obitools4/autodoc/docmd/pkg/obiseq/revcomp.md

BioSequence Reverse Complement Functionality

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.

Core Functions

• nucComplement(n byte) byte
  Returns the nucleotide complement using a lookup table (_revcmpDNA). Handles special cases:

  • . / - → unchanged (gaps)
  • [, ] → swapped ([ ↔ ])
  • A–Z letters → complemented (case-insensitive via bitwise masking)
  • Unknown characters → 'n'

• BioSequence.ReverseComplement(inplace bool) *BioSequence
  Performs reverse complement on the sequence and (if present) its quality string:

  • If inplace = false, a copy is made; original preserved.
  • Reverses indices and complements each base using nucComplement.
  • Also reverses the quality array symmetrically.
  • Caches result in sequence.revcomp for reuse.

• BioSequence._revcmpMutation() *BioSequence
  Adjusts mutation metadata (e.g., "pairing_mismatches") to reflect the reversed-complement orientation:

  • Reverses and complements symbolic mutation strings (e.g., "A>T" → "T>A").
  • Updates positional indices to match reversed sequence coordinates.

• ReverseComplementWorker(inplace bool) SeqWorker
  Returns a reusable SeqWorker function for batch processing: applies reverse complement to each sequence in a stream.

Design Notes

• Uses ASCII bitwise tricks (&31, |0x20) for case-insensitive indexing and lowercase output.
• Supports non-standard symbols (e.g., IUPAC ambiguity codes via lookup table).
• Integrates quality scores and structured attributes seamlessly.

Ideal for NGS preprocessing pipelines where orientation matters (e.g., paired-end alignment, variant calling).