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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)
20 lines
1.5 KiB
Markdown
20 lines
1.5 KiB
Markdown
## Semantic Description of `obiseq` Package Functionality
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The `obiseq` package provides core bioinformatics utilities for nucleic acid sequence manipulation in Go. It centers around two key operations:
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- **Nucleotide Complementation (`nucComplement`)**
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Implements standard Watson-Crick base pairing rules: `A↔T`, `C↔G`. It also handles ambiguous or symbolic characters (e.g., `'n' → 'n'`, `'[ ↔ ]'`), preserving non-standard symbols like gaps (`'-'`) and missing data (`'.'`). This function serves as the atomic building block for reverse-complement logic.
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- **Reverse Complementation (`BioSequence.ReverseComplement`)**
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A method on the `BioSequence` type that returns a new (or in-place modified) sequence representing:
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- The *reverse* of the original nucleotide string, followed by
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- Each base replaced with its complement (via `nucComplement`).
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The method supports two modes:
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- **Non-destructive (`inplace=false`)**: Returns a new `BioSequence`, leaving the original unchanged.
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- **In-place (`inplace=true`)**: Modifies and returns the same object for memory efficiency.
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Crucially, it preserves associated quality scores (e.g., Phred-scaled sequencing qualities), reversing their order to match the reversed sequence—ensuring correctness in downstream analyses like alignment or variant calling.
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Tests validate both functions across edge cases: degenerate bases, ambiguous symbols, and quality-aware sequences—confirming robustness for typical NGS (Next-Generation Sequencing) workflows.
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