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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)
36 lines
1.7 KiB
Markdown
36 lines
1.7 KiB
Markdown
# `NumberSequences` Function — Semantic Description
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The `NumberSequences` method assigns a unique sequential identifier (`seq_number`) to each biological sequence in an `IBioSequence` iterator, preserving consistency for paired-end reads.
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## Core Functionality
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- **Sequential numbering**: Assigns integers (starting from `start`, defaulting to 0 or user-defined) incrementally across sequences.
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- **Thread-safe**: Uses `sync.Mutex` and `atomic.Int64` to safely manage the global counter during concurrent processing.
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- **Paired-read support**: When input is paired (`IsPaired()`), both reads in a pair receive the *same* `seq_number`, ensuring alignment between mates.
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## Parallelization Strategy
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- **Default mode**: Uses multiple workers (`ParallelWorkers()`) for performance; batches are processed concurrently.
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- **Reordering mode**: If `forceReordering` is true:
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- Input iterator is batch-sorted (`SortBatches()`).
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- Parallelism disabled (1 worker) to ensure deterministic numbering order.
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## Implementation Details
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- Each goroutine processes its own split of the input iterator.
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- A shared `next_first` counter tracks the next available sequence number globally.
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- Locking ensures atomic increment and assignment, preventing race conditions.
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## Output
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Returns a new `IBioSequence` iterator:
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- Contains the same sequence batches (possibly reordered if sorted).
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- Each `BioSequence` object now carries a `"seq_number"` attribute.
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- Paired sequences are co-numbered and marked accordingly.
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## Use Cases
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- Preparing data for downstream tools requiring unique sequence IDs.
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- Maintaining cross-read identity in paired-end workflows (e.g., assembly, mapping).
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- Reproducible numbering across pipeline stages or restarts.
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