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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)
59 lines
2.7 KiB
Markdown
59 lines
2.7 KiB
Markdown
# Semantic Description of `obialign.ReadAlign`
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The `ReadAlign` function performs **paired-end read alignment** with quality-aware scoring, optimized for overlapping consensus construction in NGS data processing.
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## Core Functionality
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- **Input**: Two biological sequences (`seqA`, `seqB`) as `BioSequence` objects, plus alignment parameters:
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- `gap`: gap penalty (linear)
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- `scale`: scaling factor for quality scores
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- `delta`: extension buffer around initial overlap estimate
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- `fastScoreRel`: use relative vs absolute k-mer matching score
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## Algorithm Overview
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1. **Preprocessing & Initialization**
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- Ensures DNA scoring matrix is initialized (`_InitDNAScoreMatrix`).
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2. **Fast Overlap Estimation via 4-mer Indexing**
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- Builds a k-mer index of `seqA` using `obikmer.Index4mer`.
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- Computes optimal shift via `_FastShiftFourMer` in both forward and reverse-complement orientations.
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- Selects orientation (direct or reversed) yielding highest k-mer match count (`fastCount`) and score (`fastScore`).
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3. **Overlap Computation**
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- Determines overlap length `over` based on shift:
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```text
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over = |seqA| - shift if shift > 0
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|seqB| + shift if shift < 0
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min(|seqA|,|seqB)| otherwise
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```
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4. **Dynamic Programming Alignment**
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- If overlap is *not* identical (`fastCount + 3 < over`):
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- Extracts subregions with `delta`-buffered boundaries.
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- Calls either `_FillMatrixPeLeftAlign` (left-aligned case) or `_FillMatrixPERightAlign`.
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- Backtracks via `_Backtracking` to produce alignment path.
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- Else (near-perfect overlap):
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- Skips DP; computes score directly from quality scores using `_NucScorePartMatchMatch`.
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- Returns trivial path `[extra5, partLen]`.
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## Output
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Returns:
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| Index | Type | Meaning |
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|-------|----------|---------|
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| 0️⃣ | `int` | Final alignment score (weighted by quality) |
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| 1️⃣ | `[]int` | Alignment path (list of positions: `[startA, endA, startB, endB]` or similar) |
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| 2️⃣ | `int` | K-mer match count (`fastCount`) |
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| 3️⃣ | `int` | Overlap length (`over`) |
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| 4️⃣ | `float64` | K-mer-based score (`fastScore`) |
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| 5️⃣ | `bool` | Whether alignment was performed in direct orientation (`true`) or on reverse-complement of `seqB` |
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## Key Design Highlights
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- **Efficient pre-filtering** using 4-mers avoids full DP for nearly identical reads.
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- **Quality-aware scoring**, leveraging Phred scores via `_NucScorePartMatchMatch`.
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- Supports **asymmetric overlaps** (left/right alignment) with boundary padding (`delta`).
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- Uses preallocated memory arenas to minimize GC pressure in high-throughput pipelines.
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