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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)
18 lines
1.2 KiB
Markdown
18 lines
1.2 KiB
Markdown
# Paired-End Sequence Handling in `obiiter`
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This Go package provides semantic functionality for managing **paired-end biological sequences** within batched iterators.
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- `BioSequenceBatch` methods:
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- **`IsPaired()`**: Checks whether the batch contains paired reads.
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- **`PairedWith()`**: Returns a new batch containing only the mate (partner) of each read in the current batch.
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- **`PairTo(*BioSequenceBatch)`**: Synchronizes and pairs reads between two batches *of identical order*; fails if orders differ.
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- **`UnPair()`**: Removes pairing metadata, treating reads as unpaired.
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- `IBioSequence` (iterator) methods:
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- **`MarkAsPaired()`**: Marks the iterator as producing paired-end data.
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- **`PairTo(IBioSequence)`**: Combines two iterators into a new paired-end iterator by aligning corresponding batches and calling `PairTo` on each pair.
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- **`PairedWith()`**: Generates a new iterator yielding only the mate reads (i.e., second ends) from an existing paired-end stream.
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- **`IsPaired()`**: Returns whether the iterator was explicitly marked as paired.
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All operations preserve batched processing and concurrency via goroutines, ensuring efficient handling of large NGS datasets while maintaining semantic correctness for paired-end workflows.
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