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43 lines
2.1 KiB
Markdown
43 lines
2.1 KiB
Markdown
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# Semantic Description of `obialign` Package
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The `obialign` package provides high-performance functions for computing the **Longest Common Subsequence (LCS)** between two biological sequences, with support for error tolerance and end-gap-free alignment.
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## Core Algorithm
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- Implements a **Needleman-Wunsch** dynamic programming algorithm optimized for speed and memory efficiency.
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- Uses bit-packed encoding (`uint64`) to store score, path length, and gap status in a compact form.
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- Leverages **diagonal banding** to restrict computation only within the allowed error margin, reducing time and space complexity.
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## Scoring Scheme
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- **Match**: +1 point
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- **Mismatch or gap (indel)**: 0 points
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## Key Functions
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1. `FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[]uint64) (int, int, int)`
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- Computes LCS score and alignment length between raw byte sequences.
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- If `endgapfree` is true, ignores leading/trailing gaps (useful for read alignment).
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- Returns `(score, length, end_position)`; `end_position` marks where the LCS ends in sequence A.
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- Returns `-1, -1, -1` if the actual error count exceeds `maxError`.
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2. `FastLCSEGFScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer ...)`
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- Wrapper for `FastLCSEGFScoreByte` with end-gap-free mode enabled by default.
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- Designed for standard biosequence inputs.
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3. `FastLCSScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer ...)`
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- Computes standard LCS (including end gaps). Returns `(score, alignment_length)`.
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## Features
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- **Error-bounded**: Supports `maxError = -1` (unlimited) or a fixed max number of mismatches + gaps.
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- **Memory-efficient**: Reuses user-provided or auto-created buffers to avoid allocations during repeated calls.
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- **IUPAC-aware**: Uses `obiseq.SameIUPACNuc()` to handle ambiguous nucleotide codes (e.g., `R`, `Y`).
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- **Optimized for short reads**: Particularly suited to high-throughput sequencing data alignment tasks (e.g., in OBITools4).
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## Use Cases
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- Molecular barcode/UMI clustering
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- Read-to-reference alignment in amplicon sequencing
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- Similarity filtering of biological sequences
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