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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)
29 lines
1.8 KiB
Markdown
29 lines
1.8 KiB
Markdown
# `IFragments` Functionality Overview
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The `IFragments()` function in the `obiiter` package implements a parallelized sequence fragmentation pipeline for biological sequences. It is designed to split long nucleotide or protein sequences into smaller, overlapping fragments while preserving metadata and enabling concurrent processing.
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## Core Parameters
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- `minsize`: Minimum sequence length to skip fragmentation.
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- `length`: Desired fragment size (in bases/amino acids).
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- `overlap`: Number of overlapping residues between consecutive fragments.
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- `size`, `nworkers`: Batch size and number of worker goroutines (currently unused in active logic).
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## Workflow
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1. **Batch Sorting**: Input sequences are batched and sorted for efficient processing.
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2. **Parallel Fragmentation**:
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- Each worker processes a subset of batches independently using goroutines.
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- For each sequence longer than `minsize`, it is split into overlapping fragments of length `length` with step size = `length - overlap`.
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- The final fragment is extended to cover the remainder (fusion mode), avoiding tiny trailing pieces.
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3. **Resource Management**:
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- Original sequences are recycled (`s.Recycle()`) to optimize memory usage.
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- Fragments are reassembled into batches, sorted by source and order, then rebatched to respect memory/size limits.
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## Key Features
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- **Overlap handling**: Ensures contiguous coverage without gaps.
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- **Memory efficiency**: Uses recycling and batched output.
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- **Scalability**: Leverages Go concurrency via `nworkers`.
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- **Error safety**: Panics on subsequence errors (e.g., invalid indices).
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## Use Case
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Ideal for preparing long-read sequencing data (e.g., PacBio, Nanopore) or assembled contigs for downstream analysis requiring fixed-length inputs (e.g., k-mer indexing, ML inference).
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