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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
1.8 KiB
Markdown
33 lines
1.8 KiB
Markdown
# Semantic Description of `obiapat` Package Functionality
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The `obiapat` package provides utilities for constructing and representing **approximate sequence patterns**—flexible biological or symbolic string templates supporting mismatches, insertions, and deletions.
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## Core Functionality
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- **`MakeApatPattern(pattern string, errormax int, allowsIndel bool)`**
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Parses a pattern specification (e.g., `"A[T]C!GT"`) and returns an internal representation (`*ApatPattern`) suitable for approximate matching.
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- `pattern`: A string where:
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- Standard characters (e.g., `'A'`, `'C'`) denote exact matches.
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- Brackets `[X]` indicate *optional* or *variable positions*, e.g., ambiguity (like IUPAC codes).
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- Exclamation `!` marks positions where **errors** (substitutions) are permitted.
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- `errormax`: Maximum number of allowed errors (mismatches or indels, depending on flags).
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- `allowsIndel`: Boolean flag enabling/disabling insertion/deletion operations.
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## Behavior & Semantics
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- Returns a compiled pattern object (non-nil) on success; errors may arise from malformed input or invalid parameters.
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- Supports three modes:
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- **Exact matching** (`errormax = 0`, `allowsIndel = false`).
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- **Substitution-only approximation** (`errormax > 0`, `allowsIndel = false`).
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- **Full approximate matching with indels** (`errormax > 0`, `allowsIndel = true`).
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## Testing Coverage
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The provided test suite validates:
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- Valid pattern parsing across different configurations.
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- Correct handling of `nil` vs. non-nil output pointers.
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- Robustness against error conditions (e.g., invalid inputs would trigger expected errors).
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In summary, `obiapat` enables efficient definition and handling of *approximate regular expressions* tailored for sequence analysis in bioinformatics or pattern recognition contexts.
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