match boundary.
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4. Validates whether the mismatch region allows exactly one edit:
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- Single substitution: equal lengths, single divergent position.
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- Insertion/deletion: length differs by 1 and only one non-overlapping character remains.
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Designed for speed in **OTU/ASV dereplication or error correction** pipelines (e.g., metabarcoding), where rapid filtering of near-identical sequences is critical. Does *not* compute full alignments; optimized for binary decision-making under strict edit constraints.
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