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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
37 lines
1.8 KiB
Markdown
37 lines
1.8 KiB
Markdown
# Semantic Description of `obikmer` Package
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This Go package provides utilities for **k-mer (specifically 4-mer) counting and comparison** of biological sequences.
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## Core Functionalities
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1. **`Count4Mer(seq, buffer, counts)`**
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Counts occurrences of all possible 16-mer (4-nucleotide) subsequences in a `BioSequence`.
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- Encodes each 4-mer into an integer (0–255) using `Encode4mer`.
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- Populates a fixed-size `[256]uint16` table (`Table4mer`) with counts.
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- Reuses or allocates the `counts` buffer as needed.
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2. **`Common4Mer(count1, count2)`**
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Computes the *intersection* of two 4-mer frequency profiles: sum over all k-mers of `min(count1[k], count2[k])`.
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Used to measure shared content between sequences.
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3. **`Sum4Mer(count)`**
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Returns the total number of 4-mers in a profile (i.e., sum over all entries).
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## Distance & Similarity Bounds
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4. **`LCS4MerBounds(count1, count2)`**
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Estimates bounds for the *Longest Common Subsequence* (LCS) length between two sequences based on 4-mer profiles:
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- **Lower bound**: `common_kmers + (3 if common > 0 else 0)`
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- **Upper bound**: `min(total1, total2) + 3 − ceil((min_total – common)/4)`
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Leverages the fact that overlapping k-mers constrain possible alignments.
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5. **`Error4MerBounds(count1, count2)`**
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Estimates bounds for *alignment errors* (e.g., mismatches + indels):
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- **Upper bound**: `max_total − common_kmers + 2 * floor((common_kmers + 5)/8)`
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- **Lower bound**: `ceil(upper_bound / 4)`
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Provides fast, approximate error estimates without full alignment.
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## Use Case
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Designed for **high-performance comparison of NGS reads** (e.g., in metabarcoding), where exact alignment is too costly, and k-mer-based heuristics enable scalable similarity estimation.
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