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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)
49 lines
1.9 KiB
Markdown
49 lines
1.9 KiB
Markdown
# SuperKmer and Minimizer-Based Sliding Window Analysis
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This Go package provides functionality for extracting *super k-mers* from DNA sequences using a minimizer-based sliding window approach.
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## Core Concepts
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- **K-mers**: Substrings of length `k` from a DNA sequence.
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- **Minimizer**: The lexicographically smallest canonical *m*-mer (substring of length `m`) among all `(k − m + 1)` overlapping *m*-mers in a given k-mer.
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- **Super K-mer**: A maximal contiguous subsequence where *every* consecutive k-mer shares the **same minimizer**.
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## Data Structures
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### `SuperKmer`
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Represents a maximal region with uniform minimizer:
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- `Minimizer`: Canonical 64-bit hash of the shared m-mer.
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- `Start`, `End`: Slice-style bounds (0-indexed, exclusive end).
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- `Sequence`: Raw byte slice of the DNA subsequence.
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### `dequeItem`
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Used internally to maintain a monotone deque:
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- `position`: Index of the m-mer in the sequence.
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- `canonical`: Canonical hash value (e.g., lexicographically smallest of forward/reverse-complement).
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## Main Function
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### `ExtractSuperKmers(seq, k, m, buffer)`
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- Extracts all maximal super k-mers from `seq`.
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- Parameters validated:
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- `1 ≤ m < k`,
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- `2 ≤ k ≤ 31`,
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- sequence length ≥ `k`.
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- Uses an efficient **O(n)** time algorithm via internal iteration.
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- Supports optional preallocation (`buffer`) to reduce memory allocations.
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## Algorithm Highlights
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- Maintains a sliding window of size `k − m + 1` over *m*-mers.
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- Tracks the current minimizer using a monotone deque for O(1) updates per step.
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- Detects *minimizer transitions* to delimit super k-mer boundaries.
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## Complexity
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| Aspect | Bound |
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|---------------|-------------------------------|
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| Time | **O(n)** (linear in sequence length) |
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| Space | **O(k − m + 1)** for deque + output size |
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Useful in genome compression, read clustering, and minimizer-based alignment acceleration.
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