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24 lines
1.4 KiB
Markdown
24 lines
1.4 KiB
Markdown
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## Semantic Description of `IsPatternMatchSequence`
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The function `IsPatternMatchSequence` defines a **sequence predicate** for pattern-based matching in biological sequences (e.g., DNA/RNA), supporting fuzzy and strand-aware search.
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### Core Functionality:
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- **Input Parameters**
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- `pattern`: A regular expression-like string describing the target pattern.
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- `errormax`: Maximum allowed mismatches (substitutions only by default).
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- `bothStrand`: If true, also search on the reverse-complement strand.
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- `allowIndels`: Enables insertion/deletion errors (beyond mismatches) when set to true.
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- **Internal Workflow**
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- Parses the pattern into an automaton (`apat`) via `MakeApatPattern`.
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- Computes its reverse complement for dual-strand matching.
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- Returns a closure (`SequencePredicate`) that tests whether a given `BioSequence` matches the pattern (or its RC), within error tolerance.
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- **Matching Logic**
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- Converts input sequence to `apat` format.
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- Checks match on forward strand first; if failed and `bothStrand=true`, tries reverse complement.
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- Uses automaton-based matching (`IsMatching`) for efficient fuzzy search.
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### Semantic Use Case:
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Enables flexible, error-tolerant detection of sequence motifs (e.g., primers, barcodes) in high-throughput sequencing data—supporting both *in silico* primer design validation and read filtering in metagenomic pipelines.
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