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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
1.3 KiB
Markdown
20 lines
1.3 KiB
Markdown
# Semantic Description of `IMergeSequenceBatch` and `MergePipe`
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This code defines two related functions in the `obiiter` package for batch-wise merging of biological sequences during iteration.
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- **`IMergeSequenceBatch(na, statsOn, sizes...) IBioSequence → IBioSequence`**
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- Consumes an input sequence iterator (`IBioSequence`) and returns a new one.
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- Groups incoming sequences into batches (default size: `100`, configurable via variadic argument).
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- For each batch:
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- Collects up to `batchsize` sequences via the input iterator.
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- Applies `.Merge(na, statsOn)` on each sequence group (presumably merging reads based on `na`, e.g., nucleotide alignment or overlap).
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- Wraps merged results into a `BioSequenceBatch` with ordering metadata.
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- Emits batches asynchronously via goroutines; the output iterator is closed when input finishes.
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- **`MergePipe(na, statsOn, sizes...) Pipeable → func(IBioSequence) IBioSequence`**
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- A *pipeline combinator* (higher-order function), enabling functional composition.
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- Returns a `Pipeable` — i.e., a transformation function compatible with iterator pipelines.
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**Semantic Purpose**:
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Enables efficient, memory-smoothed merging of biological sequence reads (e.g., paired-end merges) in streaming fashion, with optional statistics tracking (`statsOn`) and configurable batching.
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