⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

autodoc/docmd/pkg/obialign/readalign.md

@@ -0,0 +1,58 @@
+# Semantic Description of `obialign.ReadAlign`
+
+The `ReadAlign` function performs **paired-end read alignment** with quality-aware scoring, optimized for overlapping consensus construction in NGS data processing.
+
+## Core Functionality
+
+- **Input**: Two biological sequences (`seqA`, `seqB`) as `BioSequence` objects, plus alignment parameters:  
+  - `gap`: gap penalty (linear)  
+  - `scale`: scaling factor for quality scores  
+  - `delta`: extension buffer around initial overlap estimate  
+  - `fastScoreRel`: use relative vs absolute k-mer matching score  
+
+## Algorithm Overview
+
+1. **Preprocessing & Initialization**  
+   - Ensures DNA scoring matrix is initialized (`_InitDNAScoreMatrix`).  
+
+2. **Fast Overlap Estimation via 4-mer Indexing**  
+   - Builds a k-mer index of `seqA` using `obikmer.Index4mer`.  
+   - Computes optimal shift via `_FastShiftFourMer` in both forward and reverse-complement orientations.  
+   - Selects orientation (direct or reversed) yielding highest k-mer match count (`fastCount`) and score (`fastScore`).  
+
+3. **Overlap Computation**  
+   - Determines overlap length `over` based on shift:  
+     ```text
+       over = |seqA| - shift    if shift > 0  
+              |seqB| + shift    if shift < 0  
+              min(|seqA|,|seqB)| otherwise
+     ```
+
+4. **Dynamic Programming Alignment**  
+   - If overlap is *not* identical (`fastCount + 3 < over`):  
+     - Extracts subregions with `delta`-buffered boundaries.  
+     - Calls either `_FillMatrixPeLeftAlign` (left-aligned case) or `_FillMatrixPERightAlign`.  
+     - Backtracks via `_Backtracking` to produce alignment path.  
+   - Else (near-perfect overlap):  
+     - Skips DP; computes score directly from quality scores using `_NucScorePartMatchMatch`.  
+     - Returns trivial path `[extra5, partLen]`.
+
+## Output
+
+Returns:  
+
+| Index | Type     | Meaning |
+|-------|----------|---------|
+| 0️⃣    | `int`     | Final alignment score (weighted by quality) |
+| 1️⃣    | `[]int`   | Alignment path (list of positions: `[startA, endA, startB, endB]` or similar) |
+| 2️⃣    | `int`     | K-mer match count (`fastCount`) |
+| 3️⃣    | `int`     | Overlap length (`over`) |
+| 4️⃣    | `float64` | K-mer-based score (`fastScore`) |
+| 5️⃣    | `bool`    | Whether alignment was performed in direct orientation (`true`) or on reverse-complement of `seqB` |
+
+## Key Design Highlights
+
+- **Efficient pre-filtering** using 4-mers avoids full DP for nearly identical reads.  
+- **Quality-aware scoring**, leveraging Phred scores via `_NucScorePartMatchMatch`.  
+- Supports **asymmetric overlaps** (left/right alignment) with boundary padding (`delta`).  
+- Uses preallocated memory arenas to minimize GC pressure in high-throughput pipelines.