⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)
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Eric Coissac
2026-04-07 08:36:50 +02:00
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# `ISequenceChunkOnMemory` Function — Semantic Description
The function `Isequencechunkonmemory`, from the Go package `obichunk`, implements **asynchronous in-memory chunking** of biological sequence data.
It consumes an iterator over `BioSequence` objects and distributes them into **heterogeneous batches** using a provided classifier. The core purpose is to group sequences by classification (e.g., sample, taxon, or feature), store each group in memory as a slice (`BioSequenceSlice`), and emit them sequentially via an output iterator.
Key features:
- **Parallel processing**: Each classification group (referred to as a *flux*) is processed in its own goroutine.
- **Thread-safe aggregation**: A mutex ensures safe concurrent updates to shared `chunks` and `sources` maps.
- **Lazy emission**: Batches are emitted only after all classification groups have been fully processed (`jobDone.Wait()`).
- **Ordered output**: Batches are emitted in increasing `order` index (0, 1, …), preserving determinism despite parallel internal processing.
- **Error handling**: Critical failures (e.g., channel retrieval errors) terminate the program with `log.Fatalf`.
Input:
- An iterator (`obiiter.IBioSequence`) of raw sequences.
- A `*obiseq.BioSequenceClassifier`, used to route each sequence into a classification bucket.
Output:
- A new iterator yielding `BioSequenceBatch` objects, each containing all sequences belonging to one classification group and its source identifier.
Use case: Efficient parallel preprocessing of high-throughput sequencing data into sample- or taxon-specific batches for downstream analysis.