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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)
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Semantic Description of KmerMap Functionality
The provided Go package implements a k-mer indexing and matching system for biological sequences (BioSequence). It supports both standard and sparse k-mer representations (where one position is masked, typically for handling ambiguous bases or symmetry).
Core Data Structures
KmerMap[T]: A generic hash map associating normalized k-mers (typeT, e.g., uint64 encoded in 2 bits per base) to lists of sequences containing them.KmerMatch: A map from sequence pointers to k-mer match counts, used for query results.
Key Features
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K-mer Normalization
- Handles both forward and reverse-complement k-mers.
- Selects the lexicographically smaller representation (canonical form).
- Supports sparse k-mers: when
SparseAt ≥ 0, the central base is ignored (replaced by#in string view), and k-mers are symmetrically normalized.
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Efficient Indexing (
Push)- Builds an index of all canonical k-mers from a set of sequences.
- Optionally limits per-k-mer storage (
maxocc), useful for filtering high-frequency k-mers (e.g., contaminants).
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Querying (
Query)- Given a query sequence, returns all sequences in the index sharing k-mers with it.
- Counts per-sequence how many shared k-mers exist (used for similarity estimation or clustering).
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Result Utilities (
KmerMatch)FilterMinCount: Remove low-count matches.Max(),Sequences(): Retrieve best match or all matched sequences.
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Construction (
NewKmerMap)- Automatically adjusts k-mer size: odd for sparse mode, even otherwise.
- Precomputes bitmasks for efficient k-mer manipulation (masking, shifting).
- Integrates progress bar during indexing.
Use Cases
- Read clustering (e.g., OTU/ASV picking).
- Error correction via k-mer abundance.
- Sequence similarity search or contamination screening.
The implementation leverages low-level bit operations for performance and memory efficiency, especially critical in large-scale NGS data processing.