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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)
35 lines
1.6 KiB
Markdown
35 lines
1.6 KiB
Markdown
# ObiDefault Package: Batch Configuration Module
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This Go module provides centralized configuration for sequence batching in Obitools, supporting both **count-based** and **memory-aware** batch processing.
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## Core Features
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- `_BatchSize` / `SetBatchSize()`
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Defines and configures the *minimum* number of sequences per batch (default: `1`).
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Used internally as `minSeqs` in `RebatchBySize`.
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- `_BatchSizeMax()` / `SetBatchSizeMax()`
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Sets the *maximum* sequences per batch (default: `2000`). Batches are flushed upon reaching this limit, regardless of memory.
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- **CLI & Environment Integration**
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Batch size is determined by `--batch-size` CLI flag and/or the `OBIBATCHSIZE` environment variable (via parsing logic not shown here but implied by comments).
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- `_BatchMem()` / `SetBatchMem(n int)`
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Configures the *maximum memory per batch* (default: `128 MB`). A value of `0` disables memory-based batching, falling back to pure count-based logic.
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- `_BatchMemStr()`
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Stores the *raw CLI string* passed to `--batch-mem` (e.g., `"256M"`, `"1G"`), enabling human-readable input parsing elsewhere.
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## Utility Functions
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- `BatchSizePtr()`, `BatchMemPtr()`
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Expose pointers to internal variables for direct modification or inter-process sharing.
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- `BatchSizeMaxPtr()`, `BatchMemStrPtr()`
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Provide read/write access to max-size and raw memory string values.
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## Design Intent
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- Separates **configuration** (defaults, CLI/env parsing) from **processing logic**, enabling modular and testable batch handling.
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- Supports both scalable, large-scale processing (via count limits) and memory-constrained environments (via soft RAM caps).
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