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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)
33 lines
1.7 KiB
Markdown
33 lines
1.7 KiB
Markdown
# Super K-mers Extraction Module (`obikmer`)
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This Go package provides efficient tools for extracting **super k-mers** from DNA sequences using *minimizer-based sliding windows*. Super k-mers are maximal contiguous subsequences sharing the same minimal canonical minimizer in a window of size `k`.
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## Core Functionality
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- **`IterSuperKmers(seq, k, m)`**
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Returns an iterator over `SuperKmer` structs. Each struct contains:
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- `Start`, `End`: genomic positions of the super k-mer in the original sequence
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- `Minimizer`: canonical minimizer value (uint64) for that segment
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- `Sequence`: the actual DNA subsequence
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- **`SuperKmer.ToBioSequence(...)`**
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Converts a raw `SuperKmer` into an enriched `obiseq.BioSequence`, embedding metadata:
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- ID: `{parentID}_superkmer_{start}_{end}`
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- Attributes: minimizer sequence (`minimizer_seq`), value, `k`, `m`, positions, and parent ID
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- **`SuperKmerWorker(k, m)`**
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A `SeqWorker` adapter for pipeline integration (e.g., with `obiiter`). Processes a full BioSequence and returns all extracted super k-mers as a slice of `BioSequence`s.
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## Algorithm Highlights
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- Uses **canonical minimizers** (forward/reverse-complement minimum) to ensure strand-invariance
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- Maintains a monotonic deque for efficient *sliding-window minimizer* tracking (O(n) time complexity)
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- Supports DNA bases `A/C/G/T/U` case-insensitively via bitmasking (`seq[i] & 31`)
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- Enforces parameter constraints: `1 ≤ m < k ≤ 31`, sequence length ≥ `k`
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## Use Cases
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- Read partitioning in metagenomics (e.g., for error correction or clustering)
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- Efficient k-mer space segmentation without storing all individual kmers
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- Integration into modular bioinformatics pipelines via `SeqWorker` interface
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