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36 lines
1.8 KiB
Markdown
36 lines
1.8 KiB
Markdown
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# Semantic Description of `obikmer` Package
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The `obikmer` package provides efficient k-mer encoding and comparison utilities for biological sequences, optimized for DNA analysis.
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## Core Functionalities
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1. **Nucleotide Encoding**
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- `EncodeNucleotide(b byte)`: Maps DNA bases (A, C, G, T/U) to 2-bit values:
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`0→A`, `1→C`, `2→G`, `3→T/U`.
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Ambiguous or non-standard characters (e.g., N, R, Y) default to `A` (`0`).
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Uses a lookup table for O(1) performance.
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2. **4-mer Encoding**
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- `Encode4mer(seq, buffer)`: Converts a biological sequence into overlapping 4-mers.
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Each k-mer is encoded as an unsigned byte (0–255), where each nucleotide contributes 2 bits.
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Supports optional buffer reuse for memory efficiency.
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3. **4-mer Indexing**
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- `Index4mer(seq, index, buffer)`: Builds an inverted index mapping each 4-mer code (0–255) to all its occurrence positions in the sequence.
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Returns `[][]int`, where rows correspond to k-mer codes and columns list positions.
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4. **Fast Sequence Comparison**
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- `FastShiftFourMer(...)`: Compares two sequences using a FASTA-like shift-scoring algorithm.
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- Uses precomputed 4-mer index of a reference sequence and encodes the query.
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- Counts co-occurring 4-mers across all possible shifts (`refpos − queryPos`).
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- Computes raw and relative scores (normalized by alignment length).
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- Returns optimal shift, count of matching 4-mers, and maximum score (raw or relative).
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## Design Highlights
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- **Memory-aware**: Supports buffer reuse to minimize allocations.
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- **Robustness**: Non-canonical bases handled gracefully (defaulting to A).
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- **Performance-oriented**: O(n) encoding and indexing; efficient hash-based shift counting.
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Intended for rapid alignment-free sequence comparison in metabarcoding or metagenomic workflows.
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