obitools4/autodoc/docmd/pkg/obiiter/paired.md

Paired-End Sequence Handling in obiiter

This Go package provides semantic functionality for managing paired-end biological sequences within batched iterators.

• BioSequenceBatch methods:

  • IsPaired(): Checks whether the batch contains paired reads.
  • PairedWith(): Returns a new batch containing only the mate (partner) of each read in the current batch.
  • PairTo(*BioSequenceBatch): Synchronizes and pairs reads between two batches of identical order; fails if orders differ.
  • UnPair(): Removes pairing metadata, treating reads as unpaired.

• IBioSequence (iterator) methods:

  • MarkAsPaired(): Marks the iterator as producing paired-end data.
  • PairTo(IBioSequence): Combines two iterators into a new paired-end iterator by aligning corresponding batches and calling PairTo on each pair.
  • PairedWith(): Generates a new iterator yielding only the mate reads (i.e., second ends) from an existing paired-end stream.
  • IsPaired(): Returns whether the iterator was explicitly marked as paired.

All operations preserve batched processing and concurrency via goroutines, ensuring efficient handling of large NGS datasets while maintaining semantic correctness for paired-end workflows.