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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)
36 lines
1.8 KiB
Markdown
36 lines
1.8 KiB
Markdown
# BioSequence Reverse Complement Functionality
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This Go package (`obiseq`) provides utilities for computing the reverse complement of biological sequences (e.g., DNA), including support for quality scores and structured metadata.
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## Core Functions
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- **`nucComplement(n byte) byte`**
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Returns the nucleotide complement using a lookup table (`_revcmpDNA`). Handles special cases:
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- `.` / `-` → unchanged (gaps)
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- `[`, `]` → swapped (`[` ↔ `]`)
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- A–Z letters → complemented (case-insensitive via bitwise masking)
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- Unknown characters → `'n'`
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- **`BioSequence.ReverseComplement(inplace bool) *BioSequence`**
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Performs reverse complement on the sequence and (if present) its quality string:
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- If `inplace = false`, a copy is made; original preserved.
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- Reverses indices and complements each base using `nucComplement`.
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- Also reverses the quality array symmetrically.
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- Caches result in `sequence.revcomp` for reuse.
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- **`BioSequence._revcmpMutation() *BioSequence`**
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Adjusts mutation metadata (e.g., `"pairing_mismatches"`) to reflect the reversed-complement orientation:
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- Reverses and complements symbolic mutation strings (e.g., `"A>T"` → `"T>A"`).
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- Updates positional indices to match reversed sequence coordinates.
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- **`ReverseComplementWorker(inplace bool) SeqWorker`**
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Returns a reusable `SeqWorker` function for batch processing: applies reverse complement to each sequence in a stream.
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## Design Notes
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- Uses ASCII bitwise tricks (`&31`, `|0x20`) for case-insensitive indexing and lowercase output.
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- Supports non-standard symbols (e.g., IUPAC ambiguity codes via lookup table).
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- Integrates quality scores and structured attributes seamlessly.
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> Ideal for NGS preprocessing pipelines where orientation matters (e.g., paired-end alignment, variant calling).
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